From 3cd8dff6bc42a3c4e6290cc050fe2a643cd630a2 Mon Sep 17 00:00:00 2001 From: Tristan Youngs Date: Mon, 27 Apr 2026 11:12:09 +0100 Subject: [PATCH 01/22] Add missing comment headers. --- src/classes/speciesAtom.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/classes/speciesAtom.cpp b/src/classes/speciesAtom.cpp index 6e0643589e..8142b6d052 100644 --- a/src/classes/speciesAtom.cpp +++ b/src/classes/speciesAtom.cpp @@ -358,6 +358,10 @@ SpeciesAtom::AtomGeometry SpeciesAtom::geometry(const SpeciesAtom *i) // Return whether the specified SpeciesAtom exists in the specified geometry bool SpeciesAtom::isGeometry(const SpeciesAtom *i, AtomGeometry geom) { return geometry(i) == geom; } +/* + * Serialisation + */ + /* * Serialisation */ From 187745ead37a3088772fcd9b52ab6bb716011c68 Mon Sep 17 00:00:00 2001 From: Tristan Youngs Date: Mon, 27 Apr 2026 11:36:03 +0100 Subject: [PATCH 02/22] Remove old and unused guessOxidationState(). --- src/classes/speciesAtom.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/classes/speciesAtom.cpp b/src/classes/speciesAtom.cpp index 8142b6d052..6e0643589e 100644 --- a/src/classes/speciesAtom.cpp +++ b/src/classes/speciesAtom.cpp @@ -358,10 +358,6 @@ SpeciesAtom::AtomGeometry SpeciesAtom::geometry(const SpeciesAtom *i) // Return whether the specified SpeciesAtom exists in the specified geometry bool SpeciesAtom::isGeometry(const SpeciesAtom *i, AtomGeometry geom) { return geometry(i) == geom; } -/* - * Serialisation - */ - /* * Serialisation */ From b4f77db032915245f11dba1bd1389106593f8722 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 29 Apr 2026 17:02:56 +0100 Subject: [PATCH 03/22] cif refactor --- src/classes/structure.cpp | 3 + src/classes/structure.h | 2 + src/gui/createGrapheneSpeciesDialog.h | 2 +- src/gui/importCIFDialog.cpp | 82 +- src/gui/importCIFDialog.h | 4 +- src/gui/models/cifAssemblyModel.h | 2 +- src/io/import/CIFImportErrorListeners.cpp | 2 +- src/io/import/CIFImportLexer.g4 | 2 +- src/io/import/CIFImportVisitor.cpp | 4 +- src/io/import/CIFImportVisitor.h | 2 +- src/io/import/CMakeLists.txt | 38 +- src/io/import/cif.cpp | 7 +- src/io/import/cif.h | 2 +- src/io/import/cifClasses.cpp | 2 +- src/nodes/CMakeLists.txt | 45 +- src/nodes/{ => cif}/cifBondingOptions.cpp | 6 +- src/nodes/{ => cif}/cifBondingOptions.h | 6 +- src/nodes/{ => cif}/cifMolecularSpecies.cpp | 4 +- src/nodes/{ => cif}/cifMolecularSpecies.h | 6 +- src/nodes/{ => cif}/cifPeriodicFramework.cpp | 4 +- src/nodes/{ => cif}/cifPeriodicFramework.h | 6 +- src/nodes/{ => cif}/cifRemoveAtomic.cpp | 6 +- src/nodes/{ => cif}/cifRemoveAtomic.h | 6 +- src/nodes/{ => cif}/cifRemoveWater.cpp | 6 +- src/nodes/{ => cif}/cifRemoveWater.h | 6 +- src/nodes/{ => cif}/cifStructureCleanup.cpp | 6 +- src/nodes/{ => cif}/cifStructureCleanup.h | 6 +- src/nodes/{ => cif}/cifSuperMolecule.cpp | 4 +- src/nodes/{ => cif}/cifSuperMolecule.h | 6 +- .../importCIFStructure.cpp} | 17 +- .../{cifLoader.h => cif/importCIFStructure.h} | 16 +- src/nodes/cif/io/CIFImportErrorListeners.cpp | 40 + src/nodes/cif/io/CIFImportErrorListeners.h | 52 + src/nodes/cif/io/CIFImportLexer.g4 | 76 + src/nodes/cif/io/CIFImportParser.g4 | 46 + src/nodes/cif/io/CIFImportVisitor.cpp | 65 + src/nodes/cif/io/CIFImportVisitor.h | 36 + src/nodes/cif/io/cifClasses.cpp | 130 ++ src/nodes/cif/io/cifClasses.h | 142 ++ src/nodes/cif/io/cifContext.cpp | 1361 +++++++++++++++++ src/nodes/cif/io/cifContext.h | 220 +++ .../{ => cif}/setCIFAtomGroupActivity.cpp | 6 +- src/nodes/{ => cif}/setCIFAtomGroupActivity.h | 6 +- src/nodes/registry.cpp | 20 +- tests/io/cif.cpp | 104 +- tests/nodes/bragg.cpp | 6 +- tests/nodes/cif.cpp | 10 +- tests/tempFile.h | 4 +- 48 files changed, 2410 insertions(+), 224 deletions(-) rename src/nodes/{ => cif}/cifBondingOptions.cpp (82%) rename src/nodes/{ => cif}/cifBondingOptions.h (90%) rename src/nodes/{ => cif}/cifMolecularSpecies.cpp (91%) rename src/nodes/{ => cif}/cifMolecularSpecies.h (90%) rename src/nodes/{ => cif}/cifPeriodicFramework.cpp (90%) rename src/nodes/{ => cif}/cifPeriodicFramework.h (91%) rename src/nodes/{ => cif}/cifRemoveAtomic.cpp (72%) rename src/nodes/{ => cif}/cifRemoveAtomic.h (87%) rename src/nodes/{ => cif}/cifRemoveWater.cpp (75%) rename src/nodes/{ => cif}/cifRemoveWater.h (87%) rename src/nodes/{ => cif}/cifStructureCleanup.cpp (79%) rename src/nodes/{ => cif}/cifStructureCleanup.h (89%) rename src/nodes/{ => cif}/cifSuperMolecule.cpp (87%) rename src/nodes/{ => cif}/cifSuperMolecule.h (88%) rename src/nodes/{cifLoader.cpp => cif/importCIFStructure.cpp} (60%) rename src/nodes/{cifLoader.h => cif/importCIFStructure.h} (69%) create mode 100644 src/nodes/cif/io/CIFImportErrorListeners.cpp create mode 100644 src/nodes/cif/io/CIFImportErrorListeners.h create mode 100644 src/nodes/cif/io/CIFImportLexer.g4 create mode 100644 src/nodes/cif/io/CIFImportParser.g4 create mode 100644 src/nodes/cif/io/CIFImportVisitor.cpp create mode 100644 src/nodes/cif/io/CIFImportVisitor.h create mode 100644 src/nodes/cif/io/cifClasses.cpp create mode 100644 src/nodes/cif/io/cifClasses.h create mode 100644 src/nodes/cif/io/cifContext.cpp create mode 100644 src/nodes/cif/io/cifContext.h rename src/nodes/{ => cif}/setCIFAtomGroupActivity.cpp (78%) rename src/nodes/{ => cif}/setCIFAtomGroupActivity.h (89%) diff --git a/src/classes/structure.cpp b/src/classes/structure.cpp index c9fad5c920..4c05cc62d9 100644 --- a/src/classes/structure.cpp +++ b/src/classes/structure.cpp @@ -103,6 +103,9 @@ int Structure::nAtoms(Atom::Presence withPresence) const { return i->isPresence(withPresence); }); } +// Return atom at index +StructureAtom *Structure::atomAt(int i) { return atoms_[i].get(); } + // Return atoms const std::vector> &Structure::atoms() const { return atoms_; } std::vector> &Structure::atoms() { return atoms_; } diff --git a/src/classes/structure.h b/src/classes/structure.h index a878d89023..f3b01f7359 100644 --- a/src/classes/structure.h +++ b/src/classes/structure.h @@ -112,6 +112,8 @@ class Structure : public Serialisable<> void removeAtoms(const std::vector &atoms); // Return the number of atoms int nAtoms(Atom::Presence withPresence = Atom::Presence::Any) const; + // Return atom at index + StructureAtom *atomAt(int i); // Return atoms const std::vector> &atoms() const; std::vector> &atoms(); diff --git a/src/gui/createGrapheneSpeciesDialog.h b/src/gui/createGrapheneSpeciesDialog.h index c265d4936c..e24b001243 100644 --- a/src/gui/createGrapheneSpeciesDialog.h +++ b/src/gui/createGrapheneSpeciesDialog.h @@ -8,8 +8,8 @@ #include "gui/selectElementDialog.h" #include "gui/ui_createGrapheneSpeciesDialog.h" #include "gui/wizard.h" -#include "io/import/cif.h" #include "main/dissolve.h" +#include "nodes/cif/io/cifContext.h" #include // Forward Declarations diff --git a/src/gui/importCIFDialog.cpp b/src/gui/importCIFDialog.cpp index 94873c163c..a94e31f3d1 100644 --- a/src/gui/importCIFDialog.cpp +++ b/src/gui/importCIFDialog.cpp @@ -13,7 +13,7 @@ #include ImportCIFDialog::ImportCIFDialog(QWidget *parent, Dissolve &dissolve) - : QDialog(parent), cifAssemblyModel_(cifHandler_.assemblies()), dissolve_(dissolve) + : QDialog(parent), cifAssemblyModel_(cifContext_.assemblies()), dissolve_(dissolve) { ui_.setupUi(this); @@ -38,7 +38,7 @@ ImportCIFDialog::ImportCIFDialog(QWidget *parent, Dissolve &dissolve) ComboEnumOptionsPopulator(ui_.DensityUnitsCombo, Units::densityUnits()); // Set display configuration - ui_.StructureViewer->setConfiguration(cifHandler_.generatedConfiguration()); + ui_.StructureViewer->setConfiguration(cifContext_.generatedConfiguration()); createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString()); } @@ -53,34 +53,34 @@ void ImportCIFDialog::updateWidgets() Locker updateLock(widgetsUpdating_); // DATA_ ID - ui_.InfoDataLabel->setText(QString::fromStdString(cifHandler_.getTagString("DATA_").value_or(""))); + ui_.InfoDataLabel->setText(QString::fromStdString(cifContext_.getTagString("DATA_").value_or(""))); // Chemical Formula - ui_.InfoChemicalFormulaLabel->setText(QString::fromStdString(cifHandler_.chemicalFormula())); + ui_.InfoChemicalFormulaLabel->setText(QString::fromStdString(cifContext_.chemicalFormula())); // Publication Data ui_.InfoPublicationTitleLabel->setText( - QString::fromStdString(cifHandler_.getTagString("_publ_section_title").value_or(""))); + QString::fromStdString(cifContext_.getTagString("_publ_section_title").value_or(""))); ui_.InfoPublicationReferenceLabel->setText(QString::fromStdString(std::format( - "{}, {}, {}, {}", cifHandler_.getTagString("_journal_name_full").value_or("N/A"), - cifHandler_.getTagString("_journal_year").value_or("N/A"), cifHandler_.getTagString("_journal_volume").value_or("N/A"), - cifHandler_.getTagString("_journal_page_first").value_or("N/A")))); + "{}, {}, {}, {}", cifContext_.getTagString("_journal_name_full").value_or("N/A"), + cifContext_.getTagString("_journal_year").value_or("N/A"), cifContext_.getTagString("_journal_volume").value_or("N/A"), + cifContext_.getTagString("_journal_page_first").value_or("N/A")))); ui_.InfoAuthorsList->clear(); - auto authors = cifHandler_.getTagStrings("_publ_author_name"); + auto authors = cifContext_.getTagStrings("_publ_author_name"); for (auto &author : authors) ui_.InfoAuthorsList->addItem(QString::fromStdString(author)); // Spacegroup - ui_.SpaceGroupsCombo->setCurrentIndex(cifHandler_.spaceGroup() - 1); + ui_.SpaceGroupsCombo->setCurrentIndex(cifContext_.spaceGroup() - 1); // Bonding - ui_.BondFromCIFRadio->setEnabled(cifHandler_.hasBondDistances()); + ui_.BondFromCIFRadio->setEnabled(cifContext_.hasBondDistances()); // Assemblies ui_.AssemblyView->expandAll(); // Configuration information - auto *cfg = cifHandler_.generatedConfiguration(); + auto *cfg = cifContext_.generatedConfiguration(); const auto *box = cfg->box(); ui_.CurrentBoxTypeLabel->setText(QString::fromStdString(std::string(Box::boxTypes().keyword(box->type())))); QString boxInfo = QString("A: %1 Å
").arg(box->axisLengths().x); @@ -95,7 +95,7 @@ void ImportCIFDialog::updateWidgets() ui_.MoleculePopulationLabel->setText(QString::number(cfg->nMolecules())); // Output - auto validSpecies = !cifHandler_.molecularSpecies().empty(); + auto validSpecies = !cifContext_.molecularSpecies().empty(); ui_.OutputMolecularRadio->setEnabled(validSpecies); ui_.OutputFrameworkRadio->setEnabled(!validSpecies); ui_.OutputSupermoleculeRadio->setEnabled(!validSpecies); @@ -106,7 +106,7 @@ void ImportCIFDialog::updateWidgets() // Update molecular species list ui_.OutputMolecularSpeciesList->clear(); - for (auto &molecularSp : cifHandler_.molecularSpecies()) + for (auto &molecularSp : cifContext_.molecularSpecies()) { ui_.OutputMolecularSpeciesList->addItem(QString::fromStdString(std::string(molecularSp.species()->name()))); } @@ -118,7 +118,7 @@ void ImportCIFDialog::updateWidgets() // Update density label void ImportCIFDialog::updateDensityLabel() { - auto *cfg = cifHandler_.generatedConfiguration(); + auto *cfg = cifContext_.generatedConfiguration(); if (!cfg) ui_.DensityUnitsLabel->setText("N/A"); else @@ -131,11 +131,11 @@ void ImportCIFDialog::updateDensityLabel() void ImportCIFDialog::on_InputFileEdit_editingFinished() { // Load the CIF file - if (!cifHandler_.read(ui_.InputFileEdit->text().toStdString())) + if (!cifContext_.read(ui_.InputFileEdit->text().toStdString())) Messenger::error("Failed to load CIF file '{}'.\n", ui_.InputFileEdit->text().toStdString()); else { - cifHandler_.generate(); + cifContext_.generate(); updateWidgets(); } } @@ -157,7 +157,7 @@ void ImportCIFDialog::on_SpaceGroupsCombo_currentIndexChanged(int index) if (widgetsUpdating_) return; - cifHandler_.setSpaceGroup((SpaceGroups::SpaceGroupId)(ui_.SpaceGroupsCombo->currentIndex() + 1)); + cifContext_.setSpaceGroup((SpaceGroups::SpaceGroupId)(ui_.SpaceGroupsCombo->currentIndex() + 1)); updateWidgets(); } @@ -166,7 +166,7 @@ void ImportCIFDialog::on_NormalOverlapToleranceRadio_clicked(bool checked) { if (checked) { - cifHandler_.setOverlapTolerance(0.1); + cifContext_.setOverlapTolerance(0.1); updateWidgets(); } } @@ -175,7 +175,7 @@ void ImportCIFDialog::on_LooseOverlapToleranceRadio_clicked(bool checked) { if (checked) { - cifHandler_.setOverlapTolerance(0.5); + cifContext_.setOverlapTolerance(0.5); updateWidgets(); } } @@ -184,7 +184,7 @@ void ImportCIFDialog::on_CalculateBondingRadio_clicked(bool checked) { if (checked) { - cifHandler_.setUseCIFBondingDefinitions(false); + cifContext_.setUseCIFBondingDefinitions(false); updateWidgets(); } } @@ -193,14 +193,14 @@ void ImportCIFDialog::on_BondFromCIFRadio_clicked(bool checked) { if (checked) { - cifHandler_.setUseCIFBondingDefinitions(true); + cifContext_.setUseCIFBondingDefinitions(true); updateWidgets(); } } void ImportCIFDialog::on_BondingPreventMetallicCheck_clicked(bool checked) { - cifHandler_.setPreventMetallicBonds(checked); + cifContext_.setPreventMetallicBonds(checked); updateWidgets(); } @@ -217,13 +217,13 @@ bool ImportCIFDialog::createMoietyRemovalNETA(std::string definition) void ImportCIFDialog::on_MoietyRemoveAtomicsCheck_clicked(bool checked) { - cifHandler_.setRemoveAtomics(checked); + cifContext_.setRemoveAtomics(checked); updateWidgets(); } void ImportCIFDialog::on_MoietyRemoveWaterCheck_clicked(bool checked) { - cifHandler_.setRemoveWaterAndCoordinateOxygens(checked); + cifContext_.setRemoveWaterAndCoordinateOxygens(checked); updateWidgets(); } @@ -236,7 +236,7 @@ void ImportCIFDialog::on_MoietyRemoveByNETACheck_clicked(bool checked) if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) return; - cifHandler_.setRemoveNETA(checked, ui_.MoietyNETARemoveFragmentsCheck->isChecked()); + cifContext_.setRemoveNETA(checked, ui_.MoietyNETARemoveFragmentsCheck->isChecked()); updateWidgets(); } @@ -245,8 +245,8 @@ void ImportCIFDialog::on_MoietyNETARemovalEdit_textEdited(const QString &text) if (!createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString())) return; - cifHandler_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), ui_.MoietyNETARemoveFragmentsCheck->isChecked()); - cifHandler_.setMoietyRemovalNETA(moietyNETA_.definitionString()); + cifContext_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), ui_.MoietyNETARemoveFragmentsCheck->isChecked()); + cifContext_.setMoietyRemovalNETA(moietyNETA_.definitionString()); updateWidgets(); } @@ -255,32 +255,32 @@ void ImportCIFDialog::on_MoietyNETARemoveFragmentsCheck_clicked(bool checked) if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) return; - cifHandler_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), checked); + cifContext_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), checked); updateWidgets(); } void ImportCIFDialog::assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &) { - cifHandler_.generate(); + cifContext_.generate(); updateWidgets(); } void ImportCIFDialog::on_RepeatASpin_valueChanged(int value) { - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); + cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); updateWidgets(); } void ImportCIFDialog::on_RepeatBSpin_valueChanged(int value) { - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); + cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); updateWidgets(); } void ImportCIFDialog::on_RepeatCSpin_valueChanged(int value) { - cifHandler_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); + cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); updateWidgets(); } @@ -300,22 +300,22 @@ void ImportCIFDialog::on_OutputSupermoleculeRadio_clicked(bool checked) {} void ImportCIFDialog::on_OKButton_clicked(bool checked) { - Flags outputFlags; + Flags outputFlags; if (ui_.OutputMolecularRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputMolecularSpecies); + outputFlags.setFlag(CIFContext::OutputFlags::OutputMolecularSpecies); else if (ui_.OutputFrameworkRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputFramework); + outputFlags.setFlag(CIFContext::OutputFlags::OutputFramework); else if (ui_.OutputSupermoleculeRadio->isChecked()) - outputFlags.setFlag(CIFHandler::OutputFlags::OutputSupermolecule); + outputFlags.setFlag(CIFContext::OutputFlags::OutputSupermolecule); // Output a configuration as well as the species for certain options - if (outputFlags.isSet(CIFHandler::OutputFlags::OutputMolecularSpecies) || - outputFlags.isSet(CIFHandler::OutputFlags::OutputFramework)) + if (outputFlags.isSet(CIFContext::OutputFlags::OutputMolecularSpecies) || + outputFlags.isSet(CIFContext::OutputFlags::OutputFramework)) { - outputFlags.setFlag(CIFHandler::OutputFlags::OutputConfiguration); + outputFlags.setFlag(CIFContext::OutputFlags::OutputConfiguration); } - cifHandler_.finalise(dissolve_.coreData(), outputFlags); + cifContext_.finalise(dissolve_.coreData(), outputFlags); accept(); } diff --git a/src/gui/importCIFDialog.h b/src/gui/importCIFDialog.h index 52133f3a42..09542002f3 100644 --- a/src/gui/importCIFDialog.h +++ b/src/gui/importCIFDialog.h @@ -7,8 +7,8 @@ #include "gui/models/cifAssemblyModel.h" #include "gui/ui_importCIFDialog.h" #include "gui/wizard.h" -#include "io/import/cif.h" #include "main/dissolve.h" +#include "nodes/cif/io/cifContext.h" #include // Forward Declarations @@ -39,7 +39,7 @@ class ImportCIFDialog : public QDialog // Main Dissolve object Dissolve &dissolve_; // CIF Handler - CIFHandler cifHandler_; + CIFContext cifContext_; // NETA for moiety removal NETADefinition moietyNETA_; diff --git a/src/gui/models/cifAssemblyModel.h b/src/gui/models/cifAssemblyModel.h index f1ba29b6d1..7ded24966d 100644 --- a/src/gui/models/cifAssemblyModel.h +++ b/src/gui/models/cifAssemblyModel.h @@ -3,7 +3,7 @@ #pragma once -#include "io/import/cif.h" +#include "nodes/cif/io/cifContext.h" #include #include diff --git a/src/io/import/CIFImportErrorListeners.cpp b/src/io/import/CIFImportErrorListeners.cpp index 6d727406f5..960fe3570d 100644 --- a/src/io/import/CIFImportErrorListeners.cpp +++ b/src/io/import/CIFImportErrorListeners.cpp @@ -1,7 +1,7 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" #include "base/messenger.h" #include "base/sysFunc.h" diff --git a/src/io/import/CIFImportLexer.g4 b/src/io/import/CIFImportLexer.g4 index 50f921c330..84f510b7fa 100644 --- a/src/io/import/CIFImportLexer.g4 +++ b/src/io/import/CIFImportLexer.g4 @@ -9,7 +9,7 @@ lexer grammar CIFImportLexer; // Add custom includes after standard ANTLR includes in both *.h and *.cpp files @lexer::postinclude { #include "base/sysFunc.h" - #include "io/import/CIFImportVisitor.h" + #include "nodes/cif/io/CIFImportVisitor.h" } // Directly precedes the lexer class declaration in the h file (e.g. for additional types etc.). diff --git a/src/io/import/CIFImportVisitor.cpp b/src/io/import/CIFImportVisitor.cpp index f0e5bec273..6b95676e03 100644 --- a/src/io/import/CIFImportVisitor.cpp +++ b/src/io/import/CIFImportVisitor.cpp @@ -1,10 +1,10 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/CIFImportVisitor.h" +#include "nodes/cif/io/CIFImportVisitor.h" #include "base/messenger.h" #include "base/sysFunc.h" -#include "io/import/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" CIFImportVisitor::CIFImportVisitor(CIFHandler::CIFTags &tags) : tags_(tags) {} diff --git a/src/io/import/CIFImportVisitor.h b/src/io/import/CIFImportVisitor.h index 20e6f554db..b73271862c 100644 --- a/src/io/import/CIFImportVisitor.h +++ b/src/io/import/CIFImportVisitor.h @@ -4,7 +4,7 @@ #pragma once #include "CIFImportParserBaseVisitor.h" -#include "io/import/cif.h" +#include "nodes/cif/io/cif.h" #include "templates/optionalRef.h" #include diff --git a/src/io/import/CMakeLists.txt b/src/io/import/CMakeLists.txt index 63ad9a0fd9..2466de48dd 100644 --- a/src/io/import/CMakeLists.txt +++ b/src/io/import/CMakeLists.txt @@ -1,32 +1,5 @@ -# CIFImport ANTLR Lexer/Parser -antlr_target(CIFImportGrammarLexer CIFImportLexer.g4 LEXER) -# PACKAGE CIFImportGrammar) -antlr_target( - CIFImportGrammarParser - CIFImportParser.g4 - PARSER - # PACKAGE CIFImportGrammar - DEPENDS_ANTLR - CIFImportGrammarLexer - COMPILE_FLAGS - -no-listener - -visitor - -lib - ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} -) - -# Append path to ANTLR parser output, and set cache variable -list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR}) -list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR}) -set(ANTLR_OUTPUT_DIRS - ${ANTLR_OUTPUT_DIRS} - CACHE INTERNAL "" -) - add_library( import - cif.cpp - cifClasses.cpp coordinates.cpp coordinates_dlpoly.cpp coordinates_epsr.cpp @@ -49,8 +22,6 @@ add_library( trajectory.cpp trajectory_dlpoly.cpp values.cpp - cif.h - cifClasses.h coordinates.h data1D.h data2D.h @@ -59,15 +30,10 @@ add_library( species.h trajectory.h values.h - CIFImportErrorListeners.cpp - CIFImportVisitor.cpp - ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} - ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS} ) target_include_directories( - import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} - ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} + import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ) -target_link_libraries(import base) +target_link_libraries(import base nodes) diff --git a/src/io/import/cif.cpp b/src/io/import/cif.cpp index d0bc116560..5724e257a5 100644 --- a/src/io/import/cif.cpp +++ b/src/io/import/cif.cpp @@ -1,7 +1,6 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/cif.h" #include "CIFImportLexer.h" #include "base/messenger.h" #include "base/sysFunc.h" @@ -11,10 +10,10 @@ #include "generator/add.h" #include "generator/box.h" #include "generator/coordinateSets.h" -#include "io/import/CIFImportErrorListeners.h" -#include "io/import/CIFImportVisitor.h" -#include "io/import/cif.h" #include "neta/neta.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "nodes/cif/io/cifContext.h" #include "templates/algorithms.h" CIFHandler::CIFHandler() diff --git a/src/io/import/cif.h b/src/io/import/cif.h index fa9f34b812..d93483db31 100644 --- a/src/io/import/cif.h +++ b/src/io/import/cif.h @@ -7,9 +7,9 @@ #include "classes/coreData.h" #include "classes/species.h" #include "data/spaceGroups.h" -#include "io/import/cifClasses.h" #include "math/matrix4.h" #include "neta/neta.h" +#include "nodes/cif/io/cifClasses.h" #include "templates/flags.h" #include diff --git a/src/io/import/cifClasses.cpp b/src/io/import/cifClasses.cpp index 433973285b..a2ba6fd5b0 100644 --- a/src/io/import/cifClasses.cpp +++ b/src/io/import/cifClasses.cpp @@ -1,7 +1,7 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/cifClasses.h" +#include "nodes/cif/io/cifClasses.h" #include "classes/empiricalFormula.h" #include "classes/molecule.h" #include "classes/species.h" diff --git a/src/nodes/CMakeLists.txt b/src/nodes/CMakeLists.txt index f26e9a23f0..88e577b828 100644 --- a/src/nodes/CMakeLists.txt +++ b/src/nodes/CMakeLists.txt @@ -10,7 +10,48 @@ file( "./*.h" ) -add_library(nodes ${node_sources} ${node_headers}) +# CIF/ANTLR +set(CIF_IO_DIR "${CMAKE_CURRENT_SOURCE_DIR}/cif/io") +set(ANTLR_CIF_PREFIX "NodeCIFImport") -target_include_directories(nodes PRIVATE ${PROJECT_SOURCE_DIR}/src) +# CIFImport ANTLR Lexer/Parser +antlr_target(CIFImportGrammarLexer "${CIF_IO_DIR}/CIFImportLexer.g4" LEXER) +# PACKAGE CIFImportGrammar) +antlr_target( + CIFImportGrammarParser + "${CIF_IO_DIR}/CIFImportParser.g4" + PARSER + # PACKAGE CIFImportGrammar + DEPENDS_ANTLR + CIFImportGrammarLexer + COMPILE_FLAGS + -no-listener + -visitor + -lib + ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} +) + +# Append path to ANTLR parser output, and set cache variable +list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR}) +list(APPEND ANTLR_OUTPUT_DIRS ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR}) +set(ANTLR_OUTPUT_DIRS + ${ANTLR_OUTPUT_DIRS} + CACHE INTERNAL "" +) + +add_library(nodes + ${node_sources} + ${node_headers} + ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} + ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS} +) + +message(STATUS "ANTLR generated products located in the following directories: ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS}, ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}") + +target_include_directories(nodes PRIVATE + ${PROJECT_SOURCE_DIR}/src + ${PROJECT_BINARY_DIR}/src + ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} + ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} +) target_link_libraries(nodes PUBLIC base ${THREADING_LINK_LIBS}) diff --git a/src/nodes/cifBondingOptions.cpp b/src/nodes/cif/cifBondingOptions.cpp similarity index 82% rename from src/nodes/cifBondingOptions.cpp rename to src/nodes/cif/cifBondingOptions.cpp index c70f0fa5d8..0d98707aa7 100644 --- a/src/nodes/cifBondingOptions.cpp +++ b/src/nodes/cif/cifBondingOptions.cpp @@ -1,16 +1,16 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifBondingOptions.h" +#include "nodes/cif/cifBondingOptions.h" CIFBondingOptionsNode::CIFBondingOptionsNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); + addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); // Options addOption("BondingTolerance", "Bonding tolerance, if calculating bonding rather than using CIF definitions", diff --git a/src/nodes/cifBondingOptions.h b/src/nodes/cif/cifBondingOptions.h similarity index 90% rename from src/nodes/cifBondingOptions.h rename to src/nodes/cif/cifBondingOptions.h index f67659187c..86097f525b 100644 --- a/src/nodes/cifBondingOptions.h +++ b/src/nodes/cif/cifBondingOptions.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFBondingOptionsNode : public Node { public: @@ -22,7 +22,7 @@ class CIFBondingOptionsNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Bonding tolerance, if calculating bonding rather than using CIF definitions Number bondingTolerance_{1.1}; // Whether to use CIF bonding definitions diff --git a/src/nodes/cifMolecularSpecies.cpp b/src/nodes/cif/cifMolecularSpecies.cpp similarity index 91% rename from src/nodes/cifMolecularSpecies.cpp rename to src/nodes/cif/cifMolecularSpecies.cpp index b47685750e..24e003f776 100644 --- a/src/nodes/cifMolecularSpecies.cpp +++ b/src/nodes/cif/cifMolecularSpecies.cpp @@ -1,14 +1,14 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifMolecularSpecies.h" +#include "nodes/cif/cifMolecularSpecies.h" #include #include CIFMolecularSpeciesNode::CIFMolecularSpeciesNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs diff --git a/src/nodes/cifMolecularSpecies.h b/src/nodes/cif/cifMolecularSpecies.h similarity index 90% rename from src/nodes/cifMolecularSpecies.h rename to src/nodes/cif/cifMolecularSpecies.h index 50df4671b8..fc842ad71a 100644 --- a/src/nodes/cifMolecularSpecies.h +++ b/src/nodes/cif/cifMolecularSpecies.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFMolecularSpeciesNode : public Node { public: @@ -22,7 +22,7 @@ class CIFMolecularSpeciesNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Supercell configuration Configuration *supercellConfiguration_{nullptr}; // Detected molecular species diff --git a/src/nodes/cifPeriodicFramework.cpp b/src/nodes/cif/cifPeriodicFramework.cpp similarity index 90% rename from src/nodes/cifPeriodicFramework.cpp rename to src/nodes/cif/cifPeriodicFramework.cpp index e47f3c193f..a80f9464e5 100644 --- a/src/nodes/cifPeriodicFramework.cpp +++ b/src/nodes/cif/cifPeriodicFramework.cpp @@ -1,12 +1,12 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifPeriodicFramework.h" +#include "nodes/cif/cifPeriodicFramework.h" CIFPeriodicFrameworkNode::CIFPeriodicFrameworkNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs diff --git a/src/nodes/cifPeriodicFramework.h b/src/nodes/cif/cifPeriodicFramework.h similarity index 91% rename from src/nodes/cifPeriodicFramework.h rename to src/nodes/cif/cifPeriodicFramework.h index 607150cbd9..d32b545bb6 100644 --- a/src/nodes/cifPeriodicFramework.h +++ b/src/nodes/cif/cifPeriodicFramework.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFPeriodicFrameworkNode : public Node { public: @@ -22,7 +22,7 @@ class CIFPeriodicFrameworkNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Supercell configuration Configuration *supercellConfiguration_{nullptr}; // Supercell species diff --git a/src/nodes/cifRemoveAtomic.cpp b/src/nodes/cif/cifRemoveAtomic.cpp similarity index 72% rename from src/nodes/cifRemoveAtomic.cpp rename to src/nodes/cif/cifRemoveAtomic.cpp index bb4ba604fb..6d18bcd696 100644 --- a/src/nodes/cifRemoveAtomic.cpp +++ b/src/nodes/cif/cifRemoveAtomic.cpp @@ -1,16 +1,16 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifRemoveAtomic.h" +#include "nodes/cif/cifRemoveAtomic.h" CIFRemoveAtomicNode::CIFRemoveAtomicNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); + addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); // Options addOption("RemoveAtomics", "Whether to remove free atomic moieties in clean-up", removeAtomics_); diff --git a/src/nodes/cifRemoveAtomic.h b/src/nodes/cif/cifRemoveAtomic.h similarity index 87% rename from src/nodes/cifRemoveAtomic.h rename to src/nodes/cif/cifRemoveAtomic.h index 4ac1c1c93a..d81d5ef38b 100644 --- a/src/nodes/cifRemoveAtomic.h +++ b/src/nodes/cif/cifRemoveAtomic.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFRemoveAtomicNode : public Node { public: @@ -22,7 +22,7 @@ class CIFRemoveAtomicNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Whether to remove free atomic moieties in clean-up bool removeAtomics_{false}; diff --git a/src/nodes/cifRemoveWater.cpp b/src/nodes/cif/cifRemoveWater.cpp similarity index 75% rename from src/nodes/cifRemoveWater.cpp rename to src/nodes/cif/cifRemoveWater.cpp index 9ac46cf7c5..d1b23f245f 100644 --- a/src/nodes/cifRemoveWater.cpp +++ b/src/nodes/cif/cifRemoveWater.cpp @@ -1,16 +1,16 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifRemoveWater.h" +#include "nodes/cif/cifRemoveWater.h" CIFRemoveWaterNode::CIFRemoveWaterNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); + addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); // Options addOption("RemoveWaterAndCoordinatedOxygens", "Whether to remove water and coordinated oxygen atoms in clean-up", diff --git a/src/nodes/cifRemoveWater.h b/src/nodes/cif/cifRemoveWater.h similarity index 87% rename from src/nodes/cifRemoveWater.h rename to src/nodes/cif/cifRemoveWater.h index 73206b1fa2..4482a3a5d0 100644 --- a/src/nodes/cifRemoveWater.h +++ b/src/nodes/cif/cifRemoveWater.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFRemoveWaterNode : public Node { public: @@ -22,7 +22,7 @@ class CIFRemoveWaterNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Whether to remove water and coordinated oxygen atoms in clean-up bool removeWaterAndCoordinatedOxygens_{false}; diff --git a/src/nodes/cifStructureCleanup.cpp b/src/nodes/cif/cifStructureCleanup.cpp similarity index 79% rename from src/nodes/cifStructureCleanup.cpp rename to src/nodes/cif/cifStructureCleanup.cpp index ae2a5c0411..2c7562130d 100644 --- a/src/nodes/cifStructureCleanup.cpp +++ b/src/nodes/cif/cifStructureCleanup.cpp @@ -1,16 +1,16 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifStructureCleanup.h" +#include "nodes/cif/cifStructureCleanup.h" CIFStructureCleanupNode::CIFStructureCleanupNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); + addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); // Options addOption("RemoveNETA", "Whether to remove by NETA definition in clean-up", removeNETA_); diff --git a/src/nodes/cifStructureCleanup.h b/src/nodes/cif/cifStructureCleanup.h similarity index 89% rename from src/nodes/cifStructureCleanup.h rename to src/nodes/cif/cifStructureCleanup.h index b0b75bd928..10ec0b8848 100644 --- a/src/nodes/cifStructureCleanup.h +++ b/src/nodes/cif/cifStructureCleanup.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFStructureCleanupNode : public Node { public: @@ -22,7 +22,7 @@ class CIFStructureCleanupNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Whether to remove by NETA definition in clean-up bool removeNETA_{false}; // Whether to expand NETA matches to fragments when removing in clean-up diff --git a/src/nodes/cifSuperMolecule.cpp b/src/nodes/cif/cifSuperMolecule.cpp similarity index 87% rename from src/nodes/cifSuperMolecule.cpp rename to src/nodes/cif/cifSuperMolecule.cpp index af8b6421c6..183079fb23 100644 --- a/src/nodes/cifSuperMolecule.cpp +++ b/src/nodes/cif/cifSuperMolecule.cpp @@ -1,12 +1,12 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifSuperMolecule.h" +#include "nodes/cif/cifSuperMolecule.h" CIFSuperMoleculeNode::CIFSuperMoleculeNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs diff --git a/src/nodes/cifSuperMolecule.h b/src/nodes/cif/cifSuperMolecule.h similarity index 88% rename from src/nodes/cifSuperMolecule.h rename to src/nodes/cif/cifSuperMolecule.h index f96e0261b4..0af23edb60 100644 --- a/src/nodes/cifSuperMolecule.h +++ b/src/nodes/cif/cifSuperMolecule.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class CIFSuperMoleculeNode : public Node { public: @@ -22,7 +22,7 @@ class CIFSuperMoleculeNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Non-periodic species const Species *nonPeriodicSpecies_{nullptr}; // Supercell species diff --git a/src/nodes/cifLoader.cpp b/src/nodes/cif/importCIFStructure.cpp similarity index 60% rename from src/nodes/cifLoader.cpp rename to src/nodes/cif/importCIFStructure.cpp index 94e692a6d9..790b113010 100644 --- a/src/nodes/cifLoader.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -1,34 +1,41 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/cifLoader.h" +#include "nodes/cif/importCIFStructure.h" #include #include #include -CIFLoaderNode::CIFLoaderNode(Graph *parentGraph) : Node(parentGraph) +ImportCIFStructureNode::ImportCIFStructureNode(Graph *parentGraph) : Node(parentGraph) { // Outputs addPointerOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); + addOutput("Structure", "Structure containing atoms and connectivity", structure_); // Option addOption("FilePath", "File path", filePath_); addOption("SpaceGroupID", "Set space group from index", spaceGroup_); } -std::string_view CIFLoaderNode::type() const { return "CIFLoader"; } +std::string_view ImportCIFStructureNode::type() const { return "ImportCIFStructure"; } -std::string_view CIFLoaderNode::summary() const { return "Load and parse a Crystallographic Information File (CIF)"; } +std::string_view ImportCIFStructureNode::summary() const +{ + return "Load and parse a Crystallographic Information File (CIF) to a structure"; +} // Run main processing -NodeConstants::ProcessResult CIFLoaderNode::process() +NodeConstants::ProcessResult ImportCIFStructureNode::process() { // Read contents of CIF file if (context_.read(filePath_)) { if (spaceGroup_ != SpaceGroups::NoSpaceGroup) context_.setSpaceGroup(spaceGroup_); + + structure_ = context_.structure(); + return NodeConstants::ProcessResult::Success; } diff --git a/src/nodes/cifLoader.h b/src/nodes/cif/importCIFStructure.h similarity index 69% rename from src/nodes/cifLoader.h rename to src/nodes/cif/importCIFStructure.h index f1aec6766b..87ecca0e49 100644 --- a/src/nodes/cifLoader.h +++ b/src/nodes/cif/importCIFStructure.h @@ -3,18 +3,16 @@ #pragma once -#include "io/import/cif.h" +#include "classes/structure.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node -class CIFLoaderNode : public Node +// ImportCIFStructure Node +class ImportCIFStructureNode : public Node { public: - using CIFContext = CIFHandler; - - public: - CIFLoaderNode(Graph *parentGraph); - ~CIFLoaderNode() override = default; + ImportCIFStructureNode(Graph *parentGraph); + ~ImportCIFStructureNode() override = default; public: std::string_view type() const override; @@ -26,6 +24,8 @@ class CIFLoaderNode : public Node private: // CIF handler context CIFContext context_; + // CIF strucutre + Structure *structure_; // Space group ID SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::SpaceGroupId::NoSpaceGroup}; // CIF filepath diff --git a/src/nodes/cif/io/CIFImportErrorListeners.cpp b/src/nodes/cif/io/CIFImportErrorListeners.cpp new file mode 100644 index 0000000000..960fe3570d --- /dev/null +++ b/src/nodes/cif/io/CIFImportErrorListeners.cpp @@ -0,0 +1,40 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "nodes/cif/io/CIFImportErrorListeners.h" +#include "base/messenger.h" +#include "base/sysFunc.h" + +/* + * CIFImport Lexer Error Listener + */ + +CIFImportLexerErrorListener::CIFImportLexerErrorListener() {} + +void CIFImportLexerErrorListener::syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *token, size_t line, + size_t charPositionInLine, const std::string &message, std::exception_ptr ep) +{ + Messenger::print("\nError in CIFImport definition on line {}, column {}.\n", line, charPositionInLine); + + // The actual error message can contain braces, so escape those to avoid breaking fmt + auto escaped = DissolveSys::replace(DissolveSys::replace(message, "{", "{{"), "}", "}}"); + + throw CIFImportExceptions::CIFImportSyntaxException(std::format("Syntax Error: {}", escaped)); +} + +/* + * CIFImport Parser Error Listener + */ + +CIFImportParserErrorListener::CIFImportParserErrorListener() {} + +void CIFImportParserErrorListener::syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *token, size_t line, + size_t charPositionInLine, const std::string &message, std::exception_ptr ep) +{ + Messenger::print("\nError in CIFImport definition on line {}, column {}.\n", line, charPositionInLine); + + // The actual error message can contain braces, so escape those to avoid breaking fmt + auto escaped = DissolveSys::replace(DissolveSys::replace(message, "{", "{{"), "}", "}}"); + + throw CIFImportExceptions::CIFImportSyntaxException(std::format("Syntax Error: {}", escaped)); +} diff --git a/src/nodes/cif/io/CIFImportErrorListeners.h b/src/nodes/cif/io/CIFImportErrorListeners.h new file mode 100644 index 0000000000..ed27e07296 --- /dev/null +++ b/src/nodes/cif/io/CIFImportErrorListeners.h @@ -0,0 +1,52 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include +#include + +namespace CIFImportExceptions +{ +// CIFImport Syntax Exception +class CIFImportSyntaxException : public std::exception +{ + public: + CIFImportSyntaxException(std::string_view message = "Undefined CIFImport Syntax Exception") : message_{message} {} + + private: + // Error message + std::string message_; + + public: + virtual const char *what() const throw() { return message_.c_str(); } +}; +} // namespace CIFImportExceptions + +// CIFImport Lexer Error Listener +class CIFImportLexerErrorListener : public antlr4::BaseErrorListener +{ + public: + CIFImportLexerErrorListener(); + + /* + * BaseErrorListener Overrides + */ + public: + void syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *, size_t line, size_t charPositionInLine, + const std::string &, std::exception_ptr ep); +}; + +// CIFImport Parser Error Listener +class CIFImportParserErrorListener : public antlr4::BaseErrorListener +{ + public: + CIFImportParserErrorListener(); + + /* + * BaseErrorListener Overrides + */ + public: + void syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *, size_t line, size_t charPositionInLine, + const std::string &, std::exception_ptr ep); +}; diff --git a/src/nodes/cif/io/CIFImportLexer.g4 b/src/nodes/cif/io/CIFImportLexer.g4 new file mode 100644 index 0000000000..84f510b7fa --- /dev/null +++ b/src/nodes/cif/io/CIFImportLexer.g4 @@ -0,0 +1,76 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +lexer grammar CIFImportLexer; + +// Lexer file header +@lexer::header {/* CIFImport ANTLR Lexer */} + +// Add custom includes after standard ANTLR includes in both *.h and *.cpp files +@lexer::postinclude { + #include "base/sysFunc.h" + #include "nodes/cif/io/CIFImportVisitor.h" +} + +// Directly precedes the lexer class declaration in the h file (e.g. for additional types etc.). +@lexer::context {/* lexer context section */} + +// Appears in the private part of the lexer in the h file. +@lexer::declarations { } + +// Appears in line with the other class member definitions in the cpp file. +@lexer::definitions {/* lexer definitions section */} + +/* + * Lexer Rules + * + * Rules defined here are based on those specified for CIF 1.1 (https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf). + * They are reproduced as faithfully as possible, with small modifications made along the way (e.g. EOL tokens are skipped rather than matched as part of tokens for the most part. + * Quotes and bracketed errors are stripped from the generated tokens. + */ + +// Fragments +fragment OrdinaryChar: '!' | '%' | '&' | '(' | ')' | '*' | '+' | ',' | '-' | '.' | '/' | '0' | '1' | '2' | '3' | '4' | '5' | '6' | '7' | '8' | '9' | ':' | '<' | '=' | '>' | '?' | '@' | [A-Z] | '\\' | '^' | '`' | [a-z] | '{' | '|' | '}' | '~'; +fragment NonBlankChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ';' | '[' | ']'; +fragment TextLeadChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ' ' | '\t' | '[' | ']'; +fragment AnyPrintChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ' ' | '\t' | ';' | '[' | ']'; +fragment EOL: [\r\n]; +fragment DIGIT: [0-9]; + +// Reserved Words +DATA_Name: ('D' | 'd') ('A' | 'a') ('T' | 't') ('A' | 'a') '_' NonBlankChar+; +LOOP_: ('L' | 'l') ('O' | 'o') ('O' | 'o') ('P' | 'p') '_'; +GLOBAL_: ('G' | 'g') ('L' | 'l') ('O' | 'o') ('B' | 'b') ('A' | 'a') ('L' | 'l') '_'; +SAVE_: ('S' | 's') ('A' | 'a') ('V' | 'v') ('E' | 'e') '_'; +SAVE_Name: ('S' | 's') ('A' | 'a') ('V' | 'v') ('E' | 'e') '_' NonBlankChar+; +STOP_: ('S' | 's') ('T' | 't') ('O' | 'o') ('P' | 'p') '_'; + +// Whitespace & Comments +WhiteSpace: [ \t\r\n]+ -> skip; +Comment: '#' AnyPrintChar*; + +// Tags & Values +Tag: '_' NonBlankChar+; +Value: '.' + | '?' + | Numeric { setText(std::string(DissolveSys::beforeChar(getText(), '('))); } + | UnquotedString + | SingleQuotedString { setText(getText().substr(1, getText().length()-2)); } + | DoubleQuotedString { setText(getText().substr(1, getText().length()-2)); } + | SemiColonTextField { setText(getText().find_first_not_of(";\r\n") != std::string::npos ? getText().substr(getText().find_first_not_of(";\r\n "), getText().find_last_not_of(";\r\n ") - getText().find_first_not_of(";\r\n ") + 1) : ""); } + ; + +// Numerics +Numeric: Number ( '(' UnsignedInteger ')' ); +Number: Integer | Float; +Integer: ('+' | '-')? UnsignedInteger; +Float: Integer Exponent +| ((DIGIT* '.' UnsignedInteger) | (DIGIT+ '.')) Exponent?; +Exponent: ('e'|'E') ('+'|'-')? UnsignedInteger+; +UnsignedInteger: DIGIT+; + +// Character Strings +UnquotedString: OrdinaryChar NonBlankChar*; +SingleQuotedString: '\'' AnyPrintChar*? '\''; +DoubleQuotedString: '"' AnyPrintChar*? '"'; +SemiColonTextField: ';' EOL* (TextLeadChar AnyPrintChar* EOL*?)* ';'; diff --git a/src/nodes/cif/io/CIFImportParser.g4 b/src/nodes/cif/io/CIFImportParser.g4 new file mode 100644 index 0000000000..d07e42512c --- /dev/null +++ b/src/nodes/cif/io/CIFImportParser.g4 @@ -0,0 +1,46 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +parser grammar CIFImportParser; + +options { + tokenVocab = CIFImportLexer; +} + +// Parser file header +@parser::header {/* CIFImport ANTLR Parser */} + +// Add custom includes after standard ANTLR includes in both *.h and *.cpp files +@parser::postinclude { } + +// Appears in the private part of the parser in the h file. +@parser::members { /* public parser declarations/members section */ } + +// Appears in the public part of the parser in the h file. +@parser::declarations {/* private parser declarations section */} + +// Appears in line with the other class member definitions in the cpp file. +@parser::definitions {/* parser definitions section */} + +/* + * CIFImport Grammar + * + * Rules defined here are based on those specified for CIF 1.1 (https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf). + * Some additional flexibility has been added, principally removing the enforced ordering of items to permit "looser" CIF files + * (of which there are many) to be read. + */ + +cif: (Comment | dataBlockHeading | dataBlock)+?; + +dataBlock: dataItems | saveFrame; + +dataBlockHeading: DATA_Name; + +saveFrame: saveFrameHeading dataItems+ SAVE_; + +saveFrameHeading: SAVE_Name; + +dataItems: name=Tag value=Value #taggedData +| loop #loopedData +; +loop: LOOP_ columns+=Tag+ values+=Value+; diff --git a/src/nodes/cif/io/CIFImportVisitor.cpp b/src/nodes/cif/io/CIFImportVisitor.cpp new file mode 100644 index 0000000000..8601d98135 --- /dev/null +++ b/src/nodes/cif/io/CIFImportVisitor.cpp @@ -0,0 +1,65 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "nodes/cif/io/CIFImportVisitor.h" +#include "base/messenger.h" +#include "base/sysFunc.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" + +CIFImportVisitor::CIFImportVisitor(CIFContext::CIFTags &tags) : tags_(tags) {} + +/* + * Data + */ + +// Extract information from tree into supplied objects +void CIFImportVisitor::extract(CIFImportParser::CifContext *tree) +{ + // Traverse the AST + visitChildren(tree); + + // Summarise + Messenger::print("Read in {} unique CIF data tags.\n", tags_.size()); +} + +/* + * Visitor Overrides + */ + +antlrcpp::Any CIFImportVisitor::visitDataBlockHeading(CIFImportParser::DataBlockHeadingContext *ctx) +{ + tags_["DATA_"].push_back(std::string(DissolveSys::afterChar(ctx->getText(), "DATA_"))); + + return visitChildren(ctx); +} + +antlrcpp::Any CIFImportVisitor::visitTaggedData(CIFImportParser::TaggedDataContext *ctx) +{ + tags_[ctx->name->getText()].push_back(ctx->value->getText()); + + return visitChildren(ctx); +} + +antlrcpp::Any CIFImportVisitor::visitLoopedData(CIFImportParser::LoopedDataContext *ctx) +{ + // Sanity check table data size + if (ctx->loop()->values.size() % ctx->loop()->columns.size()) + Messenger::exception("CIF table has {} columns (first is '{}') but {} values (and C%V != 0).\n", + ctx->loop()->columns.size(), ctx->loop()->columns.front()->getText(), ctx->loop()->values.size()); + + // Construct / retrieve dictionary elements for columns + std::vector>> columns; + for (auto *column : ctx->loop()->columns) + columns.emplace_back(tags_[column->getText()]); + + // Add values to columns - data will be in row-major order + auto colId = 0u; + for (auto *value : ctx->loop()->values) + { + columns[colId].get().emplace_back(value->getText()); + ++colId; + colId %= ctx->loop()->columns.size(); + } + + return visitChildren(ctx); +} diff --git a/src/nodes/cif/io/CIFImportVisitor.h b/src/nodes/cif/io/CIFImportVisitor.h new file mode 100644 index 0000000000..9b079f801f --- /dev/null +++ b/src/nodes/cif/io/CIFImportVisitor.h @@ -0,0 +1,36 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include "CIFImportParserBaseVisitor.h" +#include "nodes/cif/io/cifContext.h" +#include "templates/optionalRef.h" +#include + +// CIFImport Visitor for ANTLR +class CIFImportVisitor : CIFImportParserBaseVisitor +{ + public: + CIFImportVisitor(CIFContext::CIFTags &tags); + ~CIFImportVisitor() override = default; + + /* + * Data + */ + private: + // Dictionary data storage + CIFContext::CIFTags &tags_; + + public: + // Extract information from tree + void extract(CIFImportParser::CifContext *tree); + + /* + * Visitor Overrides + */ + private: + antlrcpp::Any visitDataBlockHeading(CIFImportParser::DataBlockHeadingContext *ctx) override; + antlrcpp::Any visitTaggedData(CIFImportParser::TaggedDataContext *ctx) override; + antlrcpp::Any visitLoopedData(CIFImportParser::LoopedDataContext *ctx) override; +}; diff --git a/src/nodes/cif/io/cifClasses.cpp b/src/nodes/cif/io/cifClasses.cpp new file mode 100644 index 0000000000..a2ba6fd5b0 --- /dev/null +++ b/src/nodes/cif/io/cifClasses.cpp @@ -0,0 +1,130 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "nodes/cif/io/cifClasses.h" +#include "classes/empiricalFormula.h" +#include "classes/molecule.h" +#include "classes/species.h" + +/* + * CIF Symmetry-Unique Atom + */ + +CIFSymmetryAtom::CIFSymmetryAtom(std::string_view label, Elements::Element Z, Vector3 rFrac, double occ) + : label_{label}, Z_(Z), rFrac_(rFrac), occupancy_(occ) {}; + +// Return label (from _atom_site_label) +std::string_view CIFSymmetryAtom::label() const { return label_; } + +// Return element (from _atom_site_type_symbol) +Elements::Element CIFSymmetryAtom::Z() const { return Z_; } + +// Return fractional coordinate of atom (from _atom_site_fract_[xyz]) +Vector3 CIFSymmetryAtom::rFrac() const { return rFrac_; } + +// Return site occupancy (from _atom_site_occupancy) +double CIFSymmetryAtom::occupancy() const { return occupancy_; } + +/* + * CIF Bonding Pair + */ + +CIFBondingPair::CIFBondingPair(std::string_view labelI, std::string_view labelJ, double r) + : labelI_{labelI}, labelJ_{labelJ}, r_(r) {}; + +// Return labels of involved atom i (from _geom_bond_atom_site_label_1) +std::string_view CIFBondingPair::labelI() const { return labelI_; } + +// Return labels of involved atom i (from _geom_bond_atom_site_label_2) +std::string_view CIFBondingPair::labelJ() const { return labelJ_; } + +// Return distance between bonded pair (from _geom_bond_distance) +double CIFBondingPair::r() const { return r_; } + +/* + * CIF Atom Group + */ + +CIFAtomGroup::CIFAtomGroup(std::string_view name) : name_{name} {}; + +// Group name (from _atom_site_disorder_group) +std::string_view CIFAtomGroup::name() const { return name_; } + +// Add atom to the group +void CIFAtomGroup::addAtom(const CIFSymmetryAtom &i) { atoms_.emplace_back(i); } + +// Return atoms in the group +const std::vector &CIFAtomGroup::atoms() const { return atoms_; } + +// Set whether the group is active (included in unit cell generation) +void CIFAtomGroup::setActive(bool b) { active_ = b; } + +// Return whether the group is active (included in unit cell generation) +bool CIFAtomGroup::active() const { return active_; } + +/* + * CIF Assembly + */ + +CIFAssembly::CIFAssembly(std::string_view name) : name_{name} {} + +// Return name of the assembly (from _atom_site_disorder_assembly or 'Global') +std::string_view CIFAssembly::name() const { return name_; } + +// Return all groups +std::vector &CIFAssembly::groups() { return groups_; } +const std::vector &CIFAssembly::groups() const { return groups_; } + +// Get (add or retrieve) named group +CIFAtomGroup &CIFAssembly::getGroup(std::string_view groupName) +{ + auto it = + std::find_if(groups_.begin(), groups_.end(), [groupName](const auto &group) { return group.name() == groupName; }); + if (it != groups_.end()) + return *it; + + return groups_.emplace_back(groupName); +} + +// Return the number of defined groups +int CIFAssembly::nGroups() const { return groups_.size(); } + +/* + * CIF Molecular Species + */ + +CIFMolecularSpecies::CIFMolecularSpecies() : species_(std::make_shared()) {} + +// Return species parent for molecule instances +std::shared_ptr &CIFMolecularSpecies::species() { return species_; }; +const std::shared_ptr &CIFMolecularSpecies::species() const { return species_; }; + +// Return molecule instances +const std::vector &CIFMolecularSpecies::instances() const { return instances_; } +std::vector &CIFMolecularSpecies::instances() { return instances_; } + +// Append supplied instances to our vector +void CIFMolecularSpecies::appendInstances(const std::vector &newInstances) +{ + // Increase our reservation + instances_.reserve(instances_.size() + newInstances.size()); + instances_.insert(instances_.end(), newInstances.begin(), newInstances.end()); +} + +// Return coordinates for all instances as a vector of vectors +std::vector> CIFMolecularSpecies::allInstanceCoordinates() const +{ + std::vector> coordinates; + + for (auto &instance : instances_) + { + std::vector instanceCoords; + instanceCoords.reserve(species_->nAtoms()); + for (auto &atom : instance.localAtoms()) + instanceCoords.emplace_back(atom.r()); + + coordinates.emplace_back(instanceCoords); + } + + return coordinates; +} diff --git a/src/nodes/cif/io/cifClasses.h b/src/nodes/cif/io/cifClasses.h new file mode 100644 index 0000000000..dd9dcf613d --- /dev/null +++ b/src/nodes/cif/io/cifClasses.h @@ -0,0 +1,142 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include "classes/localMolecule.h" +#include "classes/species.h" +#include "data/elements.h" +#include "math/vector3.h" +#include +#include + +// Forward Declarations +class Species; + +// CIF Symmetry-Unique Atom +class CIFSymmetryAtom +{ + public: + CIFSymmetryAtom(std::string_view label, Elements::Element Z, Vector3 rFrac, double occ); + ~CIFSymmetryAtom() = default; + + private: + // Label (from _atom_site_label) + std::string label_; + // Element (from _atom_site_type_symbol) + Elements::Element Z_; + // Fractional coordinate of atom (from _atom_site_fract_[xyz]) + Vector3 rFrac_; + // Site occupancy (from _atom_site_occupancy) + double occupancy_; + + public: + // Return label (from _atom_site_label) + std::string_view label() const; + // Return element (from _atom_site_type_symbol) + Elements::Element Z() const; + // Return fractional coordinate of atom (from _atom_site_fract_[xyz]) + Vector3 rFrac() const; + // Return site occupancy (from _atom_site_occupancy) + double occupancy() const; +}; + +// CIF Bonding Pair +class CIFBondingPair +{ + public: + CIFBondingPair(std::string_view labelI, std::string_view labelJ, double r); + ~CIFBondingPair() = default; + + private: + // Labels of involved atoms (from _geom_bond_atom_site_label_[12]) + std::string labelI_, labelJ_; + // Distance between bonded pair (from _geom_bond_distance) + double r_; + + public: + // Return labels of involved atom i (from _geom_bond_atom_site_label_1) + std::string_view labelI() const; + // Return labels of involved atom i (from _geom_bond_atom_site_label_2) + std::string_view labelJ() const; + // Return distance between bonded pair (from _geom_bond_distance) + double r() const; +}; + +// CIF Atom Group +class CIFAtomGroup +{ + public: + CIFAtomGroup(std::string_view name); + ~CIFAtomGroup() = default; + + private: + // Group name (from _atom_site_disorder_group) + std::string name_; + // Atoms in the group + std::vector atoms_; + // Whether the group is active (included in unit cell generation) + bool active_{false}; + + public: + // Group name (from _atom_site_disorder_group) + std::string_view name() const; + // Add atom to the group + void addAtom(const CIFSymmetryAtom &i); + // Return atoms in the group + const std::vector &atoms() const; + // Set whether the group is active (included in unit cell generation) + void setActive(bool b); + // Return whether the group is active (included in unit cell generation) + bool active() const; +}; + +// CIF Assembly +class CIFAssembly +{ + public: + CIFAssembly(std::string_view name); + ~CIFAssembly() = default; + + private: + // Name of the assembly (from _atom_site_disorder_assembly or 'Global') + std::string name_; + // Available atom groups + std::vector groups_; + + public: + // Return name of the assembly (from _atom_site_disorder_assembly or 'Global') + std::string_view name() const; + // Return all groups + std::vector &groups(); + const std::vector &groups() const; + // Get (add or retrieve) named group + CIFAtomGroup &getGroup(std::string_view groupName); + // Return the number of defined groups + int nGroups() const; +}; + +// CIF Repeated Molecular Species +class CIFMolecularSpecies +{ + public: + CIFMolecularSpecies(); + + private: + // Species parent for molecule instances + std::shared_ptr species_; + // Molecule instances + std::vector instances_; + + public: + // Return species parent for molecule instances + std::shared_ptr &species(); + const std::shared_ptr &species() const; + // Return molecule instances + const std::vector &instances() const; + std::vector &instances(); + // Append supplied instances to our vector + void appendInstances(const std::vector &newInstances); + // Return coordinates for all instances as a vector of vectors + std::vector> allInstanceCoordinates() const; +}; diff --git a/src/nodes/cif/io/cifContext.cpp b/src/nodes/cif/io/cifContext.cpp new file mode 100644 index 0000000000..3ac123b3d4 --- /dev/null +++ b/src/nodes/cif/io/cifContext.cpp @@ -0,0 +1,1361 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "nodes/cif/io/cifContext.h" +#include "CIFImportLexer.h" +#include "CIFImportParser.h" +#include "base/messenger.h" +#include "base/sysFunc.h" +#include "classes/coreData.h" +#include "classes/empiricalFormula.h" +#include "classes/species.h" +#include "generator/add.h" +#include "generator/box.h" +#include "generator/coordinateSets.h" +#include "neta/neta.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "templates/algorithms.h" + +CIFContext::CIFContext() +{ + unitCellConfiguration_.setName("Structural"); + unitCellSpecies_.setName("Crystal"); + cleanedUnitCellConfiguration_.setName("Cleaned"); + cleanedUnitCellSpecies_.setName("Crystal (Cleaned)"); + supercellConfiguration_.setName("Supercell"); + supercellSpecies_.setName("Crystal (Supercell)"); +} + +/* + * Raw Data + */ + +// Parse supplied file into the destination objects +bool CIFContext::parse(std::string_view filename, CIFContext::CIFTags &tags) const +{ + // Set up ANTLR input stream + std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); + if (!cifFile.is_open()) + return Messenger::error("Failed to open CIF file '{}.\n", filename); + + antlr4::ANTLRInputStream input(cifFile); + + // Create ANTLR lexer and set-up error listener + CIFImportLexer lexer(&input); + CIFImportLexerErrorListener lexerErrorListener; + lexer.removeErrorListeners(); + lexer.addErrorListener(&lexerErrorListener); + + // Generate tokens from input stream + antlr4::CommonTokenStream tokens(&lexer); + + // Create ANTLR parser and set-up error listeners + CIFImportParser parser(&tokens); + CIFImportParserErrorListener parserErrorListener; + parser.removeErrorListeners(); + parser.removeParseListeners(); + parser.addErrorListener(&lexerErrorListener); + parser.addErrorListener(&parserErrorListener); + + // Generate the AST + CIFImportParser::CifContext *tree = nullptr; + try + { + tree = parser.cif(); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + Messenger::error("{}", ex.what()); + return false; + } + + // Visit the nodes in the AST + CIFImportVisitor visitor(tags); + try + { + visitor.extract(tree); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + return Messenger::error("{}", ex.what()); + } + + return true; +} + +// Return whether the specified file parses correctly +bool CIFContext::validFile(std::string_view filename) const +{ + CIFTags tags; + return parse(filename, tags); +} + +// Read CIF data from specified file +bool CIFContext::read(std::string_view filename) +{ + assemblies_.clear(); + bondingPairs_.clear(); + tags_.clear(); + + if (!parse(filename, tags_)) + return Messenger::error("Failed to parse CIF file '{}'.\n", filename); + + /* + * Determine space group - the search order for tags is: + * + * 1. Hall symbol + * 2. Hermann-Mauginn name + * 3. Space group index + * + * In the case of 2 or 3 we also try to search for the origin choice. + * + * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection + * below fails). + */ + + // Check for Hall symbol + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); + + if (spaceGroup_ == SpaceGroups::NoSpaceGroup) + { + // Might need the coordinate system code... + auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); + + // Find a HM name + if (hasTag("_space_group_name_H-M_alt")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); + + // Find a space group index? + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); + } + + // Create symmetry-unique atoms list + auto atomSiteLabel = getTagStrings("_atom_site_label"); + auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); + auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); + auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); + auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); + auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); + auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); + auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); + if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) + return Messenger::error( + "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); + if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) + return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) + return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + for (auto n = 0; n < atomSiteFractX.size(); ++n) + { + // Get standard information + auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); + auto Z = n < atomSiteTypeSymbol.size() + ? Elements::element(atomSiteTypeSymbol[n]) + : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); + auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; + Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); + + // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: + // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly + // 2) An assembly and a group are defined - add it to that + // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group + auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; + auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; + if (assemblyName == "." && groupName != ".") + assemblyName = "Disorder"; + else if (assemblyName == "." && groupName == ".") + assemblyName = "Global"; + + if (groupName == ".") + groupName = "Default"; + + // Get the assembly and group that we're adding the atom to + auto &assembly = getAssembly(assemblyName); + auto &group = assembly.getGroup(groupName); + group.setActive(groupName == "Default" || groupName == "1"); + group.addAtom({label, Z, rFrac, occ}); + } + + // Construct bonding pairs list + auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); + auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); + auto bondDistances = getTagDoubles("_geom_bond_distance"); + if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) + { + for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) + bondingPairs_.emplace_back(i, j, r); + } + else + Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); + + return true; +} + +// Return if the specified tag exists +bool CIFContext::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } + +// Return tag data string (if it exists) assuming a single datum (first in the vector) +std::optional CIFContext::getTagString(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + return it->second.front(); +} + +// Return tag data strings (if it exists) +std::vector CIFContext::getTagStrings(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + return it->second; +} + +// Return tag data as double (if it exists) assuming a single datum (first in the vector) +std::optional CIFContext::getTagDouble(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + double result; + try + { + result = std::stod(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +// Return tag data doubles (if it exists) +std::vector CIFContext::getTagDoubles(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + std::vector v; + for (const auto &s : it->second) + { + auto d = 0.0; + try + { + d = std::stod(s); + } + catch (...) + { + Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); + } + v.push_back(d); + } + + return v; +} + +// Return tag data as integer (if it exists) assuming a single datum (first in the vector) +std::optional CIFContext::getTagInt(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + int result; + try + { + result = std::stoi(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +/* + * Processed Data + */ + +// Set space group from index +void CIFContext::setSpaceGroup(SpaceGroups::SpaceGroupId sgid) +{ + if (spaceGroup_ == sgid) + return; + + spaceGroup_ = sgid; + generate(); +} + +// Return space group information +SpaceGroups::SpaceGroupId CIFContext::spaceGroup() const { return spaceGroup_; } + +// Return cell lengths +std::optional CIFContext::getCellLengths() const +{ + auto a = getTagDouble("_cell_length_a"); + if (!a) + Messenger::error("Cell length A not defined in CIF.\n"); + auto b = getTagDouble("_cell_length_b"); + if (!b) + Messenger::error("Cell length B not defined in CIF.\n"); + auto c = getTagDouble("_cell_length_c"); + if (!c) + Messenger::error("Cell length C not defined in CIF.\n"); + + if (a && b && c) + return Vector3(a.value(), b.value(), c.value()); + else + return std::nullopt; +} + +// Return cell angles +std::optional CIFContext::getCellAngles() const +{ + auto alpha = getTagDouble("_cell_angle_alpha"); + if (!alpha) + Messenger::error("Cell angle alpha not defined in CIF.\n"); + auto beta = getTagDouble("_cell_angle_beta"); + if (!beta) + Messenger::error("Cell angle beta not defined in CIF.\n"); + auto gamma = getTagDouble("_cell_angle_gamma"); + if (!gamma) + Messenger::error("Cell angle gamma not defined in CIF.\n"); + + if (alpha && beta && gamma) + return Vector3(alpha.value(), beta.value(), gamma.value()); + else + return std::nullopt; +} + +// Return chemical formula +std::string CIFContext::chemicalFormula() const +{ + auto it = tags_.find("_chemical_formula_sum"); + return (it != tags_.end() ? it->second.front() : "Unknown"); +} + +// Get (add or retrieve) named assembly +CIFAssembly &CIFContext::getAssembly(std::string_view name) +{ + auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); + if (it != assemblies_.end()) + return *it; + + return assemblies_.emplace_back(name); +} + +// Return atom assemblies +std::vector &CIFContext::assemblies() { return assemblies_; } + +const std::vector &CIFContext::assemblies() const { return assemblies_; } + +// Return whether any bond distances are defined +bool CIFContext::hasBondDistances() const { return !bondingPairs_.empty(); } + +// Return whether a bond distance is defined for the specified label pair +std::optional CIFContext::bondDistance(std::string_view labelI, std::string_view labelJ) const +{ + auto it = std::find_if( + bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) + { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); + if (it != bondingPairs_.end()) + return it->r(); + return std::nullopt; +} + +/* + * Creation + */ + +// Create basic unit cell +bool CIFContext::createBasicUnitCell() +{ + unitCellConfiguration_.empty(); + unitCellSpecies_.clear(); + atomLabelTypes_.clear(); + + // Create temporary atom types corresponding to the unique atom labels + for (auto &a : assemblies_) + { + for (auto &g : a.groups()) + { + if (!g.active()) + continue; + + for (auto &i : g.atoms()) + { + if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) + { + atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); + } + } + } + } + + // Configure the unit cell "species" + auto cellLengths = getCellLengths(); + if (!cellLengths) + return false; + auto cellAngles = getCellAngles(); + if (!cellAngles) + return false; + unitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); + auto *box = unitCellSpecies_.box(); + + // Configuration + Messenger::setQuiet(true); + unitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); + Messenger::setQuiet(false); + + // -- Generate atoms + auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); + for (const auto &generator : symmetryGenerators) + for (auto &a : assemblies_) + for (auto &g : a.groups()) + if (g.active()) + for (auto &unique : g.atoms()) + { + // Generate folded atomic position in real space + auto r = generator * unique.rFrac(); + box->toReal(r); + r = box->fold(r); + + // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy + if (std::any_of(unitCellSpecies_.atoms().begin(), unitCellSpecies_.atoms().end(), + [&, r, box](const auto &j) + { return box->minimumDistance(r, j.r()) < overlapTolerance_; })) + continue; + + // Create the new atom + auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [&unique](const auto at) { return unique.label() == at->name(); }); + unitCellSpecies_.addAtom(unique.Z(), r, 0.0, atIt != atomLabelTypes_.end() ? atIt->get() : nullptr); + } + + // Check that we actually generated some atoms... + if (unitCellSpecies_.nAtoms() == 0) + return false; + + // Bonding + if (!preventAllBonds_) + if (useCIFBondingDefinitions_) + applyCIFBonding(&unitCellSpecies_, preventMetallicBonds_); + else + unitCellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); + + unitCellConfiguration_.addMolecule(&unitCellSpecies_); + unitCellConfiguration_.updateObjectRelationships(); + + Messenger::print("Created basic crystal unit cell - {} non-overlapping atoms.\n", unitCellSpecies_.nAtoms()); + + return true; +} + +// Create structure from basic unit cell atoms and connectivity +bool CIFContext::createStructure() +{ + // Create box for structure + auto box = unitCellConfiguration_.box(); + structure_.createBox(box->axisLengths(), box->axisAngles(), box->type() == Box::BoxType::NonPeriodic); + + // Add structural atoms + const auto &atoms = unitCellSpecies_.atoms(); + for (const auto &atom : atoms) + structure_.addAtom(atom.Z(), atom.r(), atom.q()); + + // Iterate over newly added structure atom pairs, adding any existing bonds between them if not already present + auto pairs = PairIterator(structure_.nAtoms()); + for (const auto &pair : pairs) + { + auto [i, j] = pair; + auto atomI = structure_.atomAt(i); + auto atomJ = structure_.atomAt(j); + + if (!structure_.hasBond(atomI, atomJ)) + structure_.addBond(atomI, atomJ); + } + + Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", structure_.nAtoms(), structure_.bonds().size()); + + return true; +} + +// Create the cleaned unit cell +bool CIFContext::createCleanedUnitCell() +{ + cleanedUnitCellConfiguration_.empty(); + cleanedUnitCellSpecies_.clear(); + + // Configure the species + cleanedUnitCellSpecies_.copyBasic(&unitCellSpecies_, true); + auto cellLengths = getCellLengths(); + if (!cellLengths) + return false; + auto cellAngles = getCellAngles(); + if (!cellAngles) + return false; + cleanedUnitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); + + // Configuration + Messenger::setQuiet(true); + cleanedUnitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); + Messenger::setQuiet(false); + + if (removeAtomics_) + { + std::vector indicesToRemove; + for (const auto &i : cleanedUnitCellSpecies_.atoms()) + if (i.nBonds() == 0) + indicesToRemove.push_back(i.index()); + Messenger::print("Atomic removal deleted {} atoms.\n", indicesToRemove.size()); + + // Remove selected atoms + cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); + } + + if (removeWaterAndCoordinateOxygens_) + { + NETADefinition waterVacuum("?O,nbonds=1,nh<=1|?O,nbonds>=2,-H(nbonds=1,-O)"); + if (!waterVacuum.isValid()) + { + Messenger::error("NETA definition for water removal is invalid.\n"); + return false; + } + + std::vector indicesToRemove; + for (const auto &i : cleanedUnitCellSpecies_.atoms()) + if (waterVacuum.matches(&i)) + indicesToRemove.push_back(i.index()); + Messenger::print("Water removal deleted {} atoms.\n", indicesToRemove.size()); + + // Remove selected atoms + cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); + } + + if (removeNETA_ && moietyRemovalNETA_.isValid()) + { + // Select all atoms that are in moieties where one of its atoms matches our NETA definition + std::vector indicesToRemove; + for (auto &i : cleanedUnitCellSpecies_.atoms()) + if (moietyRemovalNETA_.matches(&i)) + { + // Select all atoms that are part of the same moiety? + if (removeNETAByFragment_) + { + cleanedUnitCellSpecies_.clearAtomSelection(); + auto selection = cleanedUnitCellSpecies_.fragment(i.index()); + std::copy(selection.begin(), selection.end(), std::back_inserter(indicesToRemove)); + } + else + indicesToRemove.push_back(i.index()); + } + Messenger::print("Moiety removal deleted {} atoms.\n", indicesToRemove.size()); + + // Remove selected atoms + cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); + } + + cleanedUnitCellConfiguration_.addMolecule(&cleanedUnitCellSpecies_); + cleanedUnitCellConfiguration_.updateObjectRelationships(); + + Messenger::print("Created cleaned crystal unit cell - {} atoms after removal(s).\n", cleanedUnitCellSpecies_.nAtoms()); + + return true; +} + +// Try to detect molecules in the cell contents +bool CIFContext::detectMolecules() +{ + molecularSpecies_.clear(); + + // Try selecting within the species from the first atom - if this captures all atoms we have a bound framework... + if (cleanedUnitCellSpecies_.fragment(0).size() == cleanedUnitCellSpecies_.nAtoms()) + { + Messenger::print( + "Can't create molecular definitions since this unit cell appears to be a continuous framework/network. Consider " + "adjusting the bonding options in order to generate molecular fragments.\n"); + return false; + } + + std::vector atomMask(cleanedUnitCellSpecies_.nAtoms(), false); + + // Find all molecular species, and their instances + auto indexIterator = atomMask.begin(); + while (indexIterator != atomMask.end()) + { + // Select a fragment from the next available index + auto atomIndex = indexIterator - atomMask.begin(); + auto fragmentIndices = cleanedUnitCellSpecies_.fragment(atomIndex); + + // Create a new CIF molecular species from the fragment + auto &cifSp = molecularSpecies_.emplace_back(); + auto *sp = cifSp.species().get(); + // -- Copy selected atoms + for (auto fragAtomIndex : fragmentIndices) + { + const auto &unitCellAtom = cleanedUnitCellSpecies_.atom(fragAtomIndex); + sp->addAtom(unitCellAtom.Z(), unitCellAtom.r(), 0.0, unitCellAtom.atomType()); + } + + // Give the species a temporary unit cell so we can calculate / apply bonding + if (!preventAllBonds_) + sp->createBox(cleanedUnitCellSpecies_.box()->axisLengths(), cleanedUnitCellSpecies_.box()->axisAngles()); + if (useCIFBondingDefinitions_) + applyCIFBonding(sp, preventMetallicBonds_); + else + sp->addMissingBonds(bondingTolerance_, preventMetallicBonds_); + sp->removeBox(); + + // Set up a temporary molecule to unfold the species + LocalMolecule tempMol(sp); + tempMol.unFold(cleanedUnitCellSpecies_.box()); + for (auto &&[molAtom, spAtom] : zip(tempMol.localAtoms(), sp->atoms())) + spAtom.setR(molAtom.r()); + + // Give the species a name + sp->setName(EmpiricalFormula::formula(sp->atoms(), [&](const auto &at) { return at.Z(); })); + + // Find instances of this fragment. For large fragments that represent > 50% of the remaining atoms we don't even + // attempt to create a NETA definition etc. For cases such as framework species this will speed up detection no end. + std::vector instances; + if (fragmentIndices.size() * 2 > cleanedUnitCellSpecies_.nAtoms()) + { + // Create an instance of the current fragment + auto &mol = instances.emplace_back(sp); + for (auto i = 0; i < sp->nAtoms(); ++i) + atomMask[fragmentIndices[i]] = true; + } + else + { + // Determine the best NETA definition describing the fragment + auto &&[bestNETA, rootAtoms] = bestNETADefinition(sp); + if (rootAtoms.empty()) + return Messenger::error( + "Couldn't generate molecular partitioning for CIF - no suitable NETA definition for the " + "fragment {} could be determined.\n", + sp->name()); + + // Find instances of this fragment + instances = getSpeciesInstances(sp, atomMask, bestNETA, rootAtoms); + if (instances.empty()) + { + molecularSpecies_.clear(); + return Messenger::error("Failed to find species instances for fragment '{}'.\n", sp->name()); + } + } + + // Store the instances + cifSp.instances() = instances; + + // Search for the next valid starting index + indexIterator = std::find(std::next(indexIterator), atomMask.end(), false); + } + + Messenger::print("Partitioned unit cell into {} distinct molecular species:\n\n", molecularSpecies_.size()); + Messenger::print(" ID N Species Formula\n"); + auto count = 1; + for (const auto &cifMol : molecularSpecies_) + Messenger::print(" {:3d} {:4d} {}\n", count++, cifMol.instances().size(), + EmpiricalFormula::formula(cifMol.species()->atoms(), [](const auto &i) { return i.Z(); })); + Messenger::print(""); + + return true; +} + +// Create supercell species +bool CIFContext::createSupercell() +{ + supercellConfiguration_.empty(); + supercellSpecies_.clear(); + + // Configure the species + auto supercellLengths = cleanedUnitCellSpecies_.box()->axisLengths(); + supercellLengths.multiply(supercellRepeat_.x, supercellRepeat_.y, supercellRepeat_.z); + supercellSpecies_.createBox(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); + + // Set up configuration + Messenger::setQuiet(true); + supercellConfiguration_.createBoxAndCells(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); + Messenger::setQuiet(false); + + // Copy atoms from the Crystal species - we'll do the bonding afterwards + if (molecularSpecies_.empty()) + { + supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * + cleanedUnitCellSpecies_.nAtoms()); + for (auto ix = 0; ix < supercellRepeat_.x; ++ix) + for (auto iy = 0; iy < supercellRepeat_.y; ++iy) + for (auto iz = 0; iz < supercellRepeat_.z; ++iz) + { + Vector3 deltaR = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); + for (const auto &i : cleanedUnitCellSpecies_.atoms()) + supercellSpecies_.addAtom(i.Z(), i.r() + deltaR, 0.0, i.atomType()); + } + if (!preventAllBonds_) + if (useCIFBondingDefinitions_) + applyCIFBonding(&supercellSpecies_, preventMetallicBonds_); + else + supercellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); + + // Add the structural species to the configuration + supercellConfiguration_.addMolecule(&supercellSpecies_); + supercellConfiguration_.updateObjectRelationships(); + } + else + { + supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * + cleanedUnitCellSpecies_.nAtoms()); + + // Create images of all molecular unit cell species + for (auto &molecularSpecies : molecularSpecies_) + { + const auto *sp = molecularSpecies.species().get(); + const auto &coreInstances = molecularSpecies.instances(); + std::vector supercellInstances; + supercellInstances.reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * coreInstances.size()); + + // Loop over cell images + for (auto ix = 0; ix < supercellRepeat_.x; ++ix) + { + for (auto iy = 0; iy < supercellRepeat_.y; ++iy) + { + for (auto iz = 0; iz < supercellRepeat_.z; ++iz) + { + // Skip origin cell + if (ix == 0 && iy == 0 && iz == 0) + continue; + + // Set translation vector + auto tVec = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); + + // Create images of core molecule instances + for (auto &instance : coreInstances) + { + auto &mol = supercellInstances.emplace_back(); + mol.setSpecies(sp); + + for (auto &&[coreAtom, instanceAtom] : zip(instance.localAtoms(), mol.localAtoms())) + instanceAtom.setR(coreAtom.r() + tVec); + } + } + } + } + + // Append the new instances to our existing ones for the unit cell + molecularSpecies.appendInstances(supercellInstances); + + // Add the molecules to our configuration + for (const auto &instance : molecularSpecies.instances()) + { + auto mol = supercellConfiguration_.addMolecule(sp); + for (auto &&[molAtom, instanceAtom] : zip(mol->atoms(), instance.localAtoms())) + molAtom->setR(instanceAtom.r()); + } + } + + supercellConfiguration_.updateObjectRelationships(); + } + + Messenger::print("Created ({}, {}, {}) supercell - {} atoms total.\n", supercellRepeat_.x, supercellRepeat_.y, + supercellRepeat_.z, supercellConfiguration_.nAtoms()); + + return true; +} + +// Set overlap tolerance +void CIFContext::setOverlapTolerance(double tol) +{ + overlapTolerance_ = tol; + + generate(CIFGenerationStage::CreateBasicUnitCell); +} + +// Set whether to use CIF bonding definitions +void CIFContext::setUseCIFBondingDefinitions(bool b) +{ + if (useCIFBondingDefinitions_ == b) + return; + + useCIFBondingDefinitions_ = b; + + generate(); +} + +// Set bonding tolerance +void CIFContext::setBondingTolerance(double tol) +{ + bondingTolerance_ = tol; + + if (!useCIFBondingDefinitions_) + generate(); +} + +// Whether to ignore all bonds +void CIFContext::setPreventAllBonds(bool b) +{ + if (preventAllBonds_ == b) + return; + + preventAllBonds_ = b; + + generate(); +} + +// Set whether to prevent metallic bonding +void CIFContext::setPreventMetallicBonds(bool b) +{ + if (preventMetallicBonds_ == b) + return; + + preventMetallicBonds_ = b; + + generate(); +} + +// Set whether to remove free atomic moieties in clean-up +void CIFContext::setRemoveAtomics(bool b) +{ + if (removeAtomics_ == b) + return; + + removeAtomics_ = b; + + generate(CIFGenerationStage::CreateCleanedUnitCell); +} + +// Set whether to remove water and coordinated oxygen atoms in clean-up +void CIFContext::setRemoveWaterAndCoordinateOxygens(bool b) +{ + if (removeWaterAndCoordinateOxygens_ == b) + return; + + removeWaterAndCoordinateOxygens_ = b; + + generate(CIFGenerationStage::CreateCleanedUnitCell); +} + +// Set whether to remove by NETA definition in clean-up +void CIFContext::setRemoveNETA(bool b, bool byFragment) +{ + if (removeNETA_ == b && removeNETAByFragment_ == byFragment) + return; + + removeNETA_ = b; + removeNETAByFragment_ = byFragment; + + if (moietyRemovalNETA_.isValid()) + generate(CIFGenerationStage::CreateCleanedUnitCell); +} + +// Set NETA for moiety removal +bool CIFContext::setMoietyRemovalNETA(std::string_view netaDefinition) { return moietyRemovalNETA_.create(netaDefinition); } + +// Set supercell repeat +void CIFContext::setSupercellRepeat(const Vector3i &repeat) +{ + supercellRepeat_ = repeat; + + generate(CIFGenerationStage::CreateSupercell); +} + +// Recreate the data +bool CIFContext::generate(CIFGenerationStage fromStage) +{ + // Generate data starting from the specified stage, falling through to subsequent stages in the switch + + switch (fromStage) + { + case (CIFGenerationStage::CreateBasicUnitCell): + if (!createBasicUnitCell()) + return false; + case (CIFGenerationStage::CreateCleanedUnitCell): + if (!createCleanedUnitCell()) + return false; + case (CIFGenerationStage::DetectMolecules): + detectMolecules(); + case (CIFGenerationStage::CreateSupercell): + if (!createSupercell()) + return false; + } + + return true; +} + +// Return whether the generated data is valid +bool CIFContext::isValid() const +{ + return !molecularSpecies_.empty() || supercellSpecies_.fragment(0).size() != supercellSpecies_.nAtoms(); +} + +// Return supercell species +const Species &CIFContext::supercellSpecies() const { return supercellSpecies_; } + +// Return cleaned unit cell species +const Species &CIFContext::cleanedUnitCellSpecies() const { return cleanedUnitCellSpecies_; } + +// Return the detected molecular species +const std::vector &CIFContext::molecularSpecies() const { return molecularSpecies_; } + +// Return the generated configuration +Configuration *CIFContext::generatedConfiguration() { return &supercellConfiguration_; } + +// Return the basic unit cell configuration +Structure *CIFContext::structure() { return &structure_; } + +// Finalise, copying the required species and resulting configuration to the target CoreData +void CIFContext::finalise(CoreData &coreData, const Flags &flags) const +{ + Configuration *configuration; + + if (flags.isSet(OutputFlags::OutputMolecularSpecies)) + { + if (flags.isSet(OutputFlags::OutputConfiguration)) + { + configuration = coreData.addConfiguration(); + configuration->setName(chemicalFormula()); + + // Grab the generator + auto &generator = configuration->generator(); + + // Add Box + auto boxNode = generator.createRootNode({}); + auto cellLengths = supercellConfiguration_.box()->axisLengths(); + auto cellAngles = supercellConfiguration_.box()->axisAngles(); + boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); + boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); + + for (auto &cifMolecularSp : molecularSpecies_) + { + // Add the species + auto *sp = coreData.copySpecies(cifMolecularSp.species().get()); + + // Determine a unique suffix + auto base = sp->name(); + std::string uniqueSuffix{base}; + if (!generator.nodes().empty()) + { + // Start from the last root node + auto root = generator.nodes().back(); + auto suffix = 0; + + while (generator.rootSequence().nodeInScope(root, std::format("SymmetryCopies_{}", uniqueSuffix)) != + nullptr) + uniqueSuffix = std::format("{}_{:02d}", base, ++suffix); + } + + // We use 'CoordinateSets' here, because in this instance we are working with (CoordinateSet, Add) pairs + + // CoordinateSets + auto coordsNode = + generator.createRootNode(std::format("SymmetryCopies_{}", uniqueSuffix), sp); + coordsNode->keywords().setEnumeration("Source", CoordinateSetsGeneratorNode::CoordinateSetSource::File); + coordsNode->setSets(cifMolecularSp.allInstanceCoordinates()); + + // Add + auto addNode = generator.createRootNode(std::format("Add_{}", uniqueSuffix), coordsNode); + addNode->keywords().set("Population", NodeValueProxy(int(cifMolecularSp.instances().size()))); + addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); + addNode->keywords().set("Rotate", false); + addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); + } + } + else + { + for (auto &cifMolecularSp : molecularSpecies_) + { + coreData.copySpecies(cifMolecularSp.species().get()); + } + } + } + else + { + auto *sp = coreData.addSpecies(); + sp->copyBasic(&supercellSpecies_); + if (flags.isSet(OutputFlags::OutputSupermolecule)) + { + sp->removePeriodicBonds(); + sp->removeBox(); + } + else + sp->createBox(supercellSpecies_.box()->axisLengths(), supercellSpecies_.box()->axisAngles()); + + sp->updateIntramolecularTerms(); + + if (flags.isSet(OutputFlags::OutputConfiguration)) + { + configuration = coreData.addConfiguration(); + configuration->setName(chemicalFormula()); + + // Grab the generator + auto &generator = configuration->generator(); + + // Add Box + auto boxNode = generator.createRootNode({}); + auto cellLengths = supercellConfiguration_.box()->axisLengths(); + auto cellAngles = supercellConfiguration_.box()->axisAngles(); + boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); + boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); + + // Add + auto addNode = generator.createRootNode(std::format("Add_{}", sp->name()), sp); + addNode->keywords().set("Population", NodeValueProxy(1)); + addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); + addNode->keywords().set("Rotate", false); + addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); + } + } +} + +/* + * Helpers + */ + +// Apply CIF bonding to a given species +void CIFContext::applyCIFBonding(Species *sp, bool preventMetallicBonding) +{ + if (!hasBondDistances()) + return; + + auto *box = sp->box(); + auto pairs = PairIterator(sp->nAtoms()); + for (auto pair : pairs) + { + // Grab indices and atom references + auto [indexI, indexJ] = pair; + if (indexI == indexJ) + continue; + + auto &i = sp->atom(indexI); + auto &j = sp->atom(indexJ); + + // Prevent metallic bonding? + if (preventMetallicBonding && Elements::isMetallic(i.Z()) && Elements::isMetallic(j.Z())) + continue; + + // Retrieve distance + auto r = bondDistance(i.atomType()->name(), j.atomType()->name()); + if (!r) + continue; + else if (fabs(box->minimumDistance(i.r(), j.r()) - r.value()) < 1.0e-2) + sp->addBond(&i, &j); + } +} + +// Determine the best NETA definition for the supplied species +std::tuple> CIFContext::bestNETADefinition(Species *sp) +{ + // Set up the return value and bind its contents + std::tuple> result{NETADefinition(), {}}; + auto &&[bestNETA, rootAtoms] = result; + + // Maintain a set of atoms matched by any NETA description we generate + std::set alreadyMatched; + + // Loop over species atoms + for (auto &i : sp->atoms()) + { + // Skip this atom? + if (alreadyMatched.find(&i) != alreadyMatched.end()) + continue; + + // Create a NETA definition with this atom as the root + NETADefinition neta; + neta.create(&i, std::nullopt, + Flags(NETADefinition::NETACreationFlags::ExplicitHydrogens, + NETADefinition::NETACreationFlags::IncludeRootElement)); + + // Apply this match over the whole species + std::vector currentRootAtoms; + for (auto &j : sp->atoms()) + { + if (neta.matches(&j)) + { + currentRootAtoms.push_back(&j); + alreadyMatched.insert(&j); + } + } + + // Is this a better description? + auto better = false; + if (rootAtoms.empty() || currentRootAtoms.size() < rootAtoms.size()) + better = true; + else if (currentRootAtoms.size() == rootAtoms.size()) + { + // Replace the current match if there are more bonds on the current atom. + if (i.nBonds() > rootAtoms.front()->nBonds()) + better = true; + } + + if (better) + { + bestNETA = neta; + rootAtoms = currentRootAtoms; + } + } + + return result; +} + +// Get instances for the supplied species from the cleaned unit cell +std::vector CIFContext::getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, + const NETADefinition &neta, + const std::vector &referenceRootAtoms) +{ + if (referenceRootAtoms.empty() || !neta.isValid()) + return {}; + + // Loop over atoms in the unit cell - we'll mark any that we select as an instance so we speed things up and avoid + // duplicates + const auto &unitCellAtoms = cleanedUnitCellSpecies_.atoms(); + std::vector instances; + auto atomIndexIterator = std::find(atomMask.begin(), atomMask.end(), false); + while (atomIndexIterator != atomMask.end()) + { + // Try to match this atom / fragment + const auto atomIndex = atomIndexIterator - atomMask.begin(); + auto &atom = unitCellAtoms[atomIndex]; + auto matchedUnitCellAtoms = neta.matchedPath(&atom).set(); + if (matchedUnitCellAtoms.empty()) + { + atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); + continue; + } + + // Found a fragment that matches the NETA description - we now create a temporary instance Species which will contain + // the selected fragment atoms, reassembled into a molecule (i.e. unfolded) and with bonding applied / calculated. + // We need to copy the unit cell from the crystal so we detect bonds properly. + Species instanceSpecies; + instanceSpecies.createBox(unitCellSpecies_.box()->axisLengths(), unitCellSpecies_.box()->axisAngles()); + auto rootAtomLocalIndex = -1; + // -- Create species atoms from those matched in the unit cell by the NETA description. + for (auto &matchedAtom : matchedUnitCellAtoms) + { + auto idx = instanceSpecies.addAtom(matchedAtom->Z(), matchedAtom->r(), 0.0, matchedAtom->atomType()); + + // Store the index of the root atom in match in our instance species when we find it + if (matchedAtom == &atom) + rootAtomLocalIndex = idx; + } + // -- Store the local root atom so we can access its coordinates for the origin translation + auto &instanceSpeciesRootAtom = instanceSpecies.atom(rootAtomLocalIndex); + // -- Calculate / apply bonding + if (!preventAllBonds_) + if (useCIFBondingDefinitions_) + applyCIFBonding(&instanceSpecies, preventMetallicBonds_); + else + instanceSpecies.addMissingBonds(bondingTolerance_, preventMetallicBonds_); + + // Create a LocalMolecule as a working area for folding, translation, and rotation of the instance coordinates. + LocalMolecule instanceMolecule; + instanceMolecule.setSpecies(&instanceSpecies); + // -- Copy the coordinates off the matched unit cell atoms to our molecule and flag them as complete + auto count = 0; + for (auto &&[matchedAtom, instanceMolAtom] : zip(matchedUnitCellAtoms, instanceMolecule.localAtoms())) + { + instanceMolAtom.setR(matchedAtom->r()); + atomMask[matchedAtom->index()] = true; + } + auto &instanceMoleculeRootAtom = instanceMolecule.localAtoms()[rootAtomLocalIndex]; + + // Unfold the molecule and store the unfolded molecule coordinates back into the instance Species. + // This represents our full instance coordinates we will be storing (but not their final order) + instanceMolecule.unFold(unitCellSpecies_.box()); + for (auto &&[molAtom, spAtom] : zip(instanceMolecule.localAtoms(), instanceSpecies.atoms())) + spAtom.setR(molAtom.r()); + + /* + * Now, we have a root match atom on the current instance and a vector of possible matching sites on the reference + * species (in referenceRootAtoms). For each of the referenceRootAtoms, try to incrementally select along bonds using + * basic NETA connectivity. + */ + + // Generate basic NETA descriptions for each atom in the reference and candidate species + std::map referenceAtomNETA; + for (auto &spAtom : referenceSpecies->atoms()) + referenceAtomNETA[&spAtom] = NETADefinition(&spAtom, 1, {NETADefinition::NETACreationFlags::IncludeRootElement}); + + std::map matchMap; + for (const auto *referenceRootAtom : referenceRootAtoms) + { + // The root atom is the starting point + matchMap = matchAtom(referenceRootAtom, &instanceSpeciesRootAtom, referenceAtomNETA, {}); + if (!matchMap.empty()) + break; + } + + // Result? + if (matchMap.empty()) + { + Messenger::error("Failed to match connectivity of an instance to the reference molecule.\n"); + return {}; + } + else if (matchMap.size() != referenceSpecies->nAtoms()) + { + Messenger::error( + "Internal error - failed to match connectivity of all atoms within an instance to the reference molecule.\n"); + return {}; + } + + // Create the final instance + auto &instance = instances.emplace_back(); + instance.setSpecies(referenceSpecies); + for (const auto &[refSpeciesAtom, instanceSpeciesAtom] : matchMap) + { + instance.localAtom(refSpeciesAtom->index()).setR(instanceSpeciesAtom->r()); + } + + // Find the next available atom + atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); + } + + return instances; +} + +// Recursively check NETA description matches between the supplied atoms +std::map +CIFContext::matchAtom(const SpeciesAtom *referenceAtom, const SpeciesAtom *instanceAtom, + const std::map &refNETA, + const std::map &map) +{ + // If the reference atom NETA doesn't match the instance atom we cannot proceed + if (!refNETA.at(referenceAtom).matches(instanceAtom)) + return {}; + + // Check the map to see if we have already associated the reference atom to an instance atom, or if the instance atom + // is already associated to a different reference atom. + for (auto &&[mappedRefAtom, mappedInstanceAtom] : map) + { + // Found it - double-check to ensure that the current association matches our instance atom. If it does we can return + // the map as it currently stands. If not we return an empty map to indicate failure. + if (mappedRefAtom == referenceAtom) + { + if (mappedInstanceAtom == instanceAtom) + { + return map; + } + else + { + return {}; + } + } + else if (mappedInstanceAtom == instanceAtom) + { + return {}; + } + } + + // Copy the current map, associate our initial pair of atoms and try to extend it + auto newMap = map; + newMap[referenceAtom] = instanceAtom; + + // Cycle over bonds on the reference atom and find + for (const auto &referenceBond : referenceAtom->bonds()) + { + // Get the reference bond partner + auto *referenceBondPartner = referenceBond.get().partner(referenceAtom); + + // Try to find a match over bonds on the instance atom + std::map bondResult; + for (const auto &instanceBond : instanceAtom->bonds()) + { + // Get the instance bond partner + auto *instanceBondPartner = instanceBond.get().partner(instanceAtom); + + // Recurse + bondResult = matchAtom(referenceBondPartner, instanceBondPartner, refNETA, newMap); + if (!bondResult.empty()) + break; + } + + // If we found a suitable match recursing into the bond, store the result into newMap and continue to the next bond. + // If we didn't find a good match, we return now. + if (bondResult.empty()) + { + return {}; + } + else + { + newMap = bondResult; + } + } + + // If we get to here then we succeeded, so return the new map + return newMap; +} + +// Calculate difference metric between the supplied species and local molecule +std::pair> CIFContext::differenceMetric(const Species *species, const LocalMolecule &molecule) +{ + auto difference = 0.0; + std::vector atomIndexMap(species->nAtoms(), -1); + auto nBadAtoms = 0; + for (auto spI = 0; spI < species->nAtoms(); ++spI) + { + auto &spAtom = species->atom(spI); + + // For this species atom find the closest atom in the molecule + auto distanceSq = 1.0e6; + for (auto molI = 0; molI < molecule.nAtoms(); ++molI) + { + auto rABSq = (spAtom.r() - molecule.localAtoms()[molI].r()).magnitudeSq(); + if (rABSq < distanceSq) + { + distanceSq = rABSq; + atomIndexMap[spI] = molI; + } + } + + if (distanceSq > 0.1) + ++nBadAtoms; + + // Update the difference score + const auto &closestMolSpAtom = molecule.species()->atom(atomIndexMap[spI]); + difference += distanceSq; + if (spAtom.Z() != closestMolSpAtom.Z()) + difference += std::max(int(spAtom.Z()), int(closestMolSpAtom.Z())) * 10.0; + } + + return {difference, atomIndexMap}; +} diff --git a/src/nodes/cif/io/cifContext.h b/src/nodes/cif/io/cifContext.h new file mode 100644 index 0000000000..3f168a292f --- /dev/null +++ b/src/nodes/cif/io/cifContext.h @@ -0,0 +1,220 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include "classes/configuration.h" +#include "classes/coreData.h" +#include "classes/species.h" +#include "classes/structure.h" +#include "data/spaceGroups.h" +#include "math/matrix4.h" +#include "neta/neta.h" +#include "nodes/cif/io/cifClasses.h" +#include "templates/flags.h" +#include + +// Forward Declarations +class Box; + +// CIF Handler +class CIFContext +{ + public: + CIFContext(); + ~CIFContext() = default; + + /* + * Raw Data + */ + public: + // Data Types + using CIFTags = std::map>; + + private: + // Vector of enumerated data items + CIFTags tags_; + + private: + // Parse supplied file into the destination objects + bool parse(std::string_view filename, CIFTags &tags) const; + + public: + // Return whether the specified file parses correctly + bool validFile(std::string_view filename) const; + // Read CIF data from specified file + bool read(std::string_view filename); + // Return if the specified tag exists + bool hasTag(std::string tag) const; + // Return tag data string (if it exists) assuming a single datum (first in the vector) + std::optional getTagString(std::string tag) const; + // Return tag data strings (if it exists) + std::vector getTagStrings(std::string tag) const; + // Return tag data as double (if it exists) assuming a single datum (first in the vector) + std::optional getTagDouble(std::string tag) const; + // Return tag data doubles (if it exists) + std::vector getTagDoubles(std::string tag) const; + // Return tag data as integer (if it exists) assuming a single datum (first in the vector) + std::optional getTagInt(std::string tag) const; + + /* + * Processed Data + */ + private: + // Space group + SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::NoSpaceGroup}; + // Atom assemblies + std::vector assemblies_; + // Bond information + std::vector bondingPairs_; + + public: + // Set space group from index + void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); + // Return space group + SpaceGroups::SpaceGroupId spaceGroup() const; + // Return cell lengths + std::optional getCellLengths() const; + // Return cell angles + std::optional getCellAngles() const; + // Return chemical formula + std::string chemicalFormula() const; + // Get (add or retrieve) named assembly + CIFAssembly &getAssembly(std::string_view name); + // Return atom assemblies + std::vector &assemblies(); + const std::vector &assemblies() const; + // Return whether any bond distances are defined + bool hasBondDistances() const; + // Return whether a bond distance is defined for the specified label pair + std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; + + /* + * Creation + */ + public: + // CIF Generation Stages + enum class CIFGenerationStage + { + CreateBasicUnitCell, + CreateCleanedUnitCell, + DetectMolecules, + CreateSupercell + }; + // CIF Species Output Flags + enum OutputFlags + { + OutputConfiguration, /* Output a Configuration */ + OutputMolecularSpecies, /* Partitioning - output molecular species */ + OutputFramework, /* Partitioning - output a framework species */ + OutputSupermolecule /* Partitioning - output a supermolecule */ + }; + + private: + // Temporary atom types used for unique atom labels + std::vector> atomLabelTypes_; + // Tolerance for removal of overlapping atoms + double overlapTolerance_{0.1}; + // Whether to use CIF bonding definitions + bool useCIFBondingDefinitions_{false}; + // Bonding tolerance, if calculating bonding rather than using CIF definitions + double bondingTolerance_{1.1}; + // Whether to ignore all bonds + bool preventAllBonds_{false}; + // Whether to prevent metallic bonding + bool preventMetallicBonds_{true}; + // Whether to remove free atomic moieties in clean-up + bool removeAtomics_{false}; + // Whether to remove water and coordinated oxygen atoms in clean-up + bool removeWaterAndCoordinateOxygens_{false}; + // Whether to remove by NETA definition in clean-up + bool removeNETA_{false}; + // Whether to expand NETA matches to fragments when removing in clean-up + bool removeNETAByFragment_{false}; + // NETA for moiety removal, if specified + NETADefinition moietyRemovalNETA_; + // Supercell repeat + Vector3i supercellRepeat_{1, 1, 1}; + // Basic unit cell + Species unitCellSpecies_; + Configuration unitCellConfiguration_; + Structure structure_; + // Cleaned unit cell + Species cleanedUnitCellSpecies_; + Configuration cleanedUnitCellConfiguration_; + // Molecular definition of unit cell (if possible) + std::vector molecularSpecies_; + // Final generated result (supercell) + Species supercellSpecies_; + Configuration supercellConfiguration_; + + private: + // Create basic unit cell + bool createBasicUnitCell(); + // Create structure from basic unit cell atoms and connectivity + bool createStructure(); + // Create the cleaned unit cell + bool createCleanedUnitCell(); + // Try to detect molecules in the cell contents + bool detectMolecules(); + // Create supercell species + bool createSupercell(); + + public: + // Set overlap tolerance + void setOverlapTolerance(double tol); + // Set whether to use CIF bonding definitions + void setUseCIFBondingDefinitions(bool b); + // Set bonding tolerance + void setBondingTolerance(double tol); + // Whether to ignore all bonds + void setPreventAllBonds(bool b); + // Set whether to prevent metallic bonding + void setPreventMetallicBonds(bool b); + // Set whether to remove free atomic moieties in clean-up + void setRemoveAtomics(bool b); + // Set whether to remove water and coordinated oxygen atoms in clean-up + void setRemoveWaterAndCoordinateOxygens(bool b); + // Set whether to remove by NETA definition in clean-up + void setRemoveNETA(bool b, bool byFragment); + // Set NETA for moiety removal + bool setMoietyRemovalNETA(std::string_view netaDefinition); + // Set supercell repeat + void setSupercellRepeat(const Vector3i &repeat); + // Recreate the data + bool generate(CIFGenerationStage fromStage = CIFGenerationStage::CreateBasicUnitCell); + // Return whether the generated data is valid + bool isValid() const; + // Return supercell species + const Species &supercellSpecies() const; + // Return cleaned unit cell species + const Species &cleanedUnitCellSpecies() const; + // Return the detected molecular species + const std::vector &molecularSpecies() const; + // Return the generated configuration + Configuration *generatedConfiguration(); + // Return the basic crystal structure + Structure *structure(); + // Finalise, copying the required species and resulting configuration to the target CoreData + void finalise(CoreData &coreData, const Flags &flags = {}) const; + + /* + * Helpers + */ + private: + // Apply CIF bonding to a given species + void applyCIFBonding(Species *sp, bool preventMetallicBonding); + // Determine the best NETA definition for the supplied species + std::tuple> bestNETADefinition(Species *sp); + // Get instances of species molecules from the supplied NETA definition + std::vector getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, + const NETADefinition &neta, + const std::vector &referenceRootAtoms); + // Calculate difference metric between the supplied species and local molecule + static std::pair> differenceMetric(const Species *species, const LocalMolecule &molecule); + // Recursively check NETA description matches between the supplied atoms + std::map matchAtom(const SpeciesAtom *referenceAtom, + const SpeciesAtom *instanceAtom, + const std::map &refNETA, + const std::map &map); +}; diff --git a/src/nodes/setCIFAtomGroupActivity.cpp b/src/nodes/cif/setCIFAtomGroupActivity.cpp similarity index 78% rename from src/nodes/setCIFAtomGroupActivity.cpp rename to src/nodes/cif/setCIFAtomGroupActivity.cpp index 3f5d69a5ab..d477a7ec9e 100644 --- a/src/nodes/setCIFAtomGroupActivity.cpp +++ b/src/nodes/cif/setCIFAtomGroupActivity.cpp @@ -1,16 +1,16 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "nodes/setCIFAtomGroupActivity.h" +#include "nodes/cif/setCIFAtomGroupActivity.h" SetCIFAtomGroupActivityNode::SetCIFAtomGroupActivityNode(Graph *parentGraph) : Node(parentGraph) { // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) + addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) ->setFlags({ParameterBase::Required}); // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); + addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); // Options addOption("Assembly", "CIF assembly name", assemblyName_); diff --git a/src/nodes/setCIFAtomGroupActivity.h b/src/nodes/cif/setCIFAtomGroupActivity.h similarity index 89% rename from src/nodes/setCIFAtomGroupActivity.h rename to src/nodes/cif/setCIFAtomGroupActivity.h index 93b532af89..4d7e6f36d5 100644 --- a/src/nodes/setCIFAtomGroupActivity.h +++ b/src/nodes/cif/setCIFAtomGroupActivity.h @@ -3,10 +3,10 @@ #pragma once -#include "nodes/cifLoader.h" +#include "nodes/cif/io/cifContext.h" #include "nodes/node.h" -// CIFLoader Node +// ImportCIFStructure Node class SetCIFAtomGroupActivityNode : public Node { public: @@ -22,7 +22,7 @@ class SetCIFAtomGroupActivityNode : public Node */ private: // CIF handler context - CIFLoaderNode::CIFContext *context_{nullptr}; + CIFContext *context_{nullptr}; // Selected CIF assembly atom group name std::string atomGroupName_; // Selected CIF assembly name diff --git a/src/nodes/registry.cpp b/src/nodes/registry.cpp index 8434afe85e..8f6dbe69f7 100644 --- a/src/nodes/registry.cpp +++ b/src/nodes/registry.cpp @@ -7,14 +7,15 @@ #include "nodes/angle.h" #include "nodes/atomicMC/atomicMC.h" #include "nodes/bragg.h" -#include "nodes/cifBondingOptions.h" -#include "nodes/cifLoader.h" -#include "nodes/cifMolecularSpecies.h" -#include "nodes/cifPeriodicFramework.h" -#include "nodes/cifRemoveAtomic.h" -#include "nodes/cifRemoveWater.h" -#include "nodes/cifStructureCleanup.h" -#include "nodes/cifSuperMolecule.h" +#include "nodes/cif/cifBondingOptions.h" +#include "nodes/cif/cifMolecularSpecies.h" +#include "nodes/cif/cifPeriodicFramework.h" +#include "nodes/cif/cifRemoveAtomic.h" +#include "nodes/cif/cifRemoveWater.h" +#include "nodes/cif/cifStructureCleanup.h" +#include "nodes/cif/cifSuperMolecule.h" +#include "nodes/cif/importCIFStructure.h" +#include "nodes/cif/setCIFAtomGroupActivity.h" #include "nodes/configuration.h" #include "nodes/data1DImport.h" #include "nodes/derivative.h" @@ -40,7 +41,6 @@ #include "nodes/multiply.h" #include "nodes/neutronSQ/neutronSQ.h" #include "nodes/numberNode.h" -#include "nodes/setCIFAtomGroupActivity.h" #include "nodes/setCell.h" #include "nodes/setCoordinates.h" #include "nodes/siteRDF.h" @@ -76,7 +76,7 @@ void NodeRegistry::instantiateNodeProducers() {"CIFStructureCleanup", makeDerivedNode()}, {"Configuration", makeDerivedNode()}, {"CIFBondingOptions", makeDerivedNode()}, - {"CIFLoader", makeDerivedNode()}, + {"ImportCIFStructure", makeDerivedNode()}, {"CIFMolecularSpecies", makeDerivedNode()}, {"CIFPeriodicFramework", makeDerivedNode()}, {"CIFRemoveAtomic", makeDerivedNode()}, diff --git a/tests/io/cif.cpp b/tests/io/cif.cpp index 6486be9b6d..82031fe6a3 100644 --- a/tests/io/cif.cpp +++ b/tests/io/cif.cpp @@ -1,9 +1,9 @@ // SPDX-License-Identifier: GPL-3.0-or-later // Copyright (c) 2026 Team Dissolve and contributors -#include "io/import/cif.h" #include "classes/empiricalFormula.h" #include "io/import/species.h" +#include "nodes/cif/io/cifContext.h" #include "tests/testData.h" #include @@ -67,64 +67,64 @@ TEST_F(ImportCIFTest, Parse) for (auto &cif : cifs) { - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read(cifPath + cif)); + CIFContext cifContext; + ASSERT_TRUE(cifContext.read(cifPath + cif)); } } TEST_F(ImportCIFTest, NaCl) { - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/NaCl-1000041.cif")); - EXPECT_TRUE(cifHandler.generate()); + CIFContext cifContext; + ASSERT_TRUE(cifContext.read("cif/NaCl-1000041.cif")); + EXPECT_TRUE(cifContext.generate()); // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_225); + EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_225); constexpr double A = 5.62; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 8); + testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 8); // Calculating bonding is the default, but this gives a continuous framework... - EXPECT_EQ(cifHandler.molecularSpecies().size(), 0); + EXPECT_EQ(cifContext.molecularSpecies().size(), 0); // Get molecular species - cifHandler.setUseCIFBondingDefinitions(true); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 2); - testMolecularSpecies(cifHandler.molecularSpecies()[0], {"Na", 4, 1}); + cifContext.setUseCIFBondingDefinitions(true); + EXPECT_EQ(cifContext.molecularSpecies().size(), 2); + testMolecularSpecies(cifContext.molecularSpecies()[0], {"Na", 4, 1}); std::vector R = {{0.0, 0.0, 0.0}, {0.0, A / 2, A / 2}, {A / 2, 0.0, A / 2}, {A / 2, A / 2, 0.0}}; - for (auto &&[instance, r2] : zip(cifHandler.molecularSpecies()[0].instances(), R)) + for (auto &&[instance, r2] : zip(cifContext.molecularSpecies()[0].instances(), R)) DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), r2); - testMolecularSpecies(cifHandler.molecularSpecies()[1], {"Cl", 4, 1}); - for (auto &&[instance, r2] : zip(cifHandler.molecularSpecies()[1].instances(), R)) + testMolecularSpecies(cifContext.molecularSpecies()[1], {"Cl", 4, 1}); + for (auto &&[instance, r2] : zip(cifContext.molecularSpecies()[1].instances(), R)) DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), (r2 - A / 2).abs()); // 2x2x2 supercell - cifHandler.setSupercellRepeat({2, 2, 2}); - EXPECT_TRUE(cifHandler.generate()); - testBox(cifHandler.generatedConfiguration(), {A * 2, A * 2, A * 2}, {90, 90, 90}, 8 * 8); + cifContext.setSupercellRepeat({2, 2, 2}); + EXPECT_TRUE(cifContext.generate()); + testBox(cifContext.generatedConfiguration(), {A * 2, A * 2, A * 2}, {90, 90, 90}, 8 * 8); } TEST_F(ImportCIFTest, NaClO3) { - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/NaClO3-1010057.cif")); - EXPECT_TRUE(cifHandler.generate()); + CIFContext cifContext; + ASSERT_TRUE(cifContext.read("cif/NaClO3-1010057.cif")); + EXPECT_TRUE(cifContext.generate()); // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_198); + EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_198); constexpr double A = 6.55; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 20); + testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 20); // Turn off automatic bond calculation - there are no bonding defs in the CIF, so we expect species for each atomic // component (4 Na, 4 Cl, and 12 O) - cifHandler.setUseCIFBondingDefinitions(true); - auto &cifMols = cifHandler.molecularSpecies(); + cifContext.setUseCIFBondingDefinitions(true); + auto &cifMols = cifContext.molecularSpecies(); ASSERT_EQ(cifMols.size(), 3); testMolecularSpecies(cifMols[0], {"Na", 4, 1}); testMolecularSpecies(cifMols[1], {"Cl", 4, 1}); testMolecularSpecies(cifMols[2], {"O", 12, 1}); // Calculate bonding ourselves to get the correct species - cifHandler.setUseCIFBondingDefinitions(false); + cifContext.setUseCIFBondingDefinitions(false); ASSERT_EQ(cifMols.size(), 2); testMolecularSpecies(cifMols[0], {"Na", 4, 1}); testMolecularSpecies(cifMols[1], {"ClO3", 4, 4}); @@ -132,14 +132,14 @@ TEST_F(ImportCIFTest, NaClO3) TEST_F(ImportCIFTest, CuBTC) { - CIFHandler cifHandler; - ASSERT_TRUE(cifHandler.read("cif/CuBTC-7108574.cif")); - EXPECT_TRUE(cifHandler.generate()); + CIFContext cifContext; + ASSERT_TRUE(cifContext.read("cif/CuBTC-7108574.cif")); + EXPECT_TRUE(cifContext.generate()); // Check basic info - EXPECT_EQ(cifHandler.spaceGroup(), SpaceGroups::SpaceGroup_225); + EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_225); constexpr auto A = 26.3336; - testBox(cifHandler.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 672); + testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 672); // 16 basic formula units per unit cell constexpr auto N = 16; @@ -147,66 +147,66 @@ TEST_F(ImportCIFTest, CuBTC) // Check basic formula (which includes bound water oxygens - with no H - at this point) and using O group EmpiricalFormula::EmpiricalFormulaMap cellFormulaH = { {Elements::Cu, 3 * N}, {Elements::C, 18 * N}, {Elements::H, 6 * N}, {Elements::O, 15 * N}}; - EXPECT_EQ(EmpiricalFormula::formula(cifHandler.generatedConfiguration()->atoms(), + EXPECT_EQ(EmpiricalFormula::formula(cifContext.generatedConfiguration()->atoms(), [](const auto &i) { return i.speciesAtom()->Z(); }), EmpiricalFormula::formula(cellFormulaH)); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 2); + EXPECT_EQ(cifContext.molecularSpecies().size(), 2); // Change active assemblies to get amine-substituted structure EmpiricalFormula::EmpiricalFormulaMap cellFormulaNH2 = cellFormulaH; cellFormulaNH2[Elements::N] = 6 * N; cellFormulaNH2[Elements::H] *= 2; - cifHandler.getAssembly("A").getGroup("1").setActive(false); - cifHandler.getAssembly("B").getGroup("2").setActive(true); - cifHandler.getAssembly("C").getGroup("2").setActive(true); - EXPECT_TRUE(cifHandler.generate()); - EXPECT_EQ(EmpiricalFormula::formula(cifHandler.generatedConfiguration()->atoms(), + cifContext.getAssembly("A").getGroup("1").setActive(false); + cifContext.getAssembly("B").getGroup("2").setActive(true); + cifContext.getAssembly("C").getGroup("2").setActive(true); + EXPECT_TRUE(cifContext.generate()); + EXPECT_EQ(EmpiricalFormula::formula(cifContext.generatedConfiguration()->atoms(), [](const auto &i) { return i.speciesAtom()->Z(); }), EmpiricalFormula::formula(cellFormulaNH2)); // Remove those free oxygens so we just have a framework - cifHandler.setRemoveAtomics(true); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 0); + cifContext.setRemoveAtomics(true); + EXPECT_EQ(cifContext.molecularSpecies().size(), 0); } TEST_F(ImportCIFTest, MoleculeOrdering) { - CIFHandler cifHandler; + CIFContext cifContext; const auto cifFiles = {"cif/molecule-test-simple-ordered.cif", "cif/molecule-test-simple-unordered.cif", "cif/molecule-test-simple-unordered-rotated.cif"}; for (auto cifFile : cifFiles) { // Load the CIF file - ASSERT_TRUE(cifHandler.read(cifFile)); - EXPECT_TRUE(cifHandler.generate()); + ASSERT_TRUE(cifContext.read(cifFile)); + EXPECT_TRUE(cifContext.generate()); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 1); + EXPECT_EQ(cifContext.molecularSpecies().size(), 1); - auto &cifMolecule = cifHandler.molecularSpecies().front(); + auto &cifMolecule = cifContext.molecularSpecies().front(); EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = { {Elements::Cl, 1}, {Elements::O, 1}, {Elements::C, 1}, {Elements::H, 3}}; testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 6, 6}); - testInstanceConsistency(cifMolecule, cifHandler.cleanedUnitCellSpecies()); + testInstanceConsistency(cifMolecule, cifContext.cleanedUnitCellSpecies()); } } TEST_F(ImportCIFTest, BigMoleculeOrdering) { - CIFHandler cifHandler; + CIFContext cifContext; const auto cifFile = "cif/Bisphen_n_arenes_1517789.cif"; // Load the CIF file - ASSERT_TRUE(cifHandler.read(cifFile)); - EXPECT_TRUE(cifHandler.generate()); + ASSERT_TRUE(cifContext.read(cifFile)); + EXPECT_TRUE(cifContext.generate()); - EXPECT_EQ(cifHandler.molecularSpecies().size(), 1); + EXPECT_EQ(cifContext.molecularSpecies().size(), 1); - auto &cifMolecule = cifHandler.molecularSpecies().front(); + auto &cifMolecule = cifContext.molecularSpecies().front(); EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = {{Elements::O, 6}, {Elements::C, 51}, {Elements::H, 54}}; testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 4, 111}); - testInstanceConsistency(cifMolecule, cifHandler.cleanedUnitCellSpecies()); + testInstanceConsistency(cifMolecule, cifContext.cleanedUnitCellSpecies()); } } // namespace UnitTest diff --git a/tests/nodes/bragg.cpp b/tests/nodes/bragg.cpp index fdf3dbff60..48124b7d2c 100644 --- a/tests/nodes/bragg.cpp +++ b/tests/nodes/bragg.cpp @@ -6,7 +6,7 @@ #include "classes/speciesSites.h" #include "io/import/trajectory.h" #include "math/rangedVector3.h" -#include "nodes/cifMolecularSpecies.h" +#include "nodes/cif/cifMolecularSpecies.h" #include "nodes/gr/gr.h" #include "nodes/importConfigurationTrajectory.h" #include "nodes/iterableGraph.h" @@ -40,11 +40,11 @@ class BraggNodeTest : public ::testing::Test // Create species and configuration from MgO cif file auto root = testGraph_.dissolveGraph(); - ASSERT_TRUE(testGraph_.appendNode("CIFLoader", "CIFLoader")); + ASSERT_TRUE(testGraph_.appendNode("importCIFStructure", "importCIFStructure")); ASSERT_TRUE(testGraph_.fetchHead()->setOption("FilePath", "cif/1000053.cif")); ASSERT_TRUE(testGraph_.appendNode("CIFBondingOptions", "CIFBonds")); - ASSERT_TRUE(root->addEdge({"CIFLoader", "CIFContext", "CIFBonds", "CIFContext"})); + ASSERT_TRUE(root->addEdge({"importCIFStructure", "CIFContext", "CIFBonds", "CIFContext"})); ASSERT_TRUE(testGraph_.fetchHead()->setOption("PreventAllBonds", true)); // Create a supercell that is 5 * unitcell diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index 301a357110..04a1e5dd2e 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -3,8 +3,8 @@ #include "classes/empiricalFormula.h" #include "io/import/species.h" -#include "nodes/cifLoader.h" -#include "nodes/cifMolecularSpecies.h" +#include "nodes/cif/cifMolecularSpecies.h" +#include "nodes/cif/importCIFStructure.h" #include "tests/graphData.h" #include "tests/testData.h" #include @@ -30,7 +30,7 @@ class CIFNodeTest : public ::testing::Test void createGraph(std::string filename) { auto name = cifNameFromFile(filename); - EXPECT_TRUE(testGraph_.appendNode("CIFLoader", name)); + EXPECT_TRUE(testGraph_.appendNode("ImportCIFStructure", name)); testGraph_.fetchHead()->setOption("FilePath", path_ + filename); EXPECT_TRUE(testGraph_.appendNode("CIFBondingOptions", name + "//BondingOptions")); EXPECT_TRUE(testGraph_.appendNode("CIFRemoveAtomic", name + "//RemoveAtomic")); @@ -50,11 +50,11 @@ class CIFNodeTest : public ::testing::Test return name; } // Retrieve CIF context by filename - CIFLoaderNode::CIFContext *getContextByFileName(std::string filename) + CIFContext *getContextByFileName(std::string filename) { auto name = cifNameFromFile(filename); auto node = testGraph_.findNode(name); - auto context = node->getOutputValue("CIFContext"); + auto context = node->getOutputValue("CIFContext"); return context; } // Test Box definition diff --git a/tests/tempFile.h b/tests/tempFile.h index 661b024a7f..fa89ad26de 100644 --- a/tests/tempFile.h +++ b/tests/tempFile.h @@ -41,8 +41,8 @@ class TempFile } // Get the file name on conversion to string - operator std::string() const { return path; } - operator std::filesystem::path() const { return path; } + operator std::string() const { return path.generic_string(); } + operator std::filesystem::path() const { return path.c_str(); } private: // The actual path of the temp file From 8569e31e8a7560b92690177595eb2994b49e6d02 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 6 May 2026 14:56:08 +0100 Subject: [PATCH 04/22] delete unused files; fix typo in node name; fix structure bonding --- src/io/import/CIFImportErrorListeners.cpp | 40 - src/io/import/CIFImportErrorListeners.h | 52 - src/io/import/CIFImportLexer.g4 | 76 -- src/io/import/CIFImportParser.g4 | 46 - src/io/import/CIFImportVisitor.cpp | 65 - src/io/import/CIFImportVisitor.h | 36 - src/io/import/cif.cpp | 1328 --------------------- src/io/import/cif.h | 214 ---- src/io/import/cifClasses.cpp | 130 -- src/io/import/cifClasses.h | 142 --- src/nodes/cif/importCIFStructure.cpp | 3 + src/nodes/cif/io/cifContext.cpp | 26 +- 12 files changed, 17 insertions(+), 2141 deletions(-) delete mode 100644 src/io/import/CIFImportErrorListeners.cpp delete mode 100644 src/io/import/CIFImportErrorListeners.h delete mode 100644 src/io/import/CIFImportLexer.g4 delete mode 100644 src/io/import/CIFImportParser.g4 delete mode 100644 src/io/import/CIFImportVisitor.cpp delete mode 100644 src/io/import/CIFImportVisitor.h delete mode 100644 src/io/import/cif.cpp delete mode 100644 src/io/import/cif.h delete mode 100644 src/io/import/cifClasses.cpp delete mode 100644 src/io/import/cifClasses.h diff --git a/src/io/import/CIFImportErrorListeners.cpp b/src/io/import/CIFImportErrorListeners.cpp deleted file mode 100644 index 960fe3570d..0000000000 --- a/src/io/import/CIFImportErrorListeners.cpp +++ /dev/null @@ -1,40 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/io/CIFImportErrorListeners.h" -#include "base/messenger.h" -#include "base/sysFunc.h" - -/* - * CIFImport Lexer Error Listener - */ - -CIFImportLexerErrorListener::CIFImportLexerErrorListener() {} - -void CIFImportLexerErrorListener::syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *token, size_t line, - size_t charPositionInLine, const std::string &message, std::exception_ptr ep) -{ - Messenger::print("\nError in CIFImport definition on line {}, column {}.\n", line, charPositionInLine); - - // The actual error message can contain braces, so escape those to avoid breaking fmt - auto escaped = DissolveSys::replace(DissolveSys::replace(message, "{", "{{"), "}", "}}"); - - throw CIFImportExceptions::CIFImportSyntaxException(std::format("Syntax Error: {}", escaped)); -} - -/* - * CIFImport Parser Error Listener - */ - -CIFImportParserErrorListener::CIFImportParserErrorListener() {} - -void CIFImportParserErrorListener::syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *token, size_t line, - size_t charPositionInLine, const std::string &message, std::exception_ptr ep) -{ - Messenger::print("\nError in CIFImport definition on line {}, column {}.\n", line, charPositionInLine); - - // The actual error message can contain braces, so escape those to avoid breaking fmt - auto escaped = DissolveSys::replace(DissolveSys::replace(message, "{", "{{"), "}", "}}"); - - throw CIFImportExceptions::CIFImportSyntaxException(std::format("Syntax Error: {}", escaped)); -} diff --git a/src/io/import/CIFImportErrorListeners.h b/src/io/import/CIFImportErrorListeners.h deleted file mode 100644 index ed27e07296..0000000000 --- a/src/io/import/CIFImportErrorListeners.h +++ /dev/null @@ -1,52 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include -#include - -namespace CIFImportExceptions -{ -// CIFImport Syntax Exception -class CIFImportSyntaxException : public std::exception -{ - public: - CIFImportSyntaxException(std::string_view message = "Undefined CIFImport Syntax Exception") : message_{message} {} - - private: - // Error message - std::string message_; - - public: - virtual const char *what() const throw() { return message_.c_str(); } -}; -} // namespace CIFImportExceptions - -// CIFImport Lexer Error Listener -class CIFImportLexerErrorListener : public antlr4::BaseErrorListener -{ - public: - CIFImportLexerErrorListener(); - - /* - * BaseErrorListener Overrides - */ - public: - void syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *, size_t line, size_t charPositionInLine, - const std::string &, std::exception_ptr ep); -}; - -// CIFImport Parser Error Listener -class CIFImportParserErrorListener : public antlr4::BaseErrorListener -{ - public: - CIFImportParserErrorListener(); - - /* - * BaseErrorListener Overrides - */ - public: - void syntaxError(antlr4::Recognizer *recognizer, antlr4::Token *, size_t line, size_t charPositionInLine, - const std::string &, std::exception_ptr ep); -}; diff --git a/src/io/import/CIFImportLexer.g4 b/src/io/import/CIFImportLexer.g4 deleted file mode 100644 index 84f510b7fa..0000000000 --- a/src/io/import/CIFImportLexer.g4 +++ /dev/null @@ -1,76 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -lexer grammar CIFImportLexer; - -// Lexer file header -@lexer::header {/* CIFImport ANTLR Lexer */} - -// Add custom includes after standard ANTLR includes in both *.h and *.cpp files -@lexer::postinclude { - #include "base/sysFunc.h" - #include "nodes/cif/io/CIFImportVisitor.h" -} - -// Directly precedes the lexer class declaration in the h file (e.g. for additional types etc.). -@lexer::context {/* lexer context section */} - -// Appears in the private part of the lexer in the h file. -@lexer::declarations { } - -// Appears in line with the other class member definitions in the cpp file. -@lexer::definitions {/* lexer definitions section */} - -/* - * Lexer Rules - * - * Rules defined here are based on those specified for CIF 1.1 (https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf). - * They are reproduced as faithfully as possible, with small modifications made along the way (e.g. EOL tokens are skipped rather than matched as part of tokens for the most part. - * Quotes and bracketed errors are stripped from the generated tokens. - */ - -// Fragments -fragment OrdinaryChar: '!' | '%' | '&' | '(' | ')' | '*' | '+' | ',' | '-' | '.' | '/' | '0' | '1' | '2' | '3' | '4' | '5' | '6' | '7' | '8' | '9' | ':' | '<' | '=' | '>' | '?' | '@' | [A-Z] | '\\' | '^' | '`' | [a-z] | '{' | '|' | '}' | '~'; -fragment NonBlankChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ';' | '[' | ']'; -fragment TextLeadChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ' ' | '\t' | '[' | ']'; -fragment AnyPrintChar: OrdinaryChar | '"' | '#' | '$' | '\'' | '_' | ' ' | '\t' | ';' | '[' | ']'; -fragment EOL: [\r\n]; -fragment DIGIT: [0-9]; - -// Reserved Words -DATA_Name: ('D' | 'd') ('A' | 'a') ('T' | 't') ('A' | 'a') '_' NonBlankChar+; -LOOP_: ('L' | 'l') ('O' | 'o') ('O' | 'o') ('P' | 'p') '_'; -GLOBAL_: ('G' | 'g') ('L' | 'l') ('O' | 'o') ('B' | 'b') ('A' | 'a') ('L' | 'l') '_'; -SAVE_: ('S' | 's') ('A' | 'a') ('V' | 'v') ('E' | 'e') '_'; -SAVE_Name: ('S' | 's') ('A' | 'a') ('V' | 'v') ('E' | 'e') '_' NonBlankChar+; -STOP_: ('S' | 's') ('T' | 't') ('O' | 'o') ('P' | 'p') '_'; - -// Whitespace & Comments -WhiteSpace: [ \t\r\n]+ -> skip; -Comment: '#' AnyPrintChar*; - -// Tags & Values -Tag: '_' NonBlankChar+; -Value: '.' - | '?' - | Numeric { setText(std::string(DissolveSys::beforeChar(getText(), '('))); } - | UnquotedString - | SingleQuotedString { setText(getText().substr(1, getText().length()-2)); } - | DoubleQuotedString { setText(getText().substr(1, getText().length()-2)); } - | SemiColonTextField { setText(getText().find_first_not_of(";\r\n") != std::string::npos ? getText().substr(getText().find_first_not_of(";\r\n "), getText().find_last_not_of(";\r\n ") - getText().find_first_not_of(";\r\n ") + 1) : ""); } - ; - -// Numerics -Numeric: Number ( '(' UnsignedInteger ')' ); -Number: Integer | Float; -Integer: ('+' | '-')? UnsignedInteger; -Float: Integer Exponent -| ((DIGIT* '.' UnsignedInteger) | (DIGIT+ '.')) Exponent?; -Exponent: ('e'|'E') ('+'|'-')? UnsignedInteger+; -UnsignedInteger: DIGIT+; - -// Character Strings -UnquotedString: OrdinaryChar NonBlankChar*; -SingleQuotedString: '\'' AnyPrintChar*? '\''; -DoubleQuotedString: '"' AnyPrintChar*? '"'; -SemiColonTextField: ';' EOL* (TextLeadChar AnyPrintChar* EOL*?)* ';'; diff --git a/src/io/import/CIFImportParser.g4 b/src/io/import/CIFImportParser.g4 deleted file mode 100644 index d07e42512c..0000000000 --- a/src/io/import/CIFImportParser.g4 +++ /dev/null @@ -1,46 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -parser grammar CIFImportParser; - -options { - tokenVocab = CIFImportLexer; -} - -// Parser file header -@parser::header {/* CIFImport ANTLR Parser */} - -// Add custom includes after standard ANTLR includes in both *.h and *.cpp files -@parser::postinclude { } - -// Appears in the private part of the parser in the h file. -@parser::members { /* public parser declarations/members section */ } - -// Appears in the public part of the parser in the h file. -@parser::declarations {/* private parser declarations section */} - -// Appears in line with the other class member definitions in the cpp file. -@parser::definitions {/* parser definitions section */} - -/* - * CIFImport Grammar - * - * Rules defined here are based on those specified for CIF 1.1 (https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf). - * Some additional flexibility has been added, principally removing the enforced ordering of items to permit "looser" CIF files - * (of which there are many) to be read. - */ - -cif: (Comment | dataBlockHeading | dataBlock)+?; - -dataBlock: dataItems | saveFrame; - -dataBlockHeading: DATA_Name; - -saveFrame: saveFrameHeading dataItems+ SAVE_; - -saveFrameHeading: SAVE_Name; - -dataItems: name=Tag value=Value #taggedData -| loop #loopedData -; -loop: LOOP_ columns+=Tag+ values+=Value+; diff --git a/src/io/import/CIFImportVisitor.cpp b/src/io/import/CIFImportVisitor.cpp deleted file mode 100644 index 6b95676e03..0000000000 --- a/src/io/import/CIFImportVisitor.cpp +++ /dev/null @@ -1,65 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/io/CIFImportVisitor.h" -#include "base/messenger.h" -#include "base/sysFunc.h" -#include "nodes/cif/io/CIFImportErrorListeners.h" - -CIFImportVisitor::CIFImportVisitor(CIFHandler::CIFTags &tags) : tags_(tags) {} - -/* - * Data - */ - -// Extract information from tree into supplied objects -void CIFImportVisitor::extract(CIFImportParser::CifContext *tree) -{ - // Traverse the AST - visitChildren(tree); - - // Summarise - Messenger::print("Read in {} unique CIF data tags.\n", tags_.size()); -} - -/* - * Visitor Overrides - */ - -antlrcpp::Any CIFImportVisitor::visitDataBlockHeading(CIFImportParser::DataBlockHeadingContext *ctx) -{ - tags_["DATA_"].push_back(std::string(DissolveSys::afterChar(ctx->getText(), "DATA_"))); - - return visitChildren(ctx); -} - -antlrcpp::Any CIFImportVisitor::visitTaggedData(CIFImportParser::TaggedDataContext *ctx) -{ - tags_[ctx->name->getText()].push_back(ctx->value->getText()); - - return visitChildren(ctx); -} - -antlrcpp::Any CIFImportVisitor::visitLoopedData(CIFImportParser::LoopedDataContext *ctx) -{ - // Sanity check table data size - if (ctx->loop()->values.size() % ctx->loop()->columns.size()) - Messenger::exception("CIF table has {} columns (first is '{}') but {} values (and C%V != 0).\n", - ctx->loop()->columns.size(), ctx->loop()->columns.front()->getText(), ctx->loop()->values.size()); - - // Construct / retrieve dictionary elements for columns - std::vector>> columns; - for (auto *column : ctx->loop()->columns) - columns.emplace_back(tags_[column->getText()]); - - // Add values to columns - data will be in row-major order - auto colId = 0u; - for (auto *value : ctx->loop()->values) - { - columns[colId].get().emplace_back(value->getText()); - ++colId; - colId %= ctx->loop()->columns.size(); - } - - return visitChildren(ctx); -} diff --git a/src/io/import/CIFImportVisitor.h b/src/io/import/CIFImportVisitor.h deleted file mode 100644 index b73271862c..0000000000 --- a/src/io/import/CIFImportVisitor.h +++ /dev/null @@ -1,36 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "CIFImportParserBaseVisitor.h" -#include "nodes/cif/io/cif.h" -#include "templates/optionalRef.h" -#include - -// CIFImport Visitor for ANTLR -class CIFImportVisitor : CIFImportParserBaseVisitor -{ - public: - CIFImportVisitor(CIFHandler::CIFTags &tags); - ~CIFImportVisitor() override = default; - - /* - * Data - */ - private: - // Dictionary data storage - CIFHandler::CIFTags &tags_; - - public: - // Extract information from tree - void extract(CIFImportParser::CifContext *tree); - - /* - * Visitor Overrides - */ - private: - antlrcpp::Any visitDataBlockHeading(CIFImportParser::DataBlockHeadingContext *ctx) override; - antlrcpp::Any visitTaggedData(CIFImportParser::TaggedDataContext *ctx) override; - antlrcpp::Any visitLoopedData(CIFImportParser::LoopedDataContext *ctx) override; -}; diff --git a/src/io/import/cif.cpp b/src/io/import/cif.cpp deleted file mode 100644 index 5724e257a5..0000000000 --- a/src/io/import/cif.cpp +++ /dev/null @@ -1,1328 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "CIFImportLexer.h" -#include "base/messenger.h" -#include "base/sysFunc.h" -#include "classes/coreData.h" -#include "classes/empiricalFormula.h" -#include "classes/species.h" -#include "generator/add.h" -#include "generator/box.h" -#include "generator/coordinateSets.h" -#include "neta/neta.h" -#include "nodes/cif/io/CIFImportErrorListeners.h" -#include "nodes/cif/io/CIFImportVisitor.h" -#include "nodes/cif/io/cifContext.h" -#include "templates/algorithms.h" - -CIFHandler::CIFHandler() -{ - unitCellConfiguration_.setName("Structural"); - unitCellSpecies_.setName("Crystal"); - cleanedUnitCellConfiguration_.setName("Cleaned"); - cleanedUnitCellSpecies_.setName("Crystal (Cleaned)"); - supercellConfiguration_.setName("Supercell"); - supercellSpecies_.setName("Crystal (Supercell)"); -} - -/* - * Raw Data - */ - -// Parse supplied file into the destination objects -bool CIFHandler::parse(std::string_view filename, CIFHandler::CIFTags &tags) const -{ - // Set up ANTLR input stream - std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); - if (!cifFile.is_open()) - return Messenger::error("Failed to open CIF file '{}.\n", filename); - - antlr4::ANTLRInputStream input(cifFile); - - // Create ANTLR lexer and set-up error listener - CIFImportLexer lexer(&input); - CIFImportLexerErrorListener lexerErrorListener; - lexer.removeErrorListeners(); - lexer.addErrorListener(&lexerErrorListener); - - // Generate tokens from input stream - antlr4::CommonTokenStream tokens(&lexer); - - // Create ANTLR parser and set-up error listeners - CIFImportParser parser(&tokens); - CIFImportParserErrorListener parserErrorListener; - parser.removeErrorListeners(); - parser.removeParseListeners(); - parser.addErrorListener(&lexerErrorListener); - parser.addErrorListener(&parserErrorListener); - - // Generate the AST - CIFImportParser::CifContext *tree = nullptr; - try - { - tree = parser.cif(); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - Messenger::error("{}", ex.what()); - return false; - } - - // Visit the nodes in the AST - CIFImportVisitor visitor(tags); - try - { - visitor.extract(tree); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - return Messenger::error("{}", ex.what()); - } - - return true; -} - -// Return whether the specified file parses correctly -bool CIFHandler::validFile(std::string_view filename) const -{ - CIFTags tags; - return parse(filename, tags); -} - -// Read CIF data from specified file -bool CIFHandler::read(std::string_view filename) -{ - assemblies_.clear(); - bondingPairs_.clear(); - tags_.clear(); - - if (!parse(filename, tags_)) - return Messenger::error("Failed to parse CIF file '{}'.\n", filename); - - /* - * Determine space group - the search order for tags is: - * - * 1. Hall symbol - * 2. Hermann-Mauginn name - * 3. Space group index - * - * In the case of 2 or 3 we also try to search for the origin choice. - * - * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection - * below fails). - */ - - // Check for Hall symbol - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); - - if (spaceGroup_ == SpaceGroups::NoSpaceGroup) - { - // Might need the coordinate system code... - auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); - - // Find a HM name - if (hasTag("_space_group_name_H-M_alt")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); - - // Find a space group index? - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); - } - - // Create symmetry-unique atoms list - auto atomSiteLabel = getTagStrings("_atom_site_label"); - auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); - auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); - auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); - auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); - auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); - auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); - auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); - if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) - return Messenger::error( - "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); - if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) - return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) - return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - for (auto n = 0; n < atomSiteFractX.size(); ++n) - { - // Get standard information - auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); - auto Z = n < atomSiteTypeSymbol.size() - ? Elements::element(atomSiteTypeSymbol[n]) - : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); - auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; - Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); - - // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: - // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly - // 2) An assembly and a group are defined - add it to that - // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group - auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; - auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; - if (assemblyName == "." && groupName != ".") - assemblyName = "Disorder"; - else if (assemblyName == "." && groupName == ".") - assemblyName = "Global"; - - if (groupName == ".") - groupName = "Default"; - - // Get the assembly and group that we're adding the atom to - auto &assembly = getAssembly(assemblyName); - auto &group = assembly.getGroup(groupName); - group.setActive(groupName == "Default" || groupName == "1"); - group.addAtom({label, Z, rFrac, occ}); - } - - // Construct bonding pairs list - auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); - auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); - auto bondDistances = getTagDoubles("_geom_bond_distance"); - if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) - { - for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) - bondingPairs_.emplace_back(i, j, r); - } - else - Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); - - return true; -} - -// Return if the specified tag exists -bool CIFHandler::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } - -// Return tag data string (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagString(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - return it->second.front(); -} - -// Return tag data strings (if it exists) -std::vector CIFHandler::getTagStrings(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - return it->second; -} - -// Return tag data as double (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagDouble(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - double result; - try - { - result = std::stod(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -// Return tag data doubles (if it exists) -std::vector CIFHandler::getTagDoubles(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - std::vector v; - for (const auto &s : it->second) - { - auto d = 0.0; - try - { - d = std::stod(s); - } - catch (...) - { - Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); - } - v.push_back(d); - } - - return v; -} - -// Return tag data as integer (if it exists) assuming a single datum (first in the vector) -std::optional CIFHandler::getTagInt(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - int result; - try - { - result = std::stoi(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -/* - * Processed Data - */ - -// Set space group from index -void CIFHandler::setSpaceGroup(SpaceGroups::SpaceGroupId sgid) -{ - if (spaceGroup_ == sgid) - return; - - spaceGroup_ = sgid; - generate(); -} - -// Return space group information -SpaceGroups::SpaceGroupId CIFHandler::spaceGroup() const { return spaceGroup_; } - -// Return cell lengths -std::optional CIFHandler::getCellLengths() const -{ - auto a = getTagDouble("_cell_length_a"); - if (!a) - Messenger::error("Cell length A not defined in CIF.\n"); - auto b = getTagDouble("_cell_length_b"); - if (!b) - Messenger::error("Cell length B not defined in CIF.\n"); - auto c = getTagDouble("_cell_length_c"); - if (!c) - Messenger::error("Cell length C not defined in CIF.\n"); - - if (a && b && c) - return Vector3(a.value(), b.value(), c.value()); - else - return std::nullopt; -} - -// Return cell angles -std::optional CIFHandler::getCellAngles() const -{ - auto alpha = getTagDouble("_cell_angle_alpha"); - if (!alpha) - Messenger::error("Cell angle alpha not defined in CIF.\n"); - auto beta = getTagDouble("_cell_angle_beta"); - if (!beta) - Messenger::error("Cell angle beta not defined in CIF.\n"); - auto gamma = getTagDouble("_cell_angle_gamma"); - if (!gamma) - Messenger::error("Cell angle gamma not defined in CIF.\n"); - - if (alpha && beta && gamma) - return Vector3(alpha.value(), beta.value(), gamma.value()); - else - return std::nullopt; -} - -// Return chemical formula -std::string CIFHandler::chemicalFormula() const -{ - auto it = tags_.find("_chemical_formula_sum"); - return (it != tags_.end() ? it->second.front() : "Unknown"); -} - -// Get (add or retrieve) named assembly -CIFAssembly &CIFHandler::getAssembly(std::string_view name) -{ - auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); - if (it != assemblies_.end()) - return *it; - - return assemblies_.emplace_back(name); -} - -// Return atom assemblies -std::vector &CIFHandler::assemblies() { return assemblies_; } - -const std::vector &CIFHandler::assemblies() const { return assemblies_; } - -// Return whether any bond distances are defined -bool CIFHandler::hasBondDistances() const { return !bondingPairs_.empty(); } - -// Return whether a bond distance is defined for the specified label pair -std::optional CIFHandler::bondDistance(std::string_view labelI, std::string_view labelJ) const -{ - auto it = std::find_if( - bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) - { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); - if (it != bondingPairs_.end()) - return it->r(); - return std::nullopt; -} - -/* - * Creation - */ - -// Create basic unit cell -bool CIFHandler::createBasicUnitCell() -{ - unitCellConfiguration_.empty(); - unitCellSpecies_.clear(); - atomLabelTypes_.clear(); - - // Create temporary atom types corresponding to the unique atom labels - for (auto &a : assemblies_) - { - for (auto &g : a.groups()) - { - if (!g.active()) - continue; - - for (auto &i : g.atoms()) - { - if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) - { - atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); - } - } - } - } - - // Configure the unit cell "species" - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - unitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - auto *box = unitCellSpecies_.box(); - - // Configuration - Messenger::setQuiet(true); - unitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - // -- Generate atoms - auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); - for (const auto &generator : symmetryGenerators) - for (auto &a : assemblies_) - for (auto &g : a.groups()) - if (g.active()) - for (auto &unique : g.atoms()) - { - // Generate folded atomic position in real space - auto r = generator * unique.rFrac(); - box->toReal(r); - r = box->fold(r); - - // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy - if (std::any_of(unitCellSpecies_.atoms().begin(), unitCellSpecies_.atoms().end(), - [&, r, box](const auto &j) - { return box->minimumDistance(r, j.r()) < overlapTolerance_; })) - continue; - - // Create the new atom - auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [&unique](const auto at) { return unique.label() == at->name(); }); - unitCellSpecies_.addAtom(unique.Z(), r, 0.0, atIt != atomLabelTypes_.end() ? atIt->get() : nullptr); - } - - // Check that we actually generated some atoms... - if (unitCellSpecies_.nAtoms() == 0) - return false; - - // Bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&unitCellSpecies_, preventMetallicBonds_); - else - unitCellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - unitCellConfiguration_.addMolecule(&unitCellSpecies_); - unitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created basic crystal unit cell - {} non-overlapping atoms.\n", unitCellSpecies_.nAtoms()); - - return true; -} - -// Create the cleaned unit cell -bool CIFHandler::createCleanedUnitCell() -{ - cleanedUnitCellConfiguration_.empty(); - cleanedUnitCellSpecies_.clear(); - - // Configure the species - cleanedUnitCellSpecies_.copyBasic(&unitCellSpecies_, true); - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - cleanedUnitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - - // Configuration - Messenger::setQuiet(true); - cleanedUnitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - if (removeAtomics_) - { - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (i.nBonds() == 0) - indicesToRemove.push_back(i.index()); - Messenger::print("Atomic removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeWaterAndCoordinateOxygens_) - { - NETADefinition waterVacuum("?O,nbonds=1,nh<=1|?O,nbonds>=2,-H(nbonds=1,-O)"); - if (!waterVacuum.isValid()) - { - Messenger::error("NETA definition for water removal is invalid.\n"); - return false; - } - - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (waterVacuum.matches(&i)) - indicesToRemove.push_back(i.index()); - Messenger::print("Water removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeNETA_ && moietyRemovalNETA_.isValid()) - { - // Select all atoms that are in moieties where one of its atoms matches our NETA definition - std::vector indicesToRemove; - for (auto &i : cleanedUnitCellSpecies_.atoms()) - if (moietyRemovalNETA_.matches(&i)) - { - // Select all atoms that are part of the same moiety? - if (removeNETAByFragment_) - { - cleanedUnitCellSpecies_.clearAtomSelection(); - auto selection = cleanedUnitCellSpecies_.fragment(i.index()); - std::copy(selection.begin(), selection.end(), std::back_inserter(indicesToRemove)); - } - else - indicesToRemove.push_back(i.index()); - } - Messenger::print("Moiety removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - cleanedUnitCellConfiguration_.addMolecule(&cleanedUnitCellSpecies_); - cleanedUnitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created cleaned crystal unit cell - {} atoms after removal(s).\n", cleanedUnitCellSpecies_.nAtoms()); - - return true; -} - -// Try to detect molecules in the cell contents -bool CIFHandler::detectMolecules() -{ - molecularSpecies_.clear(); - - // Try selecting within the species from the first atom - if this captures all atoms we have a bound framework... - if (cleanedUnitCellSpecies_.fragment(0).size() == cleanedUnitCellSpecies_.nAtoms()) - { - Messenger::print( - "Can't create molecular definitions since this unit cell appears to be a continuous framework/network. Consider " - "adjusting the bonding options in order to generate molecular fragments.\n"); - return false; - } - - std::vector atomMask(cleanedUnitCellSpecies_.nAtoms(), false); - - // Find all molecular species, and their instances - auto indexIterator = atomMask.begin(); - while (indexIterator != atomMask.end()) - { - // Select a fragment from the next available index - auto atomIndex = indexIterator - atomMask.begin(); - auto fragmentIndices = cleanedUnitCellSpecies_.fragment(atomIndex); - - // Create a new CIF molecular species from the fragment - auto &cifSp = molecularSpecies_.emplace_back(); - auto *sp = cifSp.species().get(); - // -- Copy selected atoms - for (auto fragAtomIndex : fragmentIndices) - { - const auto &unitCellAtom = cleanedUnitCellSpecies_.atom(fragAtomIndex); - sp->addAtom(unitCellAtom.Z(), unitCellAtom.r(), 0.0, unitCellAtom.atomType()); - } - - // Give the species a temporary unit cell so we can calculate / apply bonding - if (!preventAllBonds_) - sp->createBox(cleanedUnitCellSpecies_.box()->axisLengths(), cleanedUnitCellSpecies_.box()->axisAngles()); - if (useCIFBondingDefinitions_) - applyCIFBonding(sp, preventMetallicBonds_); - else - sp->addMissingBonds(bondingTolerance_, preventMetallicBonds_); - sp->removeBox(); - - // Set up a temporary molecule to unfold the species - LocalMolecule tempMol(sp); - tempMol.unFold(cleanedUnitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(tempMol.localAtoms(), sp->atoms())) - spAtom.setR(molAtom.r()); - - // Give the species a name - sp->setName(EmpiricalFormula::formula(sp->atoms(), [&](const auto &at) { return at.Z(); })); - - // Find instances of this fragment. For large fragments that represent > 50% of the remaining atoms we don't even - // attempt to create a NETA definition etc. For cases such as framework species this will speed up detection no end. - std::vector instances; - if (fragmentIndices.size() * 2 > cleanedUnitCellSpecies_.nAtoms()) - { - // Create an instance of the current fragment - auto &mol = instances.emplace_back(sp); - for (auto i = 0; i < sp->nAtoms(); ++i) - atomMask[fragmentIndices[i]] = true; - } - else - { - // Determine the best NETA definition describing the fragment - auto &&[bestNETA, rootAtoms] = bestNETADefinition(sp); - if (rootAtoms.empty()) - return Messenger::error( - "Couldn't generate molecular partitioning for CIF - no suitable NETA definition for the " - "fragment {} could be determined.\n", - sp->name()); - - // Find instances of this fragment - instances = getSpeciesInstances(sp, atomMask, bestNETA, rootAtoms); - if (instances.empty()) - { - molecularSpecies_.clear(); - return Messenger::error("Failed to find species instances for fragment '{}'.\n", sp->name()); - } - } - - // Store the instances - cifSp.instances() = instances; - - // Search for the next valid starting index - indexIterator = std::find(std::next(indexIterator), atomMask.end(), false); - } - - Messenger::print("Partitioned unit cell into {} distinct molecular species:\n\n", molecularSpecies_.size()); - Messenger::print(" ID N Species Formula\n"); - auto count = 1; - for (const auto &cifMol : molecularSpecies_) - Messenger::print(" {:3d} {:4d} {}\n", count++, cifMol.instances().size(), - EmpiricalFormula::formula(cifMol.species()->atoms(), [](const auto &i) { return i.Z(); })); - Messenger::print(""); - - return true; -} - -// Create supercell species -bool CIFHandler::createSupercell() -{ - supercellConfiguration_.empty(); - supercellSpecies_.clear(); - - // Configure the species - auto supercellLengths = cleanedUnitCellSpecies_.box()->axisLengths(); - supercellLengths.multiply(supercellRepeat_.x, supercellRepeat_.y, supercellRepeat_.z); - supercellSpecies_.createBox(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - - // Set up configuration - Messenger::setQuiet(true); - supercellConfiguration_.createBoxAndCells(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - Messenger::setQuiet(false); - - // Copy atoms from the Crystal species - we'll do the bonding afterwards - if (molecularSpecies_.empty()) - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - Vector3 deltaR = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - supercellSpecies_.addAtom(i.Z(), i.r() + deltaR, 0.0, i.atomType()); - } - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&supercellSpecies_, preventMetallicBonds_); - else - supercellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Add the structural species to the configuration - supercellConfiguration_.addMolecule(&supercellSpecies_); - supercellConfiguration_.updateObjectRelationships(); - } - else - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - - // Create images of all molecular unit cell species - for (auto &molecularSpecies : molecularSpecies_) - { - const auto *sp = molecularSpecies.species().get(); - const auto &coreInstances = molecularSpecies.instances(); - std::vector supercellInstances; - supercellInstances.reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * coreInstances.size()); - - // Loop over cell images - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - { - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - { - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - // Skip origin cell - if (ix == 0 && iy == 0 && iz == 0) - continue; - - // Set translation vector - auto tVec = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - - // Create images of core molecule instances - for (auto &instance : coreInstances) - { - auto &mol = supercellInstances.emplace_back(); - mol.setSpecies(sp); - - for (auto &&[coreAtom, instanceAtom] : zip(instance.localAtoms(), mol.localAtoms())) - instanceAtom.setR(coreAtom.r() + tVec); - } - } - } - } - - // Append the new instances to our existing ones for the unit cell - molecularSpecies.appendInstances(supercellInstances); - - // Add the molecules to our configuration - for (const auto &instance : molecularSpecies.instances()) - { - auto mol = supercellConfiguration_.addMolecule(sp); - for (auto &&[molAtom, instanceAtom] : zip(mol->atoms(), instance.localAtoms())) - molAtom->setR(instanceAtom.r()); - } - } - - supercellConfiguration_.updateObjectRelationships(); - } - - Messenger::print("Created ({}, {}, {}) supercell - {} atoms total.\n", supercellRepeat_.x, supercellRepeat_.y, - supercellRepeat_.z, supercellConfiguration_.nAtoms()); - - return true; -} - -// Set overlap tolerance -void CIFHandler::setOverlapTolerance(double tol) -{ - overlapTolerance_ = tol; - - generate(CIFGenerationStage::CreateBasicUnitCell); -} - -// Set whether to use CIF bonding definitions -void CIFHandler::setUseCIFBondingDefinitions(bool b) -{ - if (useCIFBondingDefinitions_ == b) - return; - - useCIFBondingDefinitions_ = b; - - generate(); -} - -// Set bonding tolerance -void CIFHandler::setBondingTolerance(double tol) -{ - bondingTolerance_ = tol; - - if (!useCIFBondingDefinitions_) - generate(); -} - -// Whether to ignore all bonds -void CIFHandler::setPreventAllBonds(bool b) -{ - if (preventAllBonds_ == b) - return; - - preventAllBonds_ = b; - - generate(); -} - -// Set whether to prevent metallic bonding -void CIFHandler::setPreventMetallicBonds(bool b) -{ - if (preventMetallicBonds_ == b) - return; - - preventMetallicBonds_ = b; - - generate(); -} - -// Set whether to remove free atomic moieties in clean-up -void CIFHandler::setRemoveAtomics(bool b) -{ - if (removeAtomics_ == b) - return; - - removeAtomics_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove water and coordinated oxygen atoms in clean-up -void CIFHandler::setRemoveWaterAndCoordinateOxygens(bool b) -{ - if (removeWaterAndCoordinateOxygens_ == b) - return; - - removeWaterAndCoordinateOxygens_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove by NETA definition in clean-up -void CIFHandler::setRemoveNETA(bool b, bool byFragment) -{ - if (removeNETA_ == b && removeNETAByFragment_ == byFragment) - return; - - removeNETA_ = b; - removeNETAByFragment_ = byFragment; - - if (moietyRemovalNETA_.isValid()) - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set NETA for moiety removal -bool CIFHandler::setMoietyRemovalNETA(std::string_view netaDefinition) { return moietyRemovalNETA_.create(netaDefinition); } - -// Set supercell repeat -void CIFHandler::setSupercellRepeat(const Vector3i &repeat) -{ - supercellRepeat_ = repeat; - - generate(CIFGenerationStage::CreateSupercell); -} - -// Recreate the data -bool CIFHandler::generate(CIFGenerationStage fromStage) -{ - // Generate data starting from the specified stage, falling through to subsequent stages in the switch - - switch (fromStage) - { - case (CIFGenerationStage::CreateBasicUnitCell): - if (!createBasicUnitCell()) - return false; - case (CIFGenerationStage::CreateCleanedUnitCell): - if (!createCleanedUnitCell()) - return false; - case (CIFGenerationStage::DetectMolecules): - detectMolecules(); - case (CIFGenerationStage::CreateSupercell): - if (!createSupercell()) - return false; - } - - return true; -} - -// Return whether the generated data is valid -bool CIFHandler::isValid() const -{ - return !molecularSpecies_.empty() || supercellSpecies_.fragment(0).size() != supercellSpecies_.nAtoms(); -} - -// Return supercell species -const Species &CIFHandler::supercellSpecies() const { return supercellSpecies_; } - -// Return cleaned unit cell species -const Species &CIFHandler::cleanedUnitCellSpecies() const { return cleanedUnitCellSpecies_; } - -// Return the detected molecular species -const std::vector &CIFHandler::molecularSpecies() const { return molecularSpecies_; } - -// Return the generated configuration -Configuration *CIFHandler::generatedConfiguration() { return &supercellConfiguration_; } - -// Finalise, copying the required species and resulting configuration to the target CoreData -void CIFHandler::finalise(CoreData &coreData, const Flags &flags) const -{ - Configuration *configuration; - - if (flags.isSet(OutputFlags::OutputMolecularSpecies)) - { - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - for (auto &cifMolecularSp : molecularSpecies_) - { - // Add the species - auto *sp = coreData.copySpecies(cifMolecularSp.species().get()); - - // Determine a unique suffix - auto base = sp->name(); - std::string uniqueSuffix{base}; - if (!generator.nodes().empty()) - { - // Start from the last root node - auto root = generator.nodes().back(); - auto suffix = 0; - - while (generator.rootSequence().nodeInScope(root, std::format("SymmetryCopies_{}", uniqueSuffix)) != - nullptr) - uniqueSuffix = std::format("{}_{:02d}", base, ++suffix); - } - - // We use 'CoordinateSets' here, because in this instance we are working with (CoordinateSet, Add) pairs - - // CoordinateSets - auto coordsNode = - generator.createRootNode(std::format("SymmetryCopies_{}", uniqueSuffix), sp); - coordsNode->keywords().setEnumeration("Source", CoordinateSetsGeneratorNode::CoordinateSetSource::File); - coordsNode->setSets(cifMolecularSp.allInstanceCoordinates()); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", uniqueSuffix), coordsNode); - addNode->keywords().set("Population", NodeValueProxy(int(cifMolecularSp.instances().size()))); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } - else - { - for (auto &cifMolecularSp : molecularSpecies_) - { - coreData.copySpecies(cifMolecularSp.species().get()); - } - } - } - else - { - auto *sp = coreData.addSpecies(); - sp->copyBasic(&supercellSpecies_); - if (flags.isSet(OutputFlags::OutputSupermolecule)) - { - sp->removePeriodicBonds(); - sp->removeBox(); - } - else - sp->createBox(supercellSpecies_.box()->axisLengths(), supercellSpecies_.box()->axisAngles()); - - sp->updateIntramolecularTerms(); - - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", sp->name()), sp); - addNode->keywords().set("Population", NodeValueProxy(1)); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } -} - -/* - * Helpers - */ - -// Apply CIF bonding to a given species -void CIFHandler::applyCIFBonding(Species *sp, bool preventMetallicBonding) -{ - if (!hasBondDistances()) - return; - - auto *box = sp->box(); - auto pairs = PairIterator(sp->nAtoms()); - for (auto pair : pairs) - { - // Grab indices and atom references - auto [indexI, indexJ] = pair; - if (indexI == indexJ) - continue; - - auto &i = sp->atom(indexI); - auto &j = sp->atom(indexJ); - - // Prevent metallic bonding? - if (preventMetallicBonding && Elements::isMetallic(i.Z()) && Elements::isMetallic(j.Z())) - continue; - - // Retrieve distance - auto r = bondDistance(i.atomType()->name(), j.atomType()->name()); - if (!r) - continue; - else if (fabs(box->minimumDistance(i.r(), j.r()) - r.value()) < 1.0e-2) - sp->addBond(&i, &j); - } -} - -// Determine the best NETA definition for the supplied species -std::tuple> CIFHandler::bestNETADefinition(Species *sp) -{ - // Set up the return value and bind its contents - std::tuple> result{NETADefinition(), {}}; - auto &&[bestNETA, rootAtoms] = result; - - // Maintain a set of atoms matched by any NETA description we generate - std::set alreadyMatched; - - // Loop over species atoms - for (auto &i : sp->atoms()) - { - // Skip this atom? - if (alreadyMatched.find(&i) != alreadyMatched.end()) - continue; - - // Create a NETA definition with this atom as the root - NETADefinition neta; - neta.create(&i, std::nullopt, - Flags(NETADefinition::NETACreationFlags::ExplicitHydrogens, - NETADefinition::NETACreationFlags::IncludeRootElement)); - - // Apply this match over the whole species - std::vector currentRootAtoms; - for (auto &j : sp->atoms()) - { - if (neta.matches(&j)) - { - currentRootAtoms.push_back(&j); - alreadyMatched.insert(&j); - } - } - - // Is this a better description? - auto better = false; - if (rootAtoms.empty() || currentRootAtoms.size() < rootAtoms.size()) - better = true; - else if (currentRootAtoms.size() == rootAtoms.size()) - { - // Replace the current match if there are more bonds on the current atom. - if (i.nBonds() > rootAtoms.front()->nBonds()) - better = true; - } - - if (better) - { - bestNETA = neta; - rootAtoms = currentRootAtoms; - } - } - - return result; -} - -// Get instances for the supplied species from the cleaned unit cell -std::vector CIFHandler::getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms) -{ - if (referenceRootAtoms.empty() || !neta.isValid()) - return {}; - - // Loop over atoms in the unit cell - we'll mark any that we select as an instance so we speed things up and avoid - // duplicates - const auto &unitCellAtoms = cleanedUnitCellSpecies_.atoms(); - std::vector instances; - auto atomIndexIterator = std::find(atomMask.begin(), atomMask.end(), false); - while (atomIndexIterator != atomMask.end()) - { - // Try to match this atom / fragment - const auto atomIndex = atomIndexIterator - atomMask.begin(); - auto &atom = unitCellAtoms[atomIndex]; - auto matchedUnitCellAtoms = neta.matchedPath(&atom).set(); - if (matchedUnitCellAtoms.empty()) - { - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - continue; - } - - // Found a fragment that matches the NETA description - we now create a temporary instance Species which will contain - // the selected fragment atoms, reassembled into a molecule (i.e. unfolded) and with bonding applied / calculated. - // We need to copy the unit cell from the crystal so we detect bonds properly. - Species instanceSpecies; - instanceSpecies.createBox(unitCellSpecies_.box()->axisLengths(), unitCellSpecies_.box()->axisAngles()); - auto rootAtomLocalIndex = -1; - // -- Create species atoms from those matched in the unit cell by the NETA description. - for (auto &matchedAtom : matchedUnitCellAtoms) - { - auto idx = instanceSpecies.addAtom(matchedAtom->Z(), matchedAtom->r(), 0.0, matchedAtom->atomType()); - - // Store the index of the root atom in match in our instance species when we find it - if (matchedAtom == &atom) - rootAtomLocalIndex = idx; - } - // -- Store the local root atom so we can access its coordinates for the origin translation - auto &instanceSpeciesRootAtom = instanceSpecies.atom(rootAtomLocalIndex); - // -- Calculate / apply bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&instanceSpecies, preventMetallicBonds_); - else - instanceSpecies.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Create a LocalMolecule as a working area for folding, translation, and rotation of the instance coordinates. - LocalMolecule instanceMolecule; - instanceMolecule.setSpecies(&instanceSpecies); - // -- Copy the coordinates off the matched unit cell atoms to our molecule and flag them as complete - auto count = 0; - for (auto &&[matchedAtom, instanceMolAtom] : zip(matchedUnitCellAtoms, instanceMolecule.localAtoms())) - { - instanceMolAtom.setR(matchedAtom->r()); - atomMask[matchedAtom->index()] = true; - } - auto &instanceMoleculeRootAtom = instanceMolecule.localAtoms()[rootAtomLocalIndex]; - - // Unfold the molecule and store the unfolded molecule coordinates back into the instance Species. - // This represents our full instance coordinates we will be storing (but not their final order) - instanceMolecule.unFold(unitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(instanceMolecule.localAtoms(), instanceSpecies.atoms())) - spAtom.setR(molAtom.r()); - - /* - * Now, we have a root match atom on the current instance and a vector of possible matching sites on the reference - * species (in referenceRootAtoms). For each of the referenceRootAtoms, try to incrementally select along bonds using - * basic NETA connectivity. - */ - - // Generate basic NETA descriptions for each atom in the reference and candidate species - std::map referenceAtomNETA; - for (auto &spAtom : referenceSpecies->atoms()) - referenceAtomNETA[&spAtom] = NETADefinition(&spAtom, 1, {NETADefinition::NETACreationFlags::IncludeRootElement}); - - std::map matchMap; - for (const auto *referenceRootAtom : referenceRootAtoms) - { - // The root atom is the starting point - matchMap = matchAtom(referenceRootAtom, &instanceSpeciesRootAtom, referenceAtomNETA, {}); - if (!matchMap.empty()) - break; - } - - // Result? - if (matchMap.empty()) - { - Messenger::error("Failed to match connectivity of an instance to the reference molecule.\n"); - return {}; - } - else if (matchMap.size() != referenceSpecies->nAtoms()) - { - Messenger::error( - "Internal error - failed to match connectivity of all atoms within an instance to the reference molecule.\n"); - return {}; - } - - // Create the final instance - auto &instance = instances.emplace_back(); - instance.setSpecies(referenceSpecies); - for (const auto &[refSpeciesAtom, instanceSpeciesAtom] : matchMap) - { - instance.localAtom(refSpeciesAtom->index()).setR(instanceSpeciesAtom->r()); - } - - // Find the next available atom - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - } - - return instances; -} - -// Recursively check NETA description matches between the supplied atoms -std::map -CIFHandler::matchAtom(const SpeciesAtom *referenceAtom, const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map) -{ - // If the reference atom NETA doesn't match the instance atom we cannot proceed - if (!refNETA.at(referenceAtom).matches(instanceAtom)) - return {}; - - // Check the map to see if we have already associated the reference atom to an instance atom, or if the instance atom - // is already associated to a different reference atom. - for (auto &&[mappedRefAtom, mappedInstanceAtom] : map) - { - // Found it - double-check to ensure that the current association matches our instance atom. If it does we can return - // the map as it currently stands. If not we return an empty map to indicate failure. - if (mappedRefAtom == referenceAtom) - { - if (mappedInstanceAtom == instanceAtom) - { - return map; - } - else - { - return {}; - } - } - else if (mappedInstanceAtom == instanceAtom) - { - return {}; - } - } - - // Copy the current map, associate our initial pair of atoms and try to extend it - auto newMap = map; - newMap[referenceAtom] = instanceAtom; - - // Cycle over bonds on the reference atom and find - for (const auto &referenceBond : referenceAtom->bonds()) - { - // Get the reference bond partner - auto *referenceBondPartner = referenceBond.get().partner(referenceAtom); - - // Try to find a match over bonds on the instance atom - std::map bondResult; - for (const auto &instanceBond : instanceAtom->bonds()) - { - // Get the instance bond partner - auto *instanceBondPartner = instanceBond.get().partner(instanceAtom); - - // Recurse - bondResult = matchAtom(referenceBondPartner, instanceBondPartner, refNETA, newMap); - if (!bondResult.empty()) - break; - } - - // If we found a suitable match recursing into the bond, store the result into newMap and continue to the next bond. - // If we didn't find a good match, we return now. - if (bondResult.empty()) - { - return {}; - } - else - { - newMap = bondResult; - } - } - - // If we get to here then we succeeded, so return the new map - return newMap; -} - -// Calculate difference metric between the supplied species and local molecule -std::pair> CIFHandler::differenceMetric(const Species *species, const LocalMolecule &molecule) -{ - auto difference = 0.0; - std::vector atomIndexMap(species->nAtoms(), -1); - auto nBadAtoms = 0; - for (auto spI = 0; spI < species->nAtoms(); ++spI) - { - auto &spAtom = species->atom(spI); - - // For this species atom find the closest atom in the molecule - auto distanceSq = 1.0e6; - for (auto molI = 0; molI < molecule.nAtoms(); ++molI) - { - auto rABSq = (spAtom.r() - molecule.localAtoms()[molI].r()).magnitudeSq(); - if (rABSq < distanceSq) - { - distanceSq = rABSq; - atomIndexMap[spI] = molI; - } - } - - if (distanceSq > 0.1) - ++nBadAtoms; - - // Update the difference score - const auto &closestMolSpAtom = molecule.species()->atom(atomIndexMap[spI]); - difference += distanceSq; - if (spAtom.Z() != closestMolSpAtom.Z()) - difference += std::max(int(spAtom.Z()), int(closestMolSpAtom.Z())) * 10.0; - } - - return {difference, atomIndexMap}; -} diff --git a/src/io/import/cif.h b/src/io/import/cif.h deleted file mode 100644 index d93483db31..0000000000 --- a/src/io/import/cif.h +++ /dev/null @@ -1,214 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "classes/configuration.h" -#include "classes/coreData.h" -#include "classes/species.h" -#include "data/spaceGroups.h" -#include "math/matrix4.h" -#include "neta/neta.h" -#include "nodes/cif/io/cifClasses.h" -#include "templates/flags.h" -#include - -// Forward Declarations -class Box; - -// CIF Handler -class CIFHandler -{ - public: - CIFHandler(); - ~CIFHandler() = default; - - /* - * Raw Data - */ - public: - // Data Types - using CIFTags = std::map>; - - private: - // Vector of enumerated data items - CIFTags tags_; - - private: - // Parse supplied file into the destination objects - bool parse(std::string_view filename, CIFTags &tags) const; - - public: - // Return whether the specified file parses correctly - bool validFile(std::string_view filename) const; - // Read CIF data from specified file - bool read(std::string_view filename); - // Return if the specified tag exists - bool hasTag(std::string tag) const; - // Return tag data string (if it exists) assuming a single datum (first in the vector) - std::optional getTagString(std::string tag) const; - // Return tag data strings (if it exists) - std::vector getTagStrings(std::string tag) const; - // Return tag data as double (if it exists) assuming a single datum (first in the vector) - std::optional getTagDouble(std::string tag) const; - // Return tag data doubles (if it exists) - std::vector getTagDoubles(std::string tag) const; - // Return tag data as integer (if it exists) assuming a single datum (first in the vector) - std::optional getTagInt(std::string tag) const; - - /* - * Processed Data - */ - private: - // Space group - SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::NoSpaceGroup}; - // Atom assemblies - std::vector assemblies_; - // Bond information - std::vector bondingPairs_; - - public: - // Set space group from index - void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); - // Return space group - SpaceGroups::SpaceGroupId spaceGroup() const; - // Return cell lengths - std::optional getCellLengths() const; - // Return cell angles - std::optional getCellAngles() const; - // Return chemical formula - std::string chemicalFormula() const; - // Get (add or retrieve) named assembly - CIFAssembly &getAssembly(std::string_view name); - // Return atom assemblies - std::vector &assemblies(); - const std::vector &assemblies() const; - // Return whether any bond distances are defined - bool hasBondDistances() const; - // Return whether a bond distance is defined for the specified label pair - std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; - - /* - * Creation - */ - public: - // CIF Generation Stages - enum class CIFGenerationStage - { - CreateBasicUnitCell, - CreateCleanedUnitCell, - DetectMolecules, - CreateSupercell - }; - // CIF Species Output Flags - enum OutputFlags - { - OutputConfiguration, /* Output a Configuration */ - OutputMolecularSpecies, /* Partitioning - output molecular species */ - OutputFramework, /* Partitioning - output a framework species */ - OutputSupermolecule /* Partitioning - output a supermolecule */ - }; - - private: - // Temporary atom types used for unique atom labels - std::vector> atomLabelTypes_; - // Tolerance for removal of overlapping atoms - double overlapTolerance_{0.1}; - // Whether to use CIF bonding definitions - bool useCIFBondingDefinitions_{false}; - // Bonding tolerance, if calculating bonding rather than using CIF definitions - double bondingTolerance_{1.1}; - // Whether to ignore all bonds - bool preventAllBonds_{false}; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; - // Whether to remove free atomic moieties in clean-up - bool removeAtomics_{false}; - // Whether to remove water and coordinated oxygen atoms in clean-up - bool removeWaterAndCoordinateOxygens_{false}; - // Whether to remove by NETA definition in clean-up - bool removeNETA_{false}; - // Whether to expand NETA matches to fragments when removing in clean-up - bool removeNETAByFragment_{false}; - // NETA for moiety removal, if specified - NETADefinition moietyRemovalNETA_; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - // Basic unit cell - Species unitCellSpecies_; - Configuration unitCellConfiguration_; - // Cleaned unit cell - Species cleanedUnitCellSpecies_; - Configuration cleanedUnitCellConfiguration_; - // Molecular definition of unit cell (if possible) - std::vector molecularSpecies_; - // Final generated result (supercell) - Species supercellSpecies_; - Configuration supercellConfiguration_; - - private: - // Create basic unit cell - bool createBasicUnitCell(); - // Create the cleaned unit cell - bool createCleanedUnitCell(); - // Try to detect molecules in the cell contents - bool detectMolecules(); - // Create supercell species - bool createSupercell(); - - public: - // Set overlap tolerance - void setOverlapTolerance(double tol); - // Set whether to use CIF bonding definitions - void setUseCIFBondingDefinitions(bool b); - // Set bonding tolerance - void setBondingTolerance(double tol); - // Whether to ignore all bonds - void setPreventAllBonds(bool b); - // Set whether to prevent metallic bonding - void setPreventMetallicBonds(bool b); - // Set whether to remove free atomic moieties in clean-up - void setRemoveAtomics(bool b); - // Set whether to remove water and coordinated oxygen atoms in clean-up - void setRemoveWaterAndCoordinateOxygens(bool b); - // Set whether to remove by NETA definition in clean-up - void setRemoveNETA(bool b, bool byFragment); - // Set NETA for moiety removal - bool setMoietyRemovalNETA(std::string_view netaDefinition); - // Set supercell repeat - void setSupercellRepeat(const Vector3i &repeat); - // Recreate the data - bool generate(CIFGenerationStage fromStage = CIFGenerationStage::CreateBasicUnitCell); - // Return whether the generated data is valid - bool isValid() const; - // Return supercell species - const Species &supercellSpecies() const; - // Return cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; - // Return the detected molecular species - const std::vector &molecularSpecies() const; - // Return the generated configuration - Configuration *generatedConfiguration(); - // Finalise, copying the required species and resulting configuration to the target CoreData - void finalise(CoreData &coreData, const Flags &flags = {}) const; - - /* - * Helpers - */ - private: - // Apply CIF bonding to a given species - void applyCIFBonding(Species *sp, bool preventMetallicBonding); - // Determine the best NETA definition for the supplied species - std::tuple> bestNETADefinition(Species *sp); - // Get instances of species molecules from the supplied NETA definition - std::vector getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms); - // Calculate difference metric between the supplied species and local molecule - static std::pair> differenceMetric(const Species *species, const LocalMolecule &molecule); - // Recursively check NETA description matches between the supplied atoms - std::map matchAtom(const SpeciesAtom *referenceAtom, - const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map); -}; diff --git a/src/io/import/cifClasses.cpp b/src/io/import/cifClasses.cpp deleted file mode 100644 index a2ba6fd5b0..0000000000 --- a/src/io/import/cifClasses.cpp +++ /dev/null @@ -1,130 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/io/cifClasses.h" -#include "classes/empiricalFormula.h" -#include "classes/molecule.h" -#include "classes/species.h" - -/* - * CIF Symmetry-Unique Atom - */ - -CIFSymmetryAtom::CIFSymmetryAtom(std::string_view label, Elements::Element Z, Vector3 rFrac, double occ) - : label_{label}, Z_(Z), rFrac_(rFrac), occupancy_(occ) {}; - -// Return label (from _atom_site_label) -std::string_view CIFSymmetryAtom::label() const { return label_; } - -// Return element (from _atom_site_type_symbol) -Elements::Element CIFSymmetryAtom::Z() const { return Z_; } - -// Return fractional coordinate of atom (from _atom_site_fract_[xyz]) -Vector3 CIFSymmetryAtom::rFrac() const { return rFrac_; } - -// Return site occupancy (from _atom_site_occupancy) -double CIFSymmetryAtom::occupancy() const { return occupancy_; } - -/* - * CIF Bonding Pair - */ - -CIFBondingPair::CIFBondingPair(std::string_view labelI, std::string_view labelJ, double r) - : labelI_{labelI}, labelJ_{labelJ}, r_(r) {}; - -// Return labels of involved atom i (from _geom_bond_atom_site_label_1) -std::string_view CIFBondingPair::labelI() const { return labelI_; } - -// Return labels of involved atom i (from _geom_bond_atom_site_label_2) -std::string_view CIFBondingPair::labelJ() const { return labelJ_; } - -// Return distance between bonded pair (from _geom_bond_distance) -double CIFBondingPair::r() const { return r_; } - -/* - * CIF Atom Group - */ - -CIFAtomGroup::CIFAtomGroup(std::string_view name) : name_{name} {}; - -// Group name (from _atom_site_disorder_group) -std::string_view CIFAtomGroup::name() const { return name_; } - -// Add atom to the group -void CIFAtomGroup::addAtom(const CIFSymmetryAtom &i) { atoms_.emplace_back(i); } - -// Return atoms in the group -const std::vector &CIFAtomGroup::atoms() const { return atoms_; } - -// Set whether the group is active (included in unit cell generation) -void CIFAtomGroup::setActive(bool b) { active_ = b; } - -// Return whether the group is active (included in unit cell generation) -bool CIFAtomGroup::active() const { return active_; } - -/* - * CIF Assembly - */ - -CIFAssembly::CIFAssembly(std::string_view name) : name_{name} {} - -// Return name of the assembly (from _atom_site_disorder_assembly or 'Global') -std::string_view CIFAssembly::name() const { return name_; } - -// Return all groups -std::vector &CIFAssembly::groups() { return groups_; } -const std::vector &CIFAssembly::groups() const { return groups_; } - -// Get (add or retrieve) named group -CIFAtomGroup &CIFAssembly::getGroup(std::string_view groupName) -{ - auto it = - std::find_if(groups_.begin(), groups_.end(), [groupName](const auto &group) { return group.name() == groupName; }); - if (it != groups_.end()) - return *it; - - return groups_.emplace_back(groupName); -} - -// Return the number of defined groups -int CIFAssembly::nGroups() const { return groups_.size(); } - -/* - * CIF Molecular Species - */ - -CIFMolecularSpecies::CIFMolecularSpecies() : species_(std::make_shared()) {} - -// Return species parent for molecule instances -std::shared_ptr &CIFMolecularSpecies::species() { return species_; }; -const std::shared_ptr &CIFMolecularSpecies::species() const { return species_; }; - -// Return molecule instances -const std::vector &CIFMolecularSpecies::instances() const { return instances_; } -std::vector &CIFMolecularSpecies::instances() { return instances_; } - -// Append supplied instances to our vector -void CIFMolecularSpecies::appendInstances(const std::vector &newInstances) -{ - // Increase our reservation - instances_.reserve(instances_.size() + newInstances.size()); - instances_.insert(instances_.end(), newInstances.begin(), newInstances.end()); -} - -// Return coordinates for all instances as a vector of vectors -std::vector> CIFMolecularSpecies::allInstanceCoordinates() const -{ - std::vector> coordinates; - - for (auto &instance : instances_) - { - std::vector instanceCoords; - instanceCoords.reserve(species_->nAtoms()); - for (auto &atom : instance.localAtoms()) - instanceCoords.emplace_back(atom.r()); - - coordinates.emplace_back(instanceCoords); - } - - return coordinates; -} diff --git a/src/io/import/cifClasses.h b/src/io/import/cifClasses.h deleted file mode 100644 index dd9dcf613d..0000000000 --- a/src/io/import/cifClasses.h +++ /dev/null @@ -1,142 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "classes/localMolecule.h" -#include "classes/species.h" -#include "data/elements.h" -#include "math/vector3.h" -#include -#include - -// Forward Declarations -class Species; - -// CIF Symmetry-Unique Atom -class CIFSymmetryAtom -{ - public: - CIFSymmetryAtom(std::string_view label, Elements::Element Z, Vector3 rFrac, double occ); - ~CIFSymmetryAtom() = default; - - private: - // Label (from _atom_site_label) - std::string label_; - // Element (from _atom_site_type_symbol) - Elements::Element Z_; - // Fractional coordinate of atom (from _atom_site_fract_[xyz]) - Vector3 rFrac_; - // Site occupancy (from _atom_site_occupancy) - double occupancy_; - - public: - // Return label (from _atom_site_label) - std::string_view label() const; - // Return element (from _atom_site_type_symbol) - Elements::Element Z() const; - // Return fractional coordinate of atom (from _atom_site_fract_[xyz]) - Vector3 rFrac() const; - // Return site occupancy (from _atom_site_occupancy) - double occupancy() const; -}; - -// CIF Bonding Pair -class CIFBondingPair -{ - public: - CIFBondingPair(std::string_view labelI, std::string_view labelJ, double r); - ~CIFBondingPair() = default; - - private: - // Labels of involved atoms (from _geom_bond_atom_site_label_[12]) - std::string labelI_, labelJ_; - // Distance between bonded pair (from _geom_bond_distance) - double r_; - - public: - // Return labels of involved atom i (from _geom_bond_atom_site_label_1) - std::string_view labelI() const; - // Return labels of involved atom i (from _geom_bond_atom_site_label_2) - std::string_view labelJ() const; - // Return distance between bonded pair (from _geom_bond_distance) - double r() const; -}; - -// CIF Atom Group -class CIFAtomGroup -{ - public: - CIFAtomGroup(std::string_view name); - ~CIFAtomGroup() = default; - - private: - // Group name (from _atom_site_disorder_group) - std::string name_; - // Atoms in the group - std::vector atoms_; - // Whether the group is active (included in unit cell generation) - bool active_{false}; - - public: - // Group name (from _atom_site_disorder_group) - std::string_view name() const; - // Add atom to the group - void addAtom(const CIFSymmetryAtom &i); - // Return atoms in the group - const std::vector &atoms() const; - // Set whether the group is active (included in unit cell generation) - void setActive(bool b); - // Return whether the group is active (included in unit cell generation) - bool active() const; -}; - -// CIF Assembly -class CIFAssembly -{ - public: - CIFAssembly(std::string_view name); - ~CIFAssembly() = default; - - private: - // Name of the assembly (from _atom_site_disorder_assembly or 'Global') - std::string name_; - // Available atom groups - std::vector groups_; - - public: - // Return name of the assembly (from _atom_site_disorder_assembly or 'Global') - std::string_view name() const; - // Return all groups - std::vector &groups(); - const std::vector &groups() const; - // Get (add or retrieve) named group - CIFAtomGroup &getGroup(std::string_view groupName); - // Return the number of defined groups - int nGroups() const; -}; - -// CIF Repeated Molecular Species -class CIFMolecularSpecies -{ - public: - CIFMolecularSpecies(); - - private: - // Species parent for molecule instances - std::shared_ptr species_; - // Molecule instances - std::vector instances_; - - public: - // Return species parent for molecule instances - std::shared_ptr &species(); - const std::shared_ptr &species() const; - // Return molecule instances - const std::vector &instances() const; - std::vector &instances(); - // Append supplied instances to our vector - void appendInstances(const std::vector &newInstances); - // Return coordinates for all instances as a vector of vectors - std::vector> allInstanceCoordinates() const; -}; diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index 790b113010..68cb059703 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -34,6 +34,9 @@ NodeConstants::ProcessResult ImportCIFStructureNode::process() if (spaceGroup_ != SpaceGroups::NoSpaceGroup) context_.setSpaceGroup(spaceGroup_); + if (!context_.generate()) + return NodeConstants::ProcessResult::Failed; + structure_ = context_.structure(); return NodeConstants::ProcessResult::Success; diff --git a/src/nodes/cif/io/cifContext.cpp b/src/nodes/cif/io/cifContext.cpp index 3ac123b3d4..c5eb9cac68 100644 --- a/src/nodes/cif/io/cifContext.cpp +++ b/src/nodes/cif/io/cifContext.cpp @@ -490,6 +490,8 @@ bool CIFContext::createBasicUnitCell() Messenger::print("Created basic crystal unit cell - {} non-overlapping atoms.\n", unitCellSpecies_.nAtoms()); + createStructure(); + return true; } @@ -501,23 +503,23 @@ bool CIFContext::createStructure() structure_.createBox(box->axisLengths(), box->axisAngles(), box->type() == Box::BoxType::NonPeriodic); // Add structural atoms + std::map structureAtomLookUp; const auto &atoms = unitCellSpecies_.atoms(); for (const auto &atom : atoms) - structure_.addAtom(atom.Z(), atom.r(), atom.q()); + structureAtomLookUp.insert_or_assign(&atom, structure_.addAtom(atom.Z(), atom.r(), atom.q())); // Iterate over newly added structure atom pairs, adding any existing bonds between them if not already present - auto pairs = PairIterator(structure_.nAtoms()); - for (const auto &pair : pairs) - { - auto [i, j] = pair; - auto atomI = structure_.atomAt(i); - auto atomJ = structure_.atomAt(j); - - if (!structure_.hasBond(atomI, atomJ)) - structure_.addBond(atomI, atomJ); - } + for (const auto &atom : atoms) + for (const auto &bond : atom.bonds()) + { + auto i = structureAtomLookUp[bond.get().i()]; + auto j = structureAtomLookUp[bond.get().j()]; + if (!structure_.hasBond(i, j)) + structure_.addBond(i, j); + } - Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", structure_.nAtoms(), structure_.bonds().size()); + Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", + structure_.nAtoms(), structure_.bonds().size()); return true; } From 4a894fe53a291c1e3a9cce60b2cad698a2d18841 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 6 May 2026 14:59:12 +0100 Subject: [PATCH 05/22] delete unused files; fix typo in node name; fix structure bonding 2 --- tests/nodes/bragg.cpp | 4 ++-- tests/nodes/cif.cpp | 12 ++++++++---- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/tests/nodes/bragg.cpp b/tests/nodes/bragg.cpp index 48124b7d2c..b8fe94780b 100644 --- a/tests/nodes/bragg.cpp +++ b/tests/nodes/bragg.cpp @@ -40,11 +40,11 @@ class BraggNodeTest : public ::testing::Test // Create species and configuration from MgO cif file auto root = testGraph_.dissolveGraph(); - ASSERT_TRUE(testGraph_.appendNode("importCIFStructure", "importCIFStructure")); + ASSERT_TRUE(testGraph_.appendNode("ImportCIFStructure")); ASSERT_TRUE(testGraph_.fetchHead()->setOption("FilePath", "cif/1000053.cif")); ASSERT_TRUE(testGraph_.appendNode("CIFBondingOptions", "CIFBonds")); - ASSERT_TRUE(root->addEdge({"importCIFStructure", "CIFContext", "CIFBonds", "CIFContext"})); + ASSERT_TRUE(root->addEdge({"ImportCIFStructure", "CIFContext", "CIFBonds", "CIFContext"})); ASSERT_TRUE(testGraph_.fetchHead()->setOption("PreventAllBonds", true)); // Create a supercell that is 5 * unitcell diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index 04a1e5dd2e..140a7dccba 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -104,13 +104,17 @@ class CIFNodeTest : public ::testing::Test TEST_F(CIFNodeTest, Parse) { - // Test files - std::vector cifs = {"1557470.cif", "1557599.cif", "7705246.cif", "9000004.cif", "9000095.cif", "9000418.cif"}; + // Test files with expected number of structure atoms + std::vector> cifs = {{"1557470.cif", 86}, {"1557599.cif", 56}, {"7705246.cif", 364}, + {"9000004.cif", 6}, {"9000095.cif", 30}, {"9000418.cif", 64}}; - for (auto &cif : cifs) + for (auto &[cif, nStructureAtoms] : cifs) { createGraph(cif); - ASSERT_EQ(testGraph_.findNode(cifNameFromFile(cif))->run(), NodeConstants::ProcessResult::Success); + auto node = testGraph_.findNode(cifNameFromFile(cif)); + ASSERT_EQ(node->run(), NodeConstants::ProcessResult::Success); + const auto structure = node->getOutputValue("Structure"); + ASSERT_EQ(structure->atoms().size(), nStructureAtoms); } } From bc7308a7024c382d6f4dde5f4e63f4f30e217f87 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 6 May 2026 15:11:52 +0100 Subject: [PATCH 06/22] format --- tests/nodes/cif.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index 140a7dccba..0f1414694a 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -106,7 +106,7 @@ TEST_F(CIFNodeTest, Parse) { // Test files with expected number of structure atoms std::vector> cifs = {{"1557470.cif", 86}, {"1557599.cif", 56}, {"7705246.cif", 364}, - {"9000004.cif", 6}, {"9000095.cif", 30}, {"9000418.cif", 64}}; + {"9000004.cif", 6}, {"9000095.cif", 30}, {"9000418.cif", 64}}; for (auto &[cif, nStructureAtoms] : cifs) { From 98a0688378cad8aaf8e6687328525b6ee02f49a7 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 6 May 2026 15:44:58 +0100 Subject: [PATCH 07/22] format 2 --- src/io/import/CMakeLists.txt | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/io/import/CMakeLists.txt b/src/io/import/CMakeLists.txt index 2466de48dd..5e3c23a777 100644 --- a/src/io/import/CMakeLists.txt +++ b/src/io/import/CMakeLists.txt @@ -32,8 +32,6 @@ add_library( values.h ) -target_include_directories( - import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src -) +target_include_directories(import PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src) target_link_libraries(import base nodes) From 4e531e5f92f1ab69728a57ad552ccdcb41c20953 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 6 May 2026 15:52:36 +0100 Subject: [PATCH 08/22] format 3 --- src/nodes/CMakeLists.txt | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/src/nodes/CMakeLists.txt b/src/nodes/CMakeLists.txt index 88e577b828..01e5e53eef 100644 --- a/src/nodes/CMakeLists.txt +++ b/src/nodes/CMakeLists.txt @@ -39,19 +39,15 @@ set(ANTLR_OUTPUT_DIRS CACHE INTERNAL "" ) -add_library(nodes - ${node_sources} - ${node_headers} - ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} - ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS} -) +add_library(nodes ${node_sources} ${node_headers} ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS} ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}) -message(STATUS "ANTLR generated products located in the following directories: ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS}, ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}") +message( + STATUS + "ANTLR generated products located in the following directories: ${ANTLR_CIFImportGrammarLexer_CXX_OUTPUTS}, ${ANTLR_CIFImportGrammarParser_CXX_OUTPUTS}" +) -target_include_directories(nodes PRIVATE - ${PROJECT_SOURCE_DIR}/src - ${PROJECT_BINARY_DIR}/src - ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} - ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} +target_include_directories( + nodes PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} + ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} ) target_link_libraries(nodes PUBLIC base ${THREADING_LINK_LIBS}) From a33830e132043e29e010bdd95a797538f00d56c8 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Thu, 7 May 2026 14:36:20 +0100 Subject: [PATCH 09/22] break up cip context into node (strange compiler fail to find atnlr CIFImportBaseVisitor.h) --- src/nodes/cif/cifBondingOptions.cpp | 37 -- src/nodes/cif/cifBondingOptions.h | 41 -- src/nodes/cif/cifMolecularSpecies.cpp | 49 -- src/nodes/cif/cifMolecularSpecies.h | 46 -- src/nodes/cif/cifPeriodicFramework.cpp | 47 -- src/nodes/cif/cifPeriodicFramework.h | 48 -- src/nodes/cif/cifRemoveAtomic.cpp | 30 -- src/nodes/cif/cifRemoveAtomic.h | 35 -- src/nodes/cif/cifRemoveWater.cpp | 31 -- src/nodes/cif/cifRemoveWater.h | 35 -- src/nodes/cif/cifStructureCleanup.cpp | 34 -- src/nodes/cif/cifStructureCleanup.h | 39 -- src/nodes/cif/cifSuperMolecule.cpp | 37 -- src/nodes/cif/cifSuperMolecule.h | 37 -- src/nodes/cif/importCIFStructure.cpp | 520 +++++++++++++++++++++- src/nodes/cif/importCIFStructure.h | 106 ++++- src/nodes/cif/io/CIFImportVisitor.cpp | 2 +- src/nodes/cif/io/CIFImportVisitor.h | 10 +- src/nodes/cif/setCIFAtomGroupActivity.cpp | 36 -- src/nodes/cif/setCIFAtomGroupActivity.h | 39 -- src/nodes/registry.cpp | 16 - tests/nodes/bragg.cpp | 6 +- tests/nodes/cif.cpp | 10 +- 23 files changed, 626 insertions(+), 665 deletions(-) delete mode 100644 src/nodes/cif/cifBondingOptions.cpp delete mode 100644 src/nodes/cif/cifBondingOptions.h delete mode 100644 src/nodes/cif/cifMolecularSpecies.cpp delete mode 100644 src/nodes/cif/cifMolecularSpecies.h delete mode 100644 src/nodes/cif/cifPeriodicFramework.cpp delete mode 100644 src/nodes/cif/cifPeriodicFramework.h delete mode 100644 src/nodes/cif/cifRemoveAtomic.cpp delete mode 100644 src/nodes/cif/cifRemoveAtomic.h delete mode 100644 src/nodes/cif/cifRemoveWater.cpp delete mode 100644 src/nodes/cif/cifRemoveWater.h delete mode 100644 src/nodes/cif/cifStructureCleanup.cpp delete mode 100644 src/nodes/cif/cifStructureCleanup.h delete mode 100644 src/nodes/cif/cifSuperMolecule.cpp delete mode 100644 src/nodes/cif/cifSuperMolecule.h delete mode 100644 src/nodes/cif/setCIFAtomGroupActivity.cpp delete mode 100644 src/nodes/cif/setCIFAtomGroupActivity.h diff --git a/src/nodes/cif/cifBondingOptions.cpp b/src/nodes/cif/cifBondingOptions.cpp deleted file mode 100644 index 0d98707aa7..0000000000 --- a/src/nodes/cif/cifBondingOptions.cpp +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifBondingOptions.h" - -CIFBondingOptionsNode::CIFBondingOptionsNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("BondingTolerance", "Bonding tolerance, if calculating bonding rather than using CIF definitions", - bondingTolerance_); - addOption("UseCIFBondingDefinitions", "Whether to use CIF bonding definitions", useCIFBondingDefinitions_); - addOption("PreventMetallicBonds", "Whether to prevent metallic bonding", preventMetallicBonds_); - addOption("PreventAllBonds", "Whether to ignore all bonds", preventAllBonds_); -} - -std::string_view CIFBondingOptionsNode::type() const { return "CIFBondingOptions"; } - -std::string_view CIFBondingOptionsNode::summary() const { return "Apply bonding options to a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFBondingOptionsNode::process() -{ - - context_->setBondingTolerance(bondingTolerance_.asDouble()); - context_->setUseCIFBondingDefinitions(useCIFBondingDefinitions_); - context_->setPreventMetallicBonds(preventMetallicBonds_); - context_->setPreventAllBonds(preventAllBonds_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/cifBondingOptions.h b/src/nodes/cif/cifBondingOptions.h deleted file mode 100644 index 86097f525b..0000000000 --- a/src/nodes/cif/cifBondingOptions.h +++ /dev/null @@ -1,41 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFBondingOptionsNode : public Node -{ - public: - CIFBondingOptionsNode(Graph *parentGraph); - ~CIFBondingOptionsNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Bonding tolerance, if calculating bonding rather than using CIF definitions - Number bondingTolerance_{1.1}; - // Whether to use CIF bonding definitions - bool useCIFBondingDefinitions_{false}; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; - // Whether to ignore all bonds - bool preventAllBonds_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cif/cifMolecularSpecies.cpp b/src/nodes/cif/cifMolecularSpecies.cpp deleted file mode 100644 index 24e003f776..0000000000 --- a/src/nodes/cif/cifMolecularSpecies.cpp +++ /dev/null @@ -1,49 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifMolecularSpecies.h" -#include -#include - -CIFMolecularSpeciesNode::CIFMolecularSpeciesNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput>("DetectedMolecularSpecies", "Detected molecular species", molecularSpecies_); - addOutput("SupercellConfiguration", "Supercell configuration pointer", supercellConfiguration_); - - // Options - addOption("SupercellRepeat", "Supercell repeat", supercellRepeat_); -} - -std::string_view CIFMolecularSpeciesNode::type() const { return "CIFMolecularSpecies"; } - -std::string_view CIFMolecularSpeciesNode::summary() const -{ - return "Output a configuration containing individual molecules based on detected species"; -} - -// Run main processing -NodeConstants::ProcessResult CIFMolecularSpeciesNode::process() -{ - // Generate from CIF context - context_->setSupercellRepeat(supercellRepeat_); - context_->generate(); - - // Get supercell configuration - supercellConfiguration_ = context_->generatedConfiguration(); - supercellConfiguration_->setName(context_->chemicalFormula()); - - // Get detected molecular species - auto &cifMols = context_->molecularSpecies(); - molecularSpecies_.clear(); - std::ranges::copy(cifMols, std::back_inserter(molecularSpecies_)); - - return NodeConstants::ProcessResult::Success; -} - -// Get cleaned unit cell species -const Species &CIFMolecularSpeciesNode::cleanedUnitCellSpecies() const { return context_->cleanedUnitCellSpecies(); } \ No newline at end of file diff --git a/src/nodes/cif/cifMolecularSpecies.h b/src/nodes/cif/cifMolecularSpecies.h deleted file mode 100644 index fc842ad71a..0000000000 --- a/src/nodes/cif/cifMolecularSpecies.h +++ /dev/null @@ -1,46 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFMolecularSpeciesNode : public Node -{ - public: - CIFMolecularSpeciesNode(Graph *parentGraph); - ~CIFMolecularSpeciesNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Supercell configuration - Configuration *supercellConfiguration_{nullptr}; - // Detected molecular species - std::vector molecularSpecies_; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; - - /* - * Getters - */ - public: - // Get cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; -}; diff --git a/src/nodes/cif/cifPeriodicFramework.cpp b/src/nodes/cif/cifPeriodicFramework.cpp deleted file mode 100644 index a80f9464e5..0000000000 --- a/src/nodes/cif/cifPeriodicFramework.cpp +++ /dev/null @@ -1,47 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifPeriodicFramework.h" - -CIFPeriodicFrameworkNode::CIFPeriodicFrameworkNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("FrameworkSpecies", "Species", frameworkSpecies_); - addOutput("SupercellConfiguration", "Supercell configuration pointer", supercellConfiguration_); - - // Options - addOption("SupercellRepeat", "Supercell repeat", supercellRepeat_); -} - -std::string_view CIFPeriodicFrameworkNode::type() const { return "CIFPeriodicFramework"; } - -std::string_view CIFPeriodicFrameworkNode::summary() const -{ - return "Create a single species with a periodic box and all atoms in the unit cell (suitable for framework-style models)"; -} - -// Run main processing -NodeConstants::ProcessResult CIFPeriodicFrameworkNode::process() -{ - // Generate from CIF context - context_->setSupercellRepeat(supercellRepeat_); - context_->generate(); - - // Get supercell configuration - supercellConfiguration_ = context_->generatedConfiguration(); - supercellConfiguration_->setName(context_->chemicalFormula()); - - // Get framework species - supercellSpecies_->copyBasic(&(context_->supercellSpecies())); - supercellSpecies_->updateIntramolecularTerms(); - frameworkSpecies_ = supercellSpecies_.get(); - - return NodeConstants::ProcessResult::Success; -} - -// Get cleaned unit cell species -const Species &CIFPeriodicFrameworkNode::cleanedUnitCellSpecies() const { return context_->cleanedUnitCellSpecies(); } \ No newline at end of file diff --git a/src/nodes/cif/cifPeriodicFramework.h b/src/nodes/cif/cifPeriodicFramework.h deleted file mode 100644 index d32b545bb6..0000000000 --- a/src/nodes/cif/cifPeriodicFramework.h +++ /dev/null @@ -1,48 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFPeriodicFrameworkNode : public Node -{ - public: - CIFPeriodicFrameworkNode(Graph *parentGraph); - ~CIFPeriodicFrameworkNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Supercell configuration - Configuration *supercellConfiguration_{nullptr}; - // Supercell species - std::unique_ptr supercellSpecies_; - // Framework species - const Species *frameworkSpecies_{nullptr}; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; - - /* - * Getters - */ - public: - // Get cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; -}; diff --git a/src/nodes/cif/cifRemoveAtomic.cpp b/src/nodes/cif/cifRemoveAtomic.cpp deleted file mode 100644 index 6d18bcd696..0000000000 --- a/src/nodes/cif/cifRemoveAtomic.cpp +++ /dev/null @@ -1,30 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifRemoveAtomic.h" - -CIFRemoveAtomicNode::CIFRemoveAtomicNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveAtomics", "Whether to remove free atomic moieties in clean-up", removeAtomics_); -} - -std::string_view CIFRemoveAtomicNode::type() const { return "CIFRemoveAtomic"; } - -std::string_view CIFRemoveAtomicNode::summary() const { return "Remove atomics from a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFRemoveAtomicNode::process() -{ - - context_->setRemoveAtomics(removeAtomics_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/cifRemoveAtomic.h b/src/nodes/cif/cifRemoveAtomic.h deleted file mode 100644 index d81d5ef38b..0000000000 --- a/src/nodes/cif/cifRemoveAtomic.h +++ /dev/null @@ -1,35 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFRemoveAtomicNode : public Node -{ - public: - CIFRemoveAtomicNode(Graph *parentGraph); - ~CIFRemoveAtomicNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Whether to remove free atomic moieties in clean-up - bool removeAtomics_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cif/cifRemoveWater.cpp b/src/nodes/cif/cifRemoveWater.cpp deleted file mode 100644 index d1b23f245f..0000000000 --- a/src/nodes/cif/cifRemoveWater.cpp +++ /dev/null @@ -1,31 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifRemoveWater.h" - -CIFRemoveWaterNode::CIFRemoveWaterNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveWaterAndCoordinatedOxygens", "Whether to remove water and coordinated oxygen atoms in clean-up", - removeWaterAndCoordinatedOxygens_); -} - -std::string_view CIFRemoveWaterNode::type() const { return "CIFRemoveWater"; } - -std::string_view CIFRemoveWaterNode::summary() const { return "Remove water from a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFRemoveWaterNode::process() -{ - - context_->setRemoveWaterAndCoordinateOxygens(removeWaterAndCoordinatedOxygens_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/cifRemoveWater.h b/src/nodes/cif/cifRemoveWater.h deleted file mode 100644 index 4482a3a5d0..0000000000 --- a/src/nodes/cif/cifRemoveWater.h +++ /dev/null @@ -1,35 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFRemoveWaterNode : public Node -{ - public: - CIFRemoveWaterNode(Graph *parentGraph); - ~CIFRemoveWaterNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Whether to remove water and coordinated oxygen atoms in clean-up - bool removeWaterAndCoordinatedOxygens_{false}; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cif/cifStructureCleanup.cpp b/src/nodes/cif/cifStructureCleanup.cpp deleted file mode 100644 index 2c7562130d..0000000000 --- a/src/nodes/cif/cifStructureCleanup.cpp +++ /dev/null @@ -1,34 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifStructureCleanup.h" - -CIFStructureCleanupNode::CIFStructureCleanupNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("RemoveNETA", "Whether to remove by NETA definition in clean-up", removeNETA_); - addOption("removeNETAByFragment", "Whether to expand NETA matches to fragments when removing in clean-up", - removeNETAByFragment_); - addOption("MoietyRemovalNETA", "NETA for moiety removal", moietyRemovalNETA_); -} - -std::string_view CIFStructureCleanupNode::type() const { return "CIFStructureCleanup"; } - -std::string_view CIFStructureCleanupNode::summary() const { return "Clean up a CIF context"; } - -// Run main processing -NodeConstants::ProcessResult CIFStructureCleanupNode::process() -{ - - context_->setRemoveNETA(removeNETA_, removeNETAByFragment_); - context_->setMoietyRemovalNETA(std::string_view(moietyRemovalNETA_)); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/cifStructureCleanup.h b/src/nodes/cif/cifStructureCleanup.h deleted file mode 100644 index 10ec0b8848..0000000000 --- a/src/nodes/cif/cifStructureCleanup.h +++ /dev/null @@ -1,39 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFStructureCleanupNode : public Node -{ - public: - CIFStructureCleanupNode(Graph *parentGraph); - ~CIFStructureCleanupNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Whether to remove by NETA definition in clean-up - bool removeNETA_{false}; - // Whether to expand NETA matches to fragments when removing in clean-up - bool removeNETAByFragment_{false}; - // NETA for moiety removal, if specified - std::string moietyRemovalNETA_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cif/cifSuperMolecule.cpp b/src/nodes/cif/cifSuperMolecule.cpp deleted file mode 100644 index 183079fb23..0000000000 --- a/src/nodes/cif/cifSuperMolecule.cpp +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/cifSuperMolecule.h" - -CIFSuperMoleculeNode::CIFSuperMoleculeNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("NonPeriodicSpecies", "Non-periodic species", nonPeriodicSpecies_); -} - -std::string_view CIFSuperMoleculeNode::type() const { return "CIFSuperMolecule"; } - -std::string_view CIFSuperMoleculeNode::summary() const -{ - return "Create a single non-periodic species (useful for generating 'chunks' of crystal material)"; -} - -// Run main processing -NodeConstants::ProcessResult CIFSuperMoleculeNode::process() -{ - // Generate from CIF context - context_->generate(); - - // Get non-periodic species - supercellSpecies_->copyBasic(&(context_->supercellSpecies())); - supercellSpecies_->removePeriodicBonds(); - supercellSpecies_->removeBox(); - supercellSpecies_->updateIntramolecularTerms(); - nonPeriodicSpecies_ = supercellSpecies_.get(); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/cifSuperMolecule.h b/src/nodes/cif/cifSuperMolecule.h deleted file mode 100644 index 0af23edb60..0000000000 --- a/src/nodes/cif/cifSuperMolecule.h +++ /dev/null @@ -1,37 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class CIFSuperMoleculeNode : public Node -{ - public: - CIFSuperMoleculeNode(Graph *parentGraph); - ~CIFSuperMoleculeNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Non-periodic species - const Species *nonPeriodicSpecies_{nullptr}; - // Supercell species - std::unique_ptr supercellSpecies_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index 68cb059703..eb44a9b426 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -2,6 +2,20 @@ // Copyright (c) 2026 Team Dissolve and contributors #include "nodes/cif/importCIFStructure.h" +#include "CIFImportLexer.h" +#include "CIFImportParser.h" +#include "base/messenger.h" +#include "base/sysFunc.h" +#include "classes/coreData.h" +#include "classes/empiricalFormula.h" +#include "classes/species.h" +#include "generator/add.h" +#include "generator/box.h" +#include "generator/coordinateSets.h" +#include "neta/neta.h" +#include "nodes/cif/io/CIFImportErrorListeners.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "templates/algorithms.h" #include #include #include @@ -9,9 +23,7 @@ ImportCIFStructureNode::ImportCIFStructureNode(Graph *parentGraph) : Node(parentGraph) { // Outputs - addPointerOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - addOutput("Structure", "Structure containing atoms and connectivity", structure_); + addPointerOutput("Structure", "Structure containing atoms and connectivity", structure_); // Option addOption("FilePath", "File path", filePath_); @@ -29,15 +41,10 @@ std::string_view ImportCIFStructureNode::summary() const NodeConstants::ProcessResult ImportCIFStructureNode::process() { // Read contents of CIF file - if (context_.read(filePath_)) + if (read(filePath_)) { - if (spaceGroup_ != SpaceGroups::NoSpaceGroup) - context_.setSpaceGroup(spaceGroup_); - - if (!context_.generate()) - return NodeConstants::ProcessResult::Failed; - - structure_ = context_.structure(); + if (!createStructure(spaceGroup_, overlapTolerance_)) + return error("Did not successfully create a basic structure from the CIF file."); return NodeConstants::ProcessResult::Success; } @@ -46,3 +53,494 @@ NodeConstants::ProcessResult ImportCIFStructureNode::process() return NodeConstants::ProcessResult::Failed; } + +/* + * CIF I/O + */ + +/* + * Raw Data + */ + +// Parse supplied file into the destination objects +bool ImportCIFStructureNode::parse(std::string_view filename, CIFImportVisitor::CIFTags &tags) const +{ + // Set up ANTLR input stream + std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); + if (!cifFile.is_open()) + return Messenger::error("Failed to open CIF file '{}.\n", filename); + + antlr4::ANTLRInputStream input(cifFile); + + // Create ANTLR lexer and set-up error listener + CIFImportLexer lexer(&input); + CIFImportLexerErrorListener lexerErrorListener; + lexer.removeErrorListeners(); + lexer.addErrorListener(&lexerErrorListener); + + // Generate tokens from input stream + antlr4::CommonTokenStream tokens(&lexer); + + // Create ANTLR parser and set-up error listeners + CIFImportParser parser(&tokens); + CIFImportParserErrorListener parserErrorListener; + parser.removeErrorListeners(); + parser.removeParseListeners(); + parser.addErrorListener(&lexerErrorListener); + parser.addErrorListener(&parserErrorListener); + + // Generate the AST + CIFImportParser::CifContext *tree = nullptr; + try + { + tree = parser.cif(); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + Messenger::error("{}", ex.what()); + return false; + } + + // Visit the nodes in the AST + CIFImportVisitor visitor(tags); + try + { + visitor.extract(tree); + } + catch (CIFImportExceptions::CIFImportSyntaxException &ex) + { + return Messenger::error("{}", ex.what()); + } + + return true; +} + +// Return whether the specified file parses correctly +bool ImportCIFStructureNode::validFile(std::string_view filename) const +{ + CIFImportVisitor::CIFTags tags; + return parse(filename, tags); +} + +// Read CIF data from specified file +bool ImportCIFStructureNode::read(std::string_view filename) +{ + assemblies_.clear(); + bondingPairs_.clear(); + tags_.clear(); + + if (!parse(filename, tags_)) + return Messenger::error("Failed to parse CIF file '{}'.\n", filename); + + /* + * Determine space group - the search order for tags is: + * + * 1. Hall symbol + * 2. Hermann-Mauginn name + * 3. Space group index + * + * In the case of 2 or 3 we also try to search for the origin choice. + * + * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection + * below fails). + */ + + // Check for Hall symbol + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) + spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); + + if (spaceGroup_ == SpaceGroups::NoSpaceGroup) + { + // Might need the coordinate system code... + auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); + + // Find a HM name + if (hasTag("_space_group_name_H-M_alt")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) + spaceGroup_ = + SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); + + // Find a space group index? + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); + if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) + spaceGroup_ = + SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); + } + + // Create symmetry-unique atoms list + auto atomSiteLabel = getTagStrings("_atom_site_label"); + auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); + auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); + auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); + auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); + auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); + auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); + auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); + if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) + return Messenger::error( + "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); + if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) + return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) + return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", + atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); + for (auto n = 0; n < atomSiteFractX.size(); ++n) + { + // Get standard information + auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); + auto Z = n < atomSiteTypeSymbol.size() + ? Elements::element(atomSiteTypeSymbol[n]) + : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); + auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; + Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); + + // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: + // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly + // 2) An assembly and a group are defined - add it to that + // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group + auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; + auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; + if (assemblyName == "." && groupName != ".") + assemblyName = "Disorder"; + else if (assemblyName == "." && groupName == ".") + assemblyName = "Global"; + + if (groupName == ".") + groupName = "Default"; + + // Get the assembly and group that we're adding the atom to + auto &assembly = getAssembly(assemblyName); + auto &group = assembly.getGroup(groupName); + group.setActive(groupName == "Default" || groupName == "1"); + group.addAtom({label, Z, rFrac, occ}); + } + + // Construct bonding pairs list + auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); + auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); + auto bondDistances = getTagDoubles("_geom_bond_distance"); + if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) + { + for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) + bondingPairs_.emplace_back(i, j, r); + } + else + Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); + + return true; +} + +// Return if the specified tag exists +bool ImportCIFStructureNode::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } + +// Return tag data string (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagString(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + return it->second.front(); +} + +// Return tag data strings (if it exists) +std::vector ImportCIFStructureNode::getTagStrings(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + return it->second; +} + +// Return tag data as double (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagDouble(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + double result; + try + { + result = std::stod(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +// Return tag data doubles (if it exists) +std::vector ImportCIFStructureNode::getTagDoubles(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return {}; + + std::vector v; + for (const auto &s : it->second) + { + auto d = 0.0; + try + { + d = std::stod(s); + } + catch (...) + { + Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); + } + v.push_back(d); + } + + return v; +} + +// Return tag data as integer (if it exists) assuming a single datum (first in the vector) +std::optional ImportCIFStructureNode::getTagInt(std::string tag) const +{ + auto it = tags_.find(tag); + if (it == tags_.end()) + return std::nullopt; + + // Check data vector size + if (it->second.size() != 1) + Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); + + int result; + try + { + result = std::stoi(it->second.front()); + } + catch (...) + { + Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, + it->second.front()); + return std::nullopt; + } + + return result; +} + +/* + * Processed Data + */ + +// Return space group information +SpaceGroups::SpaceGroupId ImportCIFStructureNode::spaceGroup() const { return spaceGroup_; } + +// Return cell lengths +std::optional ImportCIFStructureNode::getCellLengths() const +{ + auto a = getTagDouble("_cell_length_a"); + if (!a) + Messenger::error("Cell length A not defined in CIF.\n"); + auto b = getTagDouble("_cell_length_b"); + if (!b) + Messenger::error("Cell length B not defined in CIF.\n"); + auto c = getTagDouble("_cell_length_c"); + if (!c) + Messenger::error("Cell length C not defined in CIF.\n"); + + if (a && b && c) + return Vector3(a.value(), b.value(), c.value()); + else + return std::nullopt; +} + +// Return cell angles +std::optional ImportCIFStructureNode::getCellAngles() const +{ + auto alpha = getTagDouble("_cell_angle_alpha"); + if (!alpha) + Messenger::error("Cell angle alpha not defined in CIF.\n"); + auto beta = getTagDouble("_cell_angle_beta"); + if (!beta) + Messenger::error("Cell angle beta not defined in CIF.\n"); + auto gamma = getTagDouble("_cell_angle_gamma"); + if (!gamma) + Messenger::error("Cell angle gamma not defined in CIF.\n"); + + if (alpha && beta && gamma) + return Vector3(alpha.value(), beta.value(), gamma.value()); + else + return std::nullopt; +} + +// Return chemical formula +std::string ImportCIFStructureNode::chemicalFormula() const +{ + auto it = tags_.find("_chemical_formula_sum"); + return (it != tags_.end() ? it->second.front() : "Unknown"); +} + +// Get (add or retrieve) named assembly +CIFAssembly &ImportCIFStructureNode::getAssembly(std::string_view name) +{ + auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); + if (it != assemblies_.end()) + return *it; + + return assemblies_.emplace_back(name); +} + +// Return atom assemblies +std::vector &ImportCIFStructureNode::assemblies() { return assemblies_; } + +const std::vector &ImportCIFStructureNode::assemblies() const { return assemblies_; } + +// Return whether any bond distances are defined +bool ImportCIFStructureNode::hasBondDistances() const { return !bondingPairs_.empty(); } + +// Return whether a bond distance is defined for the specified label pair +std::optional ImportCIFStructureNode::bondDistance(std::string_view labelI, std::string_view labelJ) const +{ + auto it = std::find_if( + bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) + { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); + if (it != bondingPairs_.end()) + return it->r(); + return std::nullopt; +} + +/* + * Creation + */ + +// Create structure from basic unit cell atoms and connectivity +bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, double overlapTolerance) +{ + spaceGroup_ = sgid; + + overlapTolerance_ = overlapTolerance; + + atomLabelTypes_.clear(); + + // Create temporary atom types corresponding to the unique atom labels + for (auto &a : assemblies_) + { + for (auto &g : a.groups()) + { + if (!g.active()) + continue; + + for (auto &i : g.atoms()) + { + if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) + { + atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); + } + } + } + } + + // Configure the unit cell "species" + auto cellLengths = getCellLengths(); + if (!cellLengths) + return false; + auto cellAngles = getCellAngles(); + if (!cellAngles) + return false; + + // Configuration + echo_ = false; + structure_.createBox(cellLengths.value(), cellAngles.value(), false); + echo_ = true; + + auto *box = structure_.box(); + + // -- Generate atoms + auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); + for (const auto &generator : symmetryGenerators) + for (auto &a : assemblies_) + for (auto &g : a.groups()) + if (g.active()) + for (auto &unique : g.atoms()) + { + // Generate folded atomic position in real space + auto r = generator * unique.rFrac(); + box->toReal(r); + r = box->fold(r); + + // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy + if (std::any_of(structure_.atoms().begin(), structure_.atoms().end(), [&, r, box](const auto &j) + { return box->minimumDistance(r, j->r()) < overlapTolerance_; })) + continue; + + // Create the new atom + auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), + [&unique](const auto at) { return unique.label() == at->name(); }); + structure_.addAtom(unique.Z(), r, 0.0); + } + + // Check that we actually generated some atoms... + if (structure_.nAtoms() == 0) + return false; + + // Bonding + if (!hasBondDistances()) + return true; + + auto pairs = PairIterator(structure_.nAtoms()); + for (auto pair : pairs) + { + // Grab indices and atom references + auto [indexI, indexJ] = pair; + if (indexI == indexJ) + continue; + + auto i = structure_.atomAt(indexI); + auto j = structure_.atomAt(indexJ); + + // Prevent metallic bonding? + if (preventMetallicBonds_ && Elements::isMetallic(i->Z()) && Elements::isMetallic(j->Z())) + continue; + + // Retrieve distance + auto atomTypeIdxI = i->atomTypeIndex(); + auto atomTypeIdxJ = j->atomTypeIndex(); + auto r = bondDistance(atomLabelTypes_[atomTypeIdxI]->name(), atomLabelTypes_[atomTypeIdxJ]->name()); + if (!r) + continue; + else if (!structure_.hasBond(i, j) && fabs(box->minimumDistance(i->r(), j->r()) - r.value()) < 1.0e-2) + structure_.addBond(i, j); + } + + Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", + structure_.nAtoms(), structure_.bonds().size()); + return true; +} + +/* + * End CIF I/O + */ + +/* + * Getters + */ + +// Return the basic unit cell configuration +const Structure &ImportCIFStructureNode::structure() const { return structure_; } diff --git a/src/nodes/cif/importCIFStructure.h b/src/nodes/cif/importCIFStructure.h index 87ecca0e49..b9dc9c2a48 100644 --- a/src/nodes/cif/importCIFStructure.h +++ b/src/nodes/cif/importCIFStructure.h @@ -3,9 +3,16 @@ #pragma once +#include "classes/configuration.h" +#include "classes/species.h" #include "classes/structure.h" -#include "nodes/cif/io/cifContext.h" +#include "data/spaceGroups.h" +#include "math/matrix4.h" +#include "neta/neta.h" +#include "nodes/cif/io/CIFImportVisitor.h" +#include "nodes/cif/io/cifClasses.h" #include "nodes/node.h" +#include // ImportCIFStructure Node class ImportCIFStructureNode : public Node @@ -22,14 +29,98 @@ class ImportCIFStructureNode : public Node * Definition */ private: - // CIF handler context - CIFContext context_; // CIF strucutre - Structure *structure_; + Structure structure_; // Space group ID SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::SpaceGroupId::NoSpaceGroup}; // CIF filepath std::string filePath_; + // Whether to prevent metallic bonding + bool preventMetallicBonds_{true}; + + /* + * CIF I/O + */ + + /* + * Raw Data + */ + private: + // Vector of enumerated data items + CIFImportVisitor::CIFTags tags_; + + private: + // Parse supplied file into the destination objects + bool parse(std::string_view filename, CIFImportVisitor::CIFTags &tags) const; + + public: + // Return whether the specified file parses correctly + bool validFile(std::string_view filename) const; + // Read CIF data from specified file + bool read(std::string_view filename); + // Return if the specified tag exists + bool hasTag(std::string tag) const; + // Return tag data string (if it exists) assuming a single datum (first in the vector) + std::optional getTagString(std::string tag) const; + // Return tag data strings (if it exists) + std::vector getTagStrings(std::string tag) const; + // Return tag data as double (if it exists) assuming a single datum (first in the vector) + std::optional getTagDouble(std::string tag) const; + // Return tag data doubles (if it exists) + std::vector getTagDoubles(std::string tag) const; + // Return tag data as integer (if it exists) assuming a single datum (first in the vector) + std::optional getTagInt(std::string tag) const; + + /* + * Processed Data + */ + private: + // Atom assemblies + std::vector assemblies_; + // Bond information + std::vector bondingPairs_; + + public: + // Set space group from index + void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); + // Return space group + SpaceGroups::SpaceGroupId spaceGroup() const; + // Return cell lengths + std::optional getCellLengths() const; + // Return cell angles + std::optional getCellAngles() const; + // Return chemical formula + std::string chemicalFormula() const; + // Get (add or retrieve) named assembly + CIFAssembly &getAssembly(std::string_view name); + // Return atom assemblies + std::vector &assemblies(); + const std::vector &assemblies() const; + // Return whether any bond distances are defined + bool hasBondDistances() const; + // Return whether a bond distance is defined for the specified label pair + std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; + + /* + * Creation + */ + private: + // Temporary atom types used for unique atom labels + std::vector> atomLabelTypes_; + // Tolerance for removal of overlapping atoms + double overlapTolerance_{0.1}; + + private: + // Create structure from basic unit cell atoms and connectivity + bool createStructure(SpaceGroups::SpaceGroupId sgid, double overlapTolerance); + + public: + // Set overlap tolerance + void setOverlapTolerance(double tol); + + /* + * End CIF I/O + */ /* * Processing @@ -37,4 +128,11 @@ class ImportCIFStructureNode : public Node private: // Run main processing NodeConstants::ProcessResult process() override; + + /* + * Getters + */ + public: + // Return the basic crystal structure + const Structure &structure() const; }; diff --git a/src/nodes/cif/io/CIFImportVisitor.cpp b/src/nodes/cif/io/CIFImportVisitor.cpp index 8601d98135..964af13e3b 100644 --- a/src/nodes/cif/io/CIFImportVisitor.cpp +++ b/src/nodes/cif/io/CIFImportVisitor.cpp @@ -6,7 +6,7 @@ #include "base/sysFunc.h" #include "nodes/cif/io/CIFImportErrorListeners.h" -CIFImportVisitor::CIFImportVisitor(CIFContext::CIFTags &tags) : tags_(tags) {} +CIFImportVisitor::CIFImportVisitor(CIFTags &tags) : tags_(tags) {} /* * Data diff --git a/src/nodes/cif/io/CIFImportVisitor.h b/src/nodes/cif/io/CIFImportVisitor.h index 9b079f801f..9a9374c71c 100644 --- a/src/nodes/cif/io/CIFImportVisitor.h +++ b/src/nodes/cif/io/CIFImportVisitor.h @@ -4,15 +4,19 @@ #pragma once #include "CIFImportParserBaseVisitor.h" -#include "nodes/cif/io/cifContext.h" #include "templates/optionalRef.h" #include // CIFImport Visitor for ANTLR class CIFImportVisitor : CIFImportParserBaseVisitor { + + public: + // Data Types + using CIFTags = std::map>; + public: - CIFImportVisitor(CIFContext::CIFTags &tags); + CIFImportVisitor(CIFTags &tags); ~CIFImportVisitor() override = default; /* @@ -20,7 +24,7 @@ class CIFImportVisitor : CIFImportParserBaseVisitor */ private: // Dictionary data storage - CIFContext::CIFTags &tags_; + CIFTags &tags_; public: // Extract information from tree diff --git a/src/nodes/cif/setCIFAtomGroupActivity.cpp b/src/nodes/cif/setCIFAtomGroupActivity.cpp deleted file mode 100644 index d477a7ec9e..0000000000 --- a/src/nodes/cif/setCIFAtomGroupActivity.cpp +++ /dev/null @@ -1,36 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/setCIFAtomGroupActivity.h" - -SetCIFAtomGroupActivityNode::SetCIFAtomGroupActivityNode(Graph *parentGraph) : Node(parentGraph) -{ - // Inputs - addInput("CIFContext", "CIF handling context derived from parsing of CIF file", context_) - ->setFlags({ParameterBase::Required}); - - // Outputs - addOutput("CIFContext", "CIF handling context derived from parsing of CIF file", context_); - - // Options - addOption("Assembly", "CIF assembly name", assemblyName_); - addOption("AtomGroup", "CIF atom group name", atomGroupName_); - addOption("SetActive", "Activity status of selected CIF atom group", active_); -} - -std::string_view SetCIFAtomGroupActivityNode::type() const { return "SetCIFAtomGroupActivity"; } - -std::string_view SetCIFAtomGroupActivityNode::summary() const -{ - return "Set activity of CIF assembly atom groups and apply to a CIF context"; -} - -// Run main processing -NodeConstants::ProcessResult SetCIFAtomGroupActivityNode::process() -{ - - auto &atomGroup = context_->getAssembly(assemblyName_).getGroup(atomGroupName_); - atomGroup.setActive(active_); - - return NodeConstants::ProcessResult::Success; -} diff --git a/src/nodes/cif/setCIFAtomGroupActivity.h b/src/nodes/cif/setCIFAtomGroupActivity.h deleted file mode 100644 index 4d7e6f36d5..0000000000 --- a/src/nodes/cif/setCIFAtomGroupActivity.h +++ /dev/null @@ -1,39 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include "nodes/node.h" - -// ImportCIFStructure Node -class SetCIFAtomGroupActivityNode : public Node -{ - public: - SetCIFAtomGroupActivityNode(Graph *parentGraph); - ~SetCIFAtomGroupActivityNode() override = default; - - public: - std::string_view type() const override; - std::string_view summary() const override; - - /* - * Definition - */ - private: - // CIF handler context - CIFContext *context_{nullptr}; - // Selected CIF assembly atom group name - std::string atomGroupName_; - // Selected CIF assembly name - std::string assemblyName_; - // Activity status of CIF atom group - bool active_; - - /* - * Processing - */ - private: - // Run main processing - NodeConstants::ProcessResult process() override; -}; diff --git a/src/nodes/registry.cpp b/src/nodes/registry.cpp index 8f6dbe69f7..29c1cb36c3 100644 --- a/src/nodes/registry.cpp +++ b/src/nodes/registry.cpp @@ -7,15 +7,7 @@ #include "nodes/angle.h" #include "nodes/atomicMC/atomicMC.h" #include "nodes/bragg.h" -#include "nodes/cif/cifBondingOptions.h" -#include "nodes/cif/cifMolecularSpecies.h" -#include "nodes/cif/cifPeriodicFramework.h" -#include "nodes/cif/cifRemoveAtomic.h" -#include "nodes/cif/cifRemoveWater.h" -#include "nodes/cif/cifStructureCleanup.h" -#include "nodes/cif/cifSuperMolecule.h" #include "nodes/cif/importCIFStructure.h" -#include "nodes/cif/setCIFAtomGroupActivity.h" #include "nodes/configuration.h" #include "nodes/data1DImport.h" #include "nodes/derivative.h" @@ -73,16 +65,8 @@ void NodeRegistry::instantiateNodeProducers() {"Angle", makeDerivedNode()}, {"AtomicMC", makeDerivedNode()}, {"Bragg", makeDerivedNode()}, - {"CIFStructureCleanup", makeDerivedNode()}, {"Configuration", makeDerivedNode()}, - {"CIFBondingOptions", makeDerivedNode()}, {"ImportCIFStructure", makeDerivedNode()}, - {"CIFMolecularSpecies", makeDerivedNode()}, - {"CIFPeriodicFramework", makeDerivedNode()}, - {"CIFRemoveAtomic", makeDerivedNode()}, - {"CIFRemoveWater", makeDerivedNode()}, - {"CIFSuperMolecule", makeDerivedNode()}, - {"SetCIFAtomGroupActivity", makeDerivedNode()}, {"Data1DImport", makeDerivedNode()}, {"Derivative", makeDerivedNode()}, {"DotProduct", makeDerivedNode()}, diff --git a/tests/nodes/bragg.cpp b/tests/nodes/bragg.cpp index b8fe94780b..b0ba5e13ac 100644 --- a/tests/nodes/bragg.cpp +++ b/tests/nodes/bragg.cpp @@ -6,7 +6,6 @@ #include "classes/speciesSites.h" #include "io/import/trajectory.h" #include "math/rangedVector3.h" -#include "nodes/cif/cifMolecularSpecies.h" #include "nodes/gr/gr.h" #include "nodes/importConfigurationTrajectory.h" #include "nodes/iterableGraph.h" @@ -30,7 +29,7 @@ class BraggNodeTest : public ::testing::Test TestGraph testGraph_; NeutronSQNode *neutronSQNode_{nullptr}; BraggNode *braggNode_{nullptr}; - CIFMolecularSpeciesNode *cifConfigurationNode_{nullptr}; + // CIFMolecularSpeciesNode *cifConfigurationNode_{nullptr}; const Vector3i supercellRepeat_{5, 5, 5}; protected: @@ -138,6 +137,7 @@ class BraggNodeTest : public ::testing::Test } }; +/* TEST_F(BraggNodeTest, MgO_Full) { createGraph({5, 5, 5}); @@ -1288,5 +1288,5 @@ TEST_F(BraggNodeTest, MgO_Intensities111) {939, 9.994500, {33, 6, 0}, 432, {1.128566e-25, 1.128469e-25, 1.128662e-25}}, {940, 9.999500, {33, 6, 1}, 264, {6.660584e-26, -6.738634e-26, 6.838882e-26}}})); } - +*/ } // namespace UnitTest \ No newline at end of file diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index 0f1414694a..ff6085e16a 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -3,7 +3,6 @@ #include "classes/empiricalFormula.h" #include "io/import/species.h" -#include "nodes/cif/cifMolecularSpecies.h" #include "nodes/cif/importCIFStructure.h" #include "tests/graphData.h" #include "tests/testData.h" @@ -50,12 +49,11 @@ class CIFNodeTest : public ::testing::Test return name; } // Retrieve CIF context by filename - CIFContext *getContextByFileName(std::string filename) + ImportCIFStructureNode *getContextByFileName(std::string filename) { auto name = cifNameFromFile(filename); auto node = testGraph_.findNode(name); - auto context = node->getOutputValue("CIFContext"); - return context; + return static_cast(node); } // Test Box definition void testBox(const Configuration *cfg, const Vector3 &lengths, const Vector3 &angles, int nAtoms) @@ -117,7 +115,7 @@ TEST_F(CIFNodeTest, Parse) ASSERT_EQ(structure->atoms().size(), nStructureAtoms); } } - +/* TEST_F(CIFNodeTest, NaCl) { // Load the CIF file @@ -336,5 +334,5 @@ TEST_F(CIFNodeTest, BigMoleculeOrdering) auto &unitCellSpecies = static_cast(molecularSpeciesNode)->cleanedUnitCellSpecies(); testInstanceConsistency(cifMolecule, unitCellSpecies); } - +*/ } // namespace UnitTest \ No newline at end of file From 638607e5892be6e477ee3d94691cca8d4786825a Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Thu, 7 May 2026 14:48:15 +0100 Subject: [PATCH 10/22] add option for now --- src/nodes/cif/importCIFStructure.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index eb44a9b426..e0b8d3cd53 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -27,6 +27,7 @@ ImportCIFStructureNode::ImportCIFStructureNode(Graph *parentGraph) : Node(parent // Option addOption("FilePath", "File path", filePath_); + addOption("PreventMetallicBonds", "Whether to prevent metallic bonding", preventMetallicBonds_); addOption("SpaceGroupID", "Set space group from index", spaceGroup_); } From 562c5bd4325570fedf5a2d75b2acd7cdf460f996 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Thu, 7 May 2026 15:35:24 +0100 Subject: [PATCH 11/22] fix compilation for antlr dir --- src/nodes/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/nodes/CMakeLists.txt b/src/nodes/CMakeLists.txt index 01e5e53eef..898164b0bc 100644 --- a/src/nodes/CMakeLists.txt +++ b/src/nodes/CMakeLists.txt @@ -47,7 +47,7 @@ message( ) target_include_directories( - nodes PRIVATE ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} + nodes PUBLIC ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} ) target_link_libraries(nodes PUBLIC base ${THREADING_LINK_LIBS}) From f8e89d47bcad4bbfa24d180f24c2cb1935c31b05 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Fri, 8 May 2026 07:28:14 +0100 Subject: [PATCH 12/22] fix structure bonding from cif and a few other changes --- src/nodes/CMakeLists.txt | 2 +- src/nodes/cif/importCIFStructure.cpp | 11 +++++------ src/nodes/cif/importCIFStructure.h | 4 +--- tests/nodes/cif.cpp | 10 ---------- 4 files changed, 7 insertions(+), 20 deletions(-) diff --git a/src/nodes/CMakeLists.txt b/src/nodes/CMakeLists.txt index 898164b0bc..88803e910d 100644 --- a/src/nodes/CMakeLists.txt +++ b/src/nodes/CMakeLists.txt @@ -48,6 +48,6 @@ message( target_include_directories( nodes PUBLIC ${PROJECT_SOURCE_DIR}/src ${PROJECT_BINARY_DIR}/src ${ANTLR_CIFImportGrammarLexer_OUTPUT_DIR} - ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} + ${ANTLR_CIFImportGrammarParser_OUTPUT_DIR} ) target_link_libraries(nodes PUBLIC base ${THREADING_LINK_LIBS}) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index e0b8d3cd53..ff85a594cf 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -8,7 +8,6 @@ #include "base/sysFunc.h" #include "classes/coreData.h" #include "classes/empiricalFormula.h" -#include "classes/species.h" #include "generator/add.h" #include "generator/box.h" #include "generator/coordinateSets.h" @@ -50,9 +49,7 @@ NodeConstants::ProcessResult ImportCIFStructureNode::process() return NodeConstants::ProcessResult::Success; } - error("Failed to read contents of CIF file"); - - return NodeConstants::ProcessResult::Failed; + return error("Failed to read contents of CIF file"); } /* @@ -494,7 +491,9 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou // Create the new atom auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), [&unique](const auto at) { return unique.label() == at->name(); }); - structure_.addAtom(unique.Z(), r, 0.0); + auto *structureAtom = structure_.addAtom(unique.Z(), r, 0.0); + auto atomLabelTypeIdx = std::distance(atomLabelTypes_.begin(), atIt); + structureAtom->setAtomTypeIndex(atomLabelTypeIdx); } // Check that we actually generated some atoms... @@ -543,5 +542,5 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou * Getters */ -// Return the basic unit cell configuration +// Return basic crystal structure const Structure &ImportCIFStructureNode::structure() const { return structure_; } diff --git a/src/nodes/cif/importCIFStructure.h b/src/nodes/cif/importCIFStructure.h index b9dc9c2a48..9efaea9deb 100644 --- a/src/nodes/cif/importCIFStructure.h +++ b/src/nodes/cif/importCIFStructure.h @@ -3,8 +3,6 @@ #pragma once -#include "classes/configuration.h" -#include "classes/species.h" #include "classes/structure.h" #include "data/spaceGroups.h" #include "math/matrix4.h" @@ -133,6 +131,6 @@ class ImportCIFStructureNode : public Node * Getters */ public: - // Return the basic crystal structure + // Return basic crystal structure const Structure &structure() const; }; diff --git a/tests/nodes/cif.cpp b/tests/nodes/cif.cpp index ff6085e16a..ac87de9503 100644 --- a/tests/nodes/cif.cpp +++ b/tests/nodes/cif.cpp @@ -31,16 +31,6 @@ class CIFNodeTest : public ::testing::Test auto name = cifNameFromFile(filename); EXPECT_TRUE(testGraph_.appendNode("ImportCIFStructure", name)); testGraph_.fetchHead()->setOption("FilePath", path_ + filename); - EXPECT_TRUE(testGraph_.appendNode("CIFBondingOptions", name + "//BondingOptions")); - EXPECT_TRUE(testGraph_.appendNode("CIFRemoveAtomic", name + "//RemoveAtomic")); - EXPECT_TRUE(testGraph_.appendNode("CIFRemoveWater", name + "//RemoveWater")); - EXPECT_TRUE(testGraph_.appendNode("CIFStructureCleanup", name + "//StructureCleanup")); - EXPECT_TRUE(testGraph_.appendNode("CIFMolecularSpecies", name + "//MolecularSpecies")); - testGraph_.addEdge({name, "CIFContext", name + "//BondingOptions", "CIFContext"}); - testGraph_.addEdge({name + "//BondingOptions", "CIFContext", name + "//RemoveAtomic", "CIFContext"}); - testGraph_.addEdge({name + "//RemoveAtomic", "CIFContext", name + "//RemoveWater", "CIFContext"}); - testGraph_.addEdge({name + "//RemoveWater", "CIFContext", name + "//StructureCleanup", "CIFContext"}); - testGraph_.addEdge({name + "//StructureCleanup", "CIFContext", name + "//MolecularSpecies", "CIFContext"}); } // Determine CIF node name from filename std::string cifNameFromFile(std::string filename) From 30a6b100a879783cf1744c960fe1b95feab9f5bc Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Fri, 8 May 2026 11:35:08 +0100 Subject: [PATCH 13/22] remove dissolve 1 cif context dependencies and legacy code --- src/gui/createGrapheneSpeciesDialog.cpp | 521 --------- src/gui/createGrapheneSpeciesDialog.h | 113 -- src/gui/createGrapheneSpeciesDialog.ui | 1014 ----------------- src/gui/gui.h | 4 +- src/gui/importCIFDialog.cpp | 323 ------ src/gui/importCIFDialog.h | 94 -- src/gui/importCIFDialog.ui | 1375 ----------------------- src/gui/menu_species.cpp | 7 +- src/gui/models/CMakeLists.txt | 2 - src/gui/models/cifAssemblyModel.cpp | 149 --- src/gui/models/cifAssemblyModel.h | 36 - src/nodes/cif/io/cifContext.cpp | 1363 ---------------------- src/nodes/cif/io/cifContext.h | 220 ---- tests/io/CMakeLists.txt | 1 - tests/io/cif.cpp | 212 ---- 15 files changed, 6 insertions(+), 5428 deletions(-) delete mode 100644 src/gui/createGrapheneSpeciesDialog.cpp delete mode 100644 src/gui/createGrapheneSpeciesDialog.h delete mode 100644 src/gui/createGrapheneSpeciesDialog.ui delete mode 100644 src/gui/importCIFDialog.cpp delete mode 100644 src/gui/importCIFDialog.h delete mode 100644 src/gui/importCIFDialog.ui delete mode 100644 src/gui/models/cifAssemblyModel.cpp delete mode 100644 src/gui/models/cifAssemblyModel.h delete mode 100644 src/nodes/cif/io/cifContext.cpp delete mode 100644 src/nodes/cif/io/cifContext.h delete mode 100644 tests/io/cif.cpp diff --git a/src/gui/createGrapheneSpeciesDialog.cpp b/src/gui/createGrapheneSpeciesDialog.cpp deleted file mode 100644 index 45194aa310..0000000000 --- a/src/gui/createGrapheneSpeciesDialog.cpp +++ /dev/null @@ -1,521 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "gui/createGrapheneSpeciesDialog.h" -#include "classes/empiricalFormula.h" -#include "gui/helpers/comboPopulator.h" -#include "math/mathFunc.h" -#include - -// Useful constants -const auto root3 = sqrt(3.0); -const auto oneSixthPi = M_PI / 6.0; // == 30 degrees - -CreateGrapheneSpeciesDialog::CreateGrapheneSpeciesDialog(QWidget *parent, Dissolve &dissolve) - : QDialog(parent), selectElementDialog_(this), dissolve_(dissolve) -{ - ui_.setupUi(this); - - Locker refreshLock(widgetsUpdating_); - - ui_.ElementAButton->setText(QString::fromStdString(std::string(Elements::symbol(zA_)))); - ui_.ElementBButton->setText(QString::fromStdString(std::string(Elements::symbol(zB_)))); - ui_.TerminateElementButton->setText(QString::fromStdString(std::string(Elements::symbol(zTerminate_)))); - - ui_.MSpin->setMaximum(ui_.NSpin->value()); - - // Set display configuration - ui_.StructureViewer->setSpecies(&species_); - - refreshLock.unlock(); - - calculateParameters(); - - regenerate(); -} - -/* - * Data - */ - -// Calculate parameters -void CreateGrapheneSpeciesDialog::calculateParameters() -{ - /* - * Procedure based on "Determination of the chiral indices (n,m) of carbon nanotubes by electron diffraction", - * Lu-Chan Qin, Phys. Chem. Chem. Phys. 2007, *9*, 31-48. https://doi.org/10.1039/B614121H - */ - - // Get n,m values for tube - n_ = ui_.NSpin->value(); - m_ = ui_.MSpin->value(); - - // Determine a0, the principal unit length of the structure, from the specified bond distance. See Figure 1a, noting that - // a1 == a2 == a0. - const auto r = ui_.BondLengthSpin->value(); - a0_ = r * root3; - - // Set principal vectors for reference - va1_ = Vector3(a0_, 0.0, 0.0); - va2_ = Vector3(a0_ * sin(oneSixthPi), a0_ * cos(oneSixthPi), 0.0); - - // Calculate repeat dimensions of the (n,m) sheet - // -- A is magnitude of vecA (equation 1) and represents our X dimension - A_ = a0_ * sqrt(n_ * n_ + m_ * m_ + n_ * m_); - // -- c is the magnitude of the vector perpendicular to vecA, along the tube axis, and represents our Y dimension - const auto M = std::gcd(2 * n_ + m_, n_ + 2 * m_); - c_ = sqrt(3.0) * A_ / M; - - // Determine angle alpha, describing the tilt of the sheet away from va1 (equation 3) - alpha_ = atan((sqrt(3.0) * m_) / (2 * n_ + m_)); - - // The radius of the tube is then the circumference (== A) divided by 2PI - radius_ = A_ / (2.0 * M_PI); - - dy_ = va2_.y / cos(alpha_); - H_ = round(c_ / dy_); -} - -// Find dangling atoms, defined as those which have two bonds spanning PBC of the box -std::map> CreateGrapheneSpeciesDialog::findDanglingAtoms(double localCutoff) -{ - std::map> atoms; - for (auto &i : species_.atoms()) - { - // Find all bound partners which are across the unit cell - std::vector pbcJ; - for (auto &b : i.bonds()) - { - auto *j = b.get().partner(&i); - if ((i.r() - j->r()).magnitude() > localCutoff) - pbcJ.push_back(j); - } - - if (pbcJ.size() == 2) - atoms[&i] = pbcJ; - } - - return atoms; -} - -// Get vector of atom keys from atom/neighbour map, sorted by position along indicated direction -std::vector -CreateGrapheneSpeciesDialog::getSortedByY(const std::map> &atoms) const -{ - std::vector sorted; - for (auto &&[i, _] : atoms) - sorted.push_back(i); - - std::sort(sorted.begin(), sorted.end(), [](const SpeciesAtom *a, const SpeciesAtom *b) { return a->r().y < b->r().y; }); - - return sorted; -} - -// Recursive branch function -void CreateGrapheneSpeciesDialog::extendBranch(SpeciesAtom *i, const Box *box, Vector3 &vFrac, - std::vector &branch, double localCutoff) const -{ - // Get PBC and non-PBC (local) bond partners for this atom and see what type of atom we have... - std::vector pbcJ, localJ; - for (auto &b : i->bonds()) - { - auto j = b.get().partner(i); - if ((i->r() - j->r()).magnitude() > localCutoff) - pbcJ.push_back(j); - else if (std::find(branch.begin(), branch.end(), j) == branch.end()) - localJ.push_back(j); - } - - // If all atoms are local this is a completely internally-bound atom, and we are done here. - if (pbcJ.size() == 0) - return; - - // Add ourselves to the branch - branch.push_back(i); - - // For all pbc atoms, increment the fractional direction - for (auto j : pbcJ) - vFrac += (box->getFractional(j->r()) - box->getFractional(i->r())); - - // For local atoms, recurse into them if we haven't visited them already - for (auto j : localJ) - extendBranch(j, box, vFrac, branch, localCutoff); -} - -// Regenerate species -void CreateGrapheneSpeciesDialog::regenerate() -{ - species_.clear(); - - const auto roll = ui_.RollUpCheck->isChecked(); - const auto cFactor = ui_.CFactorSpin->value(); - - // Determine a suitable periodic box for the species - we will always create one so that we get proper folding. - auto offset = Vector3(), cellLengths = Vector3(); - if (roll) - { - // Create some extra space and set an offset so the tube is central in XZ - cellLengths = {radius_ * 3, c_ * cFactor, radius_ * 3}; - offset = Vector3(radius_ * 1.5, 0.0, radius_ * 1.5); - } - else - { - cellLengths = {A_, c_ * cFactor, sheetZ_}; - offset = Vector3(0.0, 0.0, sheetZ_ * 0.5); - } - species_.createBox(cellLengths, {90, 90, 90}); - - /* - * Generate the full coordinates of the sheet. This process is based on equations 7 - 9, but does not follow it precisely. - * Specifically, the innermost loop to translate the primary helix pair is originally stated to run over j (here 'i') from - * 0 - (m-1) inclusive, but this does not generate the correct number of copies for most cases. Instead, the number of - * required helix copies 'H' is calculated from c and the rotated y component of va2 (see earlier). - */ - for (auto j = 0; j < n_ + m_; ++j) - { - // Primary helix atoms (equation 7) - auto x1j = j * a0_ * cos(alpha_); - auto y1j = -j * a0_ * sin(alpha_); - - // Secondary helix atoms (equation 8) - auto x2j = x1j - (a0_ / sqrt(3.0)) * cos(oneSixthPi - alpha_); - auto y2j = y1j - (a0_ / sqrt(3.0)) * sin(oneSixthPi - alpha_); - - // Create H copies of the helix pairs, multiplied by the extension factor along C - for (auto i = 0; i < H_ * cFactor; ++i) - { - // Generate translation vector for this copy (equation 9) - auto delta = Vector3(-i * a0_ * sin(oneSixthPi - alpha_), i * a0_ * cos(oneSixthPi - alpha_), 0.0); - auto r1 = delta + Vector3(x1j, y1j, 0.0); - auto r2 = delta + Vector3(x2j, y2j, 0.0); - - // Get new helix pair coordinates - Vector3 p1, p2; - if (roll) - { - // Wrap the X coordinate (== real position on circumference) onto a tube of radius 'radius', applying the - // offset we set earlier when creating the periodic box so as to put it in the centre of XZ. - p1 = species_.box()->fold( - offset + Vector3(radius_ * sin(2.0 * M_PI * r1.x / A_), r1.y, radius_ * cos(2.0 * M_PI * r1.x / A_))); - p2 = species_.box()->fold( - offset + Vector3(radius_ * sin(2.0 * M_PI * r2.x / A_), r2.y, radius_ * cos(2.0 * M_PI * r2.x / A_))); - } - else - { - p1 = species_.box()->fold(r1); - p2 = species_.box()->fold(r2); - } - - // Check for overlaps with existing atoms - easier and more efficient to do this now as we go. - auto add1 = true, add2 = true; - for (auto &existing : species_.atoms()) - { - if (add1) - add1 = (p1 - existing.r()).magnitude() > 0.1; - if (add2) - add2 = (p2 - existing.r()).magnitude() > 0.1; - if (!add1 && !add2) - break; - } - if (add1) - species_.addAtom(zA_, p1); - if (add2) - species_.addAtom(zB_, p2); - } - } - - // Finalise the species - if (ui_.PeriodicRadio->isChecked()) - { - species_.recalculateIntermolecularTerms(1.1); - } - else if (ui_.NonPeriodicRadio->isChecked()) - { - species_.recalculateIntermolecularTerms(1.1); - - if (ui_.TidyEndsCheck->isChecked()) - { - // Find all atoms which have two bonds spanning PBC of the box - auto localCutoff = ui_.BondLengthSpin->value() * 1.01; - const auto atoms = findDanglingAtoms(localCutoff); - auto sorted = getSortedByY(atoms); - - // Pass 1 - Move all atoms along the PBC bond vectors - while (!sorted.empty()) - { - auto i = sorted.back(); - auto &pbcJ = atoms.at(i); - - // Determine the fractional average vector to the pbc atoms - Vector3 vFrac; - for (auto j : pbcJ) - vFrac += species_.box()->getFractional(j->r()) - species_.box()->getFractional(i->r()); - - // Make this a sensible translation vector - divide elements by their abs value to make unitary and round - for (auto n = 0; n < 3; ++n) - vFrac[n] = fabs(vFrac[n]) < 0.5 ? 0.0 : round(vFrac[n] / fabs(vFrac[n])); - vFrac.multiply(cellLengths); - - // Translate the atom - i->setCoordinates(i->r() + vFrac); - - // Remove this atom from the vector, along with any that were in its pbc neighbour lists - for (auto j : pbcJ) - { - auto it = std::ranges::find(sorted, j); - if (it != sorted.end()) - sorted.erase(it); - } - - sorted.pop_back(); - } - - // Pass 2 - We may have generated some "branches" inadvertently, so rebond, find any singly-bound atoms and check - auto branchEnd = findDanglingAtoms(localCutoff); - std::vector indicesToRemove; - for (auto &&[i, _] : branchEnd) - { - // For this atom we will step along bonds until we find an atom with three non-PBC bonds - this marks a fully - // "internal" atom which does not need (and should not be) translated, and the end of the linear branch we're - // interested in. Along the way we maintain a fractional translation vector based on all PBC bonds we encounter - // which will inform the direction we might want to move the branch. Or we could just remove it. - - Vector3 vFrac; - std::vector branch; - extendBranch(i, species_.box(), vFrac, branch, localCutoff); - auto maxEl = vFrac.absMaxElement(); - Vector3 tVec; - tVec.set(maxEl, round(vFrac.get(maxEl) / fabs(vFrac.get(maxEl)))); - tVec.multiply(cellLengths); - ; - - // Translate or remove the branch? - for (auto j : branch) - if (ui_.RemoveBranchesCheck->isChecked()) - indicesToRemove.push_back(j->index()); - else - j->setCoordinates(j->r() + tVec); - } - - // Final tidy-up - remove any branch atoms if required - species_.removeAtoms(indicesToRemove); - } - - species_.removeBox(); - species_.recalculateIntermolecularTerms(1.1); - - // Terminate? - if (ui_.TerminateCheck->isChecked()) - { - auto rT = ui_.TerminateBondLengthSpin->value(); - auto excludeA = !ui_.TerminateACheck->isChecked(); - auto excludeB = !ui_.TerminateBCheck->isChecked(); - - // Any atom with just two bonds can be terminated - for (auto &i : species_.atoms()) - { - if ((i.nBonds() != 2) || (excludeA && i.Z() == zA_) || (excludeB && i.Z() == zB_)) - continue; - - // Get average bond vector - auto v = (i.r() - i.bond(0).partner(&i)->r()) + (i.r() - i.bond(1).partner(&i)->r()); - v.normalise(); - - species_.addAtom(zTerminate_, i.r() + v * rT); - } - - species_.recalculateIntermolecularTerms(1.1); - } - } - else - { - species_.recalculateIntermolecularTerms(1.1); - species_.removeBox(); - } -} - -/* - * UI - */ - -// Update all controls -void CreateGrapheneSpeciesDialog::updateWidgets() -{ - Locker updateLock(widgetsUpdating_); - - // Sheet properties - ui_.ALabel->setText(QString("%1 \u212B").arg(A_, 0, 'f', 3)); - ui_.CLabel->setText(QString("%1 (%2) \u212B").arg(c_, 0, 'f', 3).arg(c_ * ui_.CFactorSpin->value(), 0, 'f', 3)); - ui_.AlphaLabel->setText(QString("%1\u00B0").arg(DissolveMath::toDegrees(alpha_), 0, 'f', 3)); - ui_.HLabel->setText(QString("%1 (%2)").arg(H_).arg(H_ * ui_.CFactorSpin->value())); - ui_.RadiusLabel->setText(QString("%1 \u212B").arg(radius_, 0, 'f', 3)); - - // Final cell properties - ui_.CellALabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().x, 0, 'f', 3)); - ui_.CellBLabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().y, 0, 'f', 3)); - ui_.CellCLabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().z, 0, 'f', 3)); - - // Configuration information - const auto *box = species_.box(); - ui_.CurrentBoxTypeLabel->setText(QString::fromStdString(std::string(Box::boxTypes().keyword(box->type())))); - QString boxInfo = QString("A: %1 Å
").arg(box->axisLengths().x); - boxInfo += QString("B: %1 Å
").arg(box->axisLengths().y); - boxInfo += QString("C: %1 Å
").arg(box->axisLengths().z); - boxInfo += QString("α: %1°
").arg(box->axisAngles().x); - boxInfo += QString("β: %1°
").arg(box->axisAngles().y); - boxInfo += QString("γ: %1°").arg(box->axisAngles().z); - ui_.CurrentBoxFrame->setToolTip(boxInfo); - - ui_.AtomPopulationLabel->setText(QString::number(species_.nAtoms())); - - // Structure - ui_.StructureViewer->postRedisplay(); -} - -void CreateGrapheneSpeciesDialog::on_NSpin_valueChanged(int value) -{ - if (widgetsUpdating_.isLocked()) - return; - - // MSpin's upper value is our current value - ui_.MSpin->setMaximum(value); - - calculateParameters(); - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_MSpin_valueChanged(int value) -{ - calculateParameters(); - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_ElementAButton_clicked(bool checked) -{ - auto Z = selectElementDialog_.selectElement(zA_); - if (Z == Elements::Unknown) - return; - zA_ = Z; - ui_.ElementAButton->setText(QString::fromStdString(std::string(Elements::symbol(zA_)))); - - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_ElementBButton_clicked(bool checked) -{ - auto Z = selectElementDialog_.selectElement(zB_); - if (Z == Elements::Unknown) - return; - zB_ = Z; - ui_.ElementBButton->setText(QString::fromStdString(std::string(Elements::symbol(zB_)))); - - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_BondLengthSpin_valueChanged(double value) -{ - calculateParameters(); - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_CFactorSpin_valueChanged(int value) -{ - calculateParameters(); - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_RollUpCheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_PeriodicRadio_clicked(bool checked) -{ - if (widgetsUpdating_) - return; - - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_PseudoPeriodicRadio_clicked(bool checked) -{ - if (widgetsUpdating_) - return; - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_NonPeriodicRadio_clicked(bool checked) -{ - if (widgetsUpdating_) - return; - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TidyEndsCheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_RemoveBranchesCheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TerminateCheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TerminateElementButton_clicked(bool checked) -{ - auto Z = selectElementDialog_.selectElement(zB_); - if (Z == Elements::Unknown) - return; - zTerminate_ = Z; - ui_.TerminateElementButton->setText(QString::fromStdString(std::string(Elements::symbol(zTerminate_)))); - - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TerminateBondLengthSpin_valueChanged(double value) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TerminateACheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_TerminateBCheck_clicked(bool checked) -{ - regenerate(); - updateWidgets(); -} - -void CreateGrapheneSpeciesDialog::on_OKButton_clicked(bool checked) -{ - // Copy the species to the main Dissolve instance and set its new name - auto *sp = dissolve_.coreData().copySpecies(&species_); - sp->setName(std::format("Nanotube-({},{})", ui_.NSpin->value(), ui_.MSpin->value())); - - accept(); -} - -void CreateGrapheneSpeciesDialog::on_CancelButton_clicked(bool checked) { reject(); } diff --git a/src/gui/createGrapheneSpeciesDialog.h b/src/gui/createGrapheneSpeciesDialog.h deleted file mode 100644 index e24b001243..0000000000 --- a/src/gui/createGrapheneSpeciesDialog.h +++ /dev/null @@ -1,113 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "base/lock.h" -#include "gui/models/cifAssemblyModel.h" -#include "gui/selectElementDialog.h" -#include "gui/ui_createGrapheneSpeciesDialog.h" -#include "gui/wizard.h" -#include "main/dissolve.h" -#include "nodes/cif/io/cifContext.h" -#include - -// Forward Declarations -class Dissolve; -class Species; - -// Create Graphene Species Dialog -class CreateGrapheneSpeciesDialog : public QDialog -{ - Q_OBJECT - - public: - CreateGrapheneSpeciesDialog(QWidget *parent, Dissolve &dissolve); - ~CreateGrapheneSpeciesDialog() = default; - - private: - // Main form declaration - Ui::CreateGrapheneSpeciesDialog ui_; - // Temporary core data - CoreData temporaryCoreData_; - - /* - * Data - */ - private: - // Main Dissolve object - Dissolve &dissolve_; - // Elements in nanotube - Elements::Element zA_{Elements::Element::C}, zB_{Elements::Element::N}, zTerminate_{Elements::H}; - // Generated nanotube species - Species species_; - // Chirality parameters - int n_{0}, m_{0}; - // Sheet width (A) and height (c) - double A_{0.0}, c_{0.0}; - // Representative unit length - double a0_{0.0}; - // Principal vectors - Vector3 va1_, va2_; - // Angle between principal vector va1 and the sheet vector - double alpha_{0.0}; - // Radius of resulting tube - double radius_{0.0}; - // Delta along y between helices - double dy_{0.0}; - // Number of helices required - int H_{0}; - // Default size of unit cell for sheet - const double sheetZ_{10.0}; - - private: - // Calculate parameters - void calculateParameters(); - // Find dangling atoms, defined as those which have two bonds spanning PBC of the box - std::map> findDanglingAtoms(double localCutoff); - // Get vector of atom keys from atom/neighbour map, sorted by position along y - std::vector getSortedByY(const std::map> &atoms) const; - // Recursive branch function - void extendBranch(SpeciesAtom *i, const Box *box, Vector3 &vFrac, std::vector &branch, - double localCutoff) const; - // Regenerate species - void regenerate(); - - /* - * UI - */ - private: - // Widget update lock - Lock widgetsUpdating_; - // Element selection dialog - SelectElementDialog selectElementDialog_; - - private: - // Update all controls - void updateWidgets(); - - private Q_SLOTS: - // Sheet Definition - void on_NSpin_valueChanged(int value); - void on_MSpin_valueChanged(int value); - void on_ElementAButton_clicked(bool checked); - void on_ElementBButton_clicked(bool checked); - void on_BondLengthSpin_valueChanged(double value); - // Sheet Transforms - void on_CFactorSpin_valueChanged(int value); - void on_RollUpCheck_clicked(bool checked); - // Output Options - void on_PeriodicRadio_clicked(bool checked); - void on_PseudoPeriodicRadio_clicked(bool checked); - void on_NonPeriodicRadio_clicked(bool checked); - void on_TidyEndsCheck_clicked(bool checked); - void on_RemoveBranchesCheck_clicked(bool checked); - void on_TerminateCheck_clicked(bool checked); - void on_TerminateElementButton_clicked(bool checked); - void on_TerminateBondLengthSpin_valueChanged(double value); - void on_TerminateACheck_clicked(bool checked); - void on_TerminateBCheck_clicked(bool checked); - // Dialog - void on_OKButton_clicked(bool checked); - void on_CancelButton_clicked(bool checked); -}; diff --git a/src/gui/createGrapheneSpeciesDialog.ui b/src/gui/createGrapheneSpeciesDialog.ui deleted file mode 100644 index add06c593f..0000000000 --- a/src/gui/createGrapheneSpeciesDialog.ui +++ /dev/null @@ -1,1014 +0,0 @@ - - - CreateGrapheneSpeciesDialog - - - Qt::ApplicationModal - - - - 0 - 0 - 1227 - 835 - - - - - 10 - - - - Create Graphene Species - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - - 0 - 0 - - - - - 4 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Sheet Definition - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - N - - - - - - - 1 - - - 1000 - - - 5 - - - - - - - M - - - - - - - 0 - - - 1000 - - - 0 - - - - - - - Element A - - - - - - - ElementA - - - - - - - Element B - - - - - - - ElementB - - - - - - - Bond Length - - - - - - - 3 - - - 0.100000000000000 - - - 0.010000000000000 - - - 1.420000000000000 - - - - - - - Qt::Horizontal - - - - - - - - 10 - true - - - - Sheet repeat dimension along x, or circumference if rolled into a tube - - - A - - - - - - - Sheet repeat dimension along x, or circumference if rolled into a tube - - - 0 - - - - - - - - 10 - true - - - - Axial length of sheet along the y direction - - - c - - - - - - - Axial length of sheet along the y direction - - - 0 - - - - - - - - 10 - true - - - - Angle alpha between principal vector a1 and the x axis of the repeat unit cell - - - ɑ - - - - - - - Angle alpha between principal vector a1 and the x axis of the repeat unit cell - - - 0 - - - - - - - - 10 - true - - - - Number of repeated translations of the primary helix required (adjusted value in brackets) - - - H - - - - - - - Number of repeated translations of the primary helix required (adjusted value in brackets) - - - 0 - - - - - - - - - - Sheet Transforms - - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Whether to roll up the sheet about the y axis to form a nanotube - - - Roll - - - - - - - - 10 - true - - - - Radius, if rolled into a nanotube - - - Radius - - - - - - - Radius, if rolled into a nanotube - - - 0 - - - - - - - Multiplier for the sheet along the c axis - - - c Factor - - - - - - - Multiplier for the sheet along the c axis - - - 1 - - - 100 - - - - - - - - - - - 0 - 0 - - - - Cell Properties - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 0 - 0 - - - - - 10 - true - - - - A - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - - 0 - 0 - - - - - 10 - true - - - - B - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - - 0 - 0 - - - - - 10 - true - - - - C - - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - - - - - - 0.0 - - - - - - - 0.0 - - - - - - - 0.0 - - - - - - - - - - Output Options - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Periodic - - - true - - - - - - - Pseudo-periodic - - - - - - - Non-periodic - - - false - - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 20 - 20 - - - - - - - - 4 - - - - - Tidy the ends of non-periodic sheets, moving dangling atoms to leave complete rings - - - Tidy Ends - - - true - - - - - - - Whether to remove any remaining branches rather than try to translate them into a meaningful position (requires Tidy Ends) - - - Remove branches - - - - - - - Terminate? - - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 20 - 20 - - - - - - - - - - Element - - - - - - - ElementA - - - - - - - Bond Length - - - - - - - 3 - - - 0.100000000000000 - - - 0.010000000000000 - - - 1.000000000000000 - - - - - - - Terminate A - - - true - - - - - - - Terminate B - - - true - - - - - - - - - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - - - 1 - 0 - - - - - - - Preview - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/configuration.svg:/general/icons/configuration.svg - - - true - - - - - - - - 0 - 0 - - - - - 10 - false - - - - Orthorhombic - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - - - - Number of atoms in the configuration - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/spheres_on.svg:/general/icons/spheres_on.svg - - - true - - - - - - - - 0 - 0 - - - - 0 - - - - - - - - - - - - - 3 - 0 - - - - - 300 - 300 - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - - 1 - 0 - - - - - - - - - - - - - - - - - - - Qt::Horizontal - - - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - - 10 - true - - - - Cancel - - - - - - - - 10 - true - - - - OK - - - - - - - - - - SpeciesViewer - QWidget -
gui/speciesViewer.h
- 1 - - - - NSpin - MSpin - ElementAButton - ElementBButton - BondLengthSpin - CancelButton - OKButton - CurrentBoxToolButton - AtomPopulationToolButton - - - - - - diff --git a/src/gui/gui.h b/src/gui/gui.h index b350024f37..451d55d26a 100644 --- a/src/gui/gui.h +++ b/src/gui/gui.h @@ -166,11 +166,11 @@ class DissolveWindow : public QMainWindow void on_SpeciesCreateAtomicAction_triggered(bool checked); void on_SpeciesCreateDrawAction_triggered(bool checked); void on_SpeciesCreateFromExistingAction_triggered(bool checked); - void on_SpeciesCreateGrapheneAction_triggered(bool checked); + // void on_SpeciesCreateGrapheneAction_triggered(bool checked); void on_SpeciesImportFromDissolveAction_triggered(bool checked); void on_SpeciesImportFromXYZAction_triggered(bool checked); void on_SpeciesImportLigParGenAction_triggered(bool checked); - void on_SpeciesImportFromCIFAction_triggered(bool checked); + // void on_SpeciesImportFromCIFAction_triggered(bool checked); void on_SpeciesRenameAction_triggered(bool checked); void on_SpeciesDeleteAction_triggered(bool checked); void on_SpeciesAddForcefieldTermsAction_triggered(bool checked); diff --git a/src/gui/importCIFDialog.cpp b/src/gui/importCIFDialog.cpp deleted file mode 100644 index a94e31f3d1..0000000000 --- a/src/gui/importCIFDialog.cpp +++ /dev/null @@ -1,323 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "gui/importCIFDialog.h" -#include "base/units.h" -#include "classes/empiricalFormula.h" -#include "classes/pairIterator.h" -#include "generator/box.h" -#include "gui/helpers/comboPopulator.h" -#include -#include -#include -#include - -ImportCIFDialog::ImportCIFDialog(QWidget *parent, Dissolve &dissolve) - : QDialog(parent), cifAssemblyModel_(cifContext_.assemblies()), dissolve_(dissolve) -{ - ui_.setupUi(this); - - Locker refreshLock(widgetsUpdating_); - - // Add spacegroups to combo - for (auto n = 1; n < SpaceGroups::nSpaceGroupIds; ++n) - ui_.SpaceGroupsCombo->addItem( - QString::fromStdString(std::string(SpaceGroups::formattedInformation((SpaceGroups::SpaceGroupId)n)))); - ui_.SpaceGroupsCombo->setCurrentIndex(-1); - - // Set assembly view model - ui_.AssemblyView->setModel(&cifAssemblyModel_); - ui_.AssemblyView->update(); - ui_.AssemblyView->expandAll(); - connect(&cifAssemblyModel_, SIGNAL(dataChanged(const QModelIndex &, const QModelIndex &, const QList &)), this, - SLOT(assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &))); - connect(&cifAssemblyModel_, SIGNAL(dataChanged(const QModelIndex &, const QModelIndex &, const QList &)), - ui_.AssemblyView, SLOT(expandAll())); - - // Populate density units combo - ComboEnumOptionsPopulator(ui_.DensityUnitsCombo, Units::densityUnits()); - - // Set display configuration - ui_.StructureViewer->setConfiguration(cifContext_.generatedConfiguration()); - - createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString()); -} - -/* - * UI - */ - -// Update all controls -void ImportCIFDialog::updateWidgets() -{ - Locker updateLock(widgetsUpdating_); - - // DATA_ ID - ui_.InfoDataLabel->setText(QString::fromStdString(cifContext_.getTagString("DATA_").value_or(""))); - - // Chemical Formula - ui_.InfoChemicalFormulaLabel->setText(QString::fromStdString(cifContext_.chemicalFormula())); - - // Publication Data - ui_.InfoPublicationTitleLabel->setText( - QString::fromStdString(cifContext_.getTagString("_publ_section_title").value_or(""))); - ui_.InfoPublicationReferenceLabel->setText(QString::fromStdString(std::format( - "{}, {}, {}, {}", cifContext_.getTagString("_journal_name_full").value_or("N/A"), - cifContext_.getTagString("_journal_year").value_or("N/A"), cifContext_.getTagString("_journal_volume").value_or("N/A"), - cifContext_.getTagString("_journal_page_first").value_or("N/A")))); - ui_.InfoAuthorsList->clear(); - auto authors = cifContext_.getTagStrings("_publ_author_name"); - for (auto &author : authors) - ui_.InfoAuthorsList->addItem(QString::fromStdString(author)); - - // Spacegroup - ui_.SpaceGroupsCombo->setCurrentIndex(cifContext_.spaceGroup() - 1); - - // Bonding - ui_.BondFromCIFRadio->setEnabled(cifContext_.hasBondDistances()); - - // Assemblies - ui_.AssemblyView->expandAll(); - - // Configuration information - auto *cfg = cifContext_.generatedConfiguration(); - const auto *box = cfg->box(); - ui_.CurrentBoxTypeLabel->setText(QString::fromStdString(std::string(Box::boxTypes().keyword(box->type())))); - QString boxInfo = QString("A: %1 Å
").arg(box->axisLengths().x); - boxInfo += QString("B: %1 Å
").arg(box->axisLengths().y); - boxInfo += QString("C: %1 Å
").arg(box->axisLengths().z); - boxInfo += QString("α: %1°
").arg(box->axisAngles().x); - boxInfo += QString("β: %1°
").arg(box->axisAngles().y); - boxInfo += QString("γ: %1°").arg(box->axisAngles().z); - ui_.CurrentBoxFrame->setToolTip(boxInfo); - updateDensityLabel(); - ui_.AtomPopulationLabel->setText(QString::number(cfg->nAtoms())); - ui_.MoleculePopulationLabel->setText(QString::number(cfg->nMolecules())); - - // Output - auto validSpecies = !cifContext_.molecularSpecies().empty(); - ui_.OutputMolecularRadio->setEnabled(validSpecies); - ui_.OutputFrameworkRadio->setEnabled(!validSpecies); - ui_.OutputSupermoleculeRadio->setEnabled(!validSpecies); - if (validSpecies) - ui_.OutputMolecularRadio->setChecked(true); - else if (ui_.OutputMolecularRadio->isChecked()) - ui_.OutputFrameworkRadio->setChecked(true); - - // Update molecular species list - ui_.OutputMolecularSpeciesList->clear(); - for (auto &molecularSp : cifContext_.molecularSpecies()) - { - ui_.OutputMolecularSpeciesList->addItem(QString::fromStdString(std::string(molecularSp.species()->name()))); - } - - // Structure - ui_.StructureViewer->postRedisplay(); -} - -// Update density label -void ImportCIFDialog::updateDensityLabel() -{ - auto *cfg = cifContext_.generatedConfiguration(); - if (!cfg) - ui_.DensityUnitsLabel->setText("N/A"); - else - { - auto rho = ui_.DensityUnitsCombo->currentIndex() == 0 ? cfg->atomicDensity() : cfg->chemicalDensity(); - ui_.DensityUnitsLabel->setText(rho ? QString::number(*rho) : "--"); - } -} - -void ImportCIFDialog::on_InputFileEdit_editingFinished() -{ - // Load the CIF file - if (!cifContext_.read(ui_.InputFileEdit->text().toStdString())) - Messenger::error("Failed to load CIF file '{}'.\n", ui_.InputFileEdit->text().toStdString()); - else - { - cifContext_.generate(); - updateWidgets(); - } -} - -void ImportCIFDialog::on_InputFileSelectButton_clicked(bool checked) -{ - QString inputFile = QFileDialog::getOpenFileName(this, "Choose CIF file to open", QDir().absolutePath(), - "CIF files (*.cif);;All files (*)"); - if (inputFile.isEmpty()) - return; - - // Set input file in edit - ui_.InputFileEdit->setText(inputFile); - on_InputFileEdit_editingFinished(); -} - -void ImportCIFDialog::on_SpaceGroupsCombo_currentIndexChanged(int index) -{ - if (widgetsUpdating_) - return; - - cifContext_.setSpaceGroup((SpaceGroups::SpaceGroupId)(ui_.SpaceGroupsCombo->currentIndex() + 1)); - - updateWidgets(); -} - -void ImportCIFDialog::on_NormalOverlapToleranceRadio_clicked(bool checked) -{ - if (checked) - { - cifContext_.setOverlapTolerance(0.1); - updateWidgets(); - } -} - -void ImportCIFDialog::on_LooseOverlapToleranceRadio_clicked(bool checked) -{ - if (checked) - { - cifContext_.setOverlapTolerance(0.5); - updateWidgets(); - } -} - -void ImportCIFDialog::on_CalculateBondingRadio_clicked(bool checked) -{ - if (checked) - { - cifContext_.setUseCIFBondingDefinitions(false); - updateWidgets(); - } -} - -void ImportCIFDialog::on_BondFromCIFRadio_clicked(bool checked) -{ - if (checked) - { - cifContext_.setUseCIFBondingDefinitions(true); - updateWidgets(); - } -} - -void ImportCIFDialog::on_BondingPreventMetallicCheck_clicked(bool checked) -{ - cifContext_.setPreventMetallicBonds(checked); - - updateWidgets(); -} - -// Create / check NETA definition for moiety removal -bool ImportCIFDialog::createMoietyRemovalNETA(std::string definition) -{ - auto result = moietyNETA_.create(definition); - - ui_.MoietyNETARemovalIndicator->setOK(result); - - return result; -} - -void ImportCIFDialog::on_MoietyRemoveAtomicsCheck_clicked(bool checked) -{ - cifContext_.setRemoveAtomics(checked); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyRemoveWaterCheck_clicked(bool checked) -{ - cifContext_.setRemoveWaterAndCoordinateOxygens(checked); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyRemoveByNETACheck_clicked(bool checked) -{ - // Set state of associated controls - ui_.MoietyNETARemovalEdit->setEnabled(checked); - ui_.MoietyNETARemoveFragmentsCheck->setEnabled(checked); - - if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) - return; - - cifContext_.setRemoveNETA(checked, ui_.MoietyNETARemoveFragmentsCheck->isChecked()); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyNETARemovalEdit_textEdited(const QString &text) -{ - if (!createMoietyRemovalNETA(ui_.MoietyNETARemovalEdit->text().toStdString())) - return; - - cifContext_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), ui_.MoietyNETARemoveFragmentsCheck->isChecked()); - cifContext_.setMoietyRemovalNETA(moietyNETA_.definitionString()); - updateWidgets(); -} - -void ImportCIFDialog::on_MoietyNETARemoveFragmentsCheck_clicked(bool checked) -{ - if (ui_.MoietyNETARemovalIndicator->state() != CheckIndicator::OKState) - return; - - cifContext_.setRemoveNETA(ui_.MoietyRemoveByNETACheck->isChecked(), checked); - updateWidgets(); -} - -void ImportCIFDialog::assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &) -{ - cifContext_.generate(); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatASpin_valueChanged(int value) -{ - cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatBSpin_valueChanged(int value) -{ - cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_RepeatCSpin_valueChanged(int value) -{ - - cifContext_.setSupercellRepeat({ui_.RepeatASpin->value(), ui_.RepeatBSpin->value(), ui_.RepeatCSpin->value()}); - updateWidgets(); -} - -void ImportCIFDialog::on_DensityUnitsCombo_currentIndexChanged(int index) -{ - if (widgetsUpdating_) - return; - - updateDensityLabel(); -} - -void ImportCIFDialog::on_OutputMolecularRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OutputFrameworkRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OutputSupermoleculeRadio_clicked(bool checked) {} - -void ImportCIFDialog::on_OKButton_clicked(bool checked) -{ - Flags outputFlags; - if (ui_.OutputMolecularRadio->isChecked()) - outputFlags.setFlag(CIFContext::OutputFlags::OutputMolecularSpecies); - else if (ui_.OutputFrameworkRadio->isChecked()) - outputFlags.setFlag(CIFContext::OutputFlags::OutputFramework); - else if (ui_.OutputSupermoleculeRadio->isChecked()) - outputFlags.setFlag(CIFContext::OutputFlags::OutputSupermolecule); - - // Output a configuration as well as the species for certain options - if (outputFlags.isSet(CIFContext::OutputFlags::OutputMolecularSpecies) || - outputFlags.isSet(CIFContext::OutputFlags::OutputFramework)) - { - outputFlags.setFlag(CIFContext::OutputFlags::OutputConfiguration); - } - - cifContext_.finalise(dissolve_.coreData(), outputFlags); - - accept(); -} - -void ImportCIFDialog::on_CancelButton_clicked(bool checked) { reject(); } diff --git a/src/gui/importCIFDialog.h b/src/gui/importCIFDialog.h deleted file mode 100644 index 09542002f3..0000000000 --- a/src/gui/importCIFDialog.h +++ /dev/null @@ -1,94 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "base/lock.h" -#include "gui/models/cifAssemblyModel.h" -#include "gui/ui_importCIFDialog.h" -#include "gui/wizard.h" -#include "main/dissolve.h" -#include "nodes/cif/io/cifContext.h" -#include - -// Forward Declarations -class Dissolve; -class Species; - -// Import CIF Dialog -class ImportCIFDialog : public QDialog -{ - Q_OBJECT - - public: - ImportCIFDialog(QWidget *parent, Dissolve &dissolve); - ~ImportCIFDialog() = default; - - private: - // Main form declaration - Ui::ImportCIFDialog ui_; - // Model for CIF assemblies - CIFAssemblyModel cifAssemblyModel_; - // Temporary core data - CoreData temporaryCoreData_; - - /* - * Data - */ - private: - // Main Dissolve object - Dissolve &dissolve_; - // CIF Handler - CIFContext cifContext_; - // NETA for moiety removal - NETADefinition moietyNETA_; - - private: - // Create / check NETA definition for moiety removal - bool createMoietyRemovalNETA(std::string definition); - - /* - * UI - */ - private: - // Widget update lock - Lock widgetsUpdating_; - // Update all controls - void updateWidgets(); - // Update density label - void updateDensityLabel(); - - private Q_SLOTS: - // CIF File / Information - void on_InputFileEdit_editingFinished(); - void on_InputFileSelectButton_clicked(bool checked); - void on_SpaceGroupsCombo_currentIndexChanged(int index); - // Overlap - void on_NormalOverlapToleranceRadio_clicked(bool checked); - void on_LooseOverlapToleranceRadio_clicked(bool checked); - // Bonding - void on_CalculateBondingRadio_clicked(bool checked); - void on_BondingPreventMetallicCheck_clicked(bool checked); - void on_BondFromCIFRadio_clicked(bool checked); - // CleanUp - void on_MoietyRemoveAtomicsCheck_clicked(bool checked); - void on_MoietyRemoveWaterCheck_clicked(bool checked); - void on_MoietyRemoveByNETACheck_clicked(bool checked); - void on_MoietyNETARemovalEdit_textEdited(const QString &text); - void on_MoietyNETARemoveFragmentsCheck_clicked(bool checked); - // Assemblies - void assembliesChanged(const QModelIndex &, const QModelIndex &, const QList &); - // Supercell - void on_RepeatASpin_valueChanged(int value); - void on_RepeatBSpin_valueChanged(int value); - void on_RepeatCSpin_valueChanged(int value); - // Preview - void on_DensityUnitsCombo_currentIndexChanged(int index); - // Output - void on_OutputMolecularRadio_clicked(bool checked); - void on_OutputFrameworkRadio_clicked(bool checked); - void on_OutputSupermoleculeRadio_clicked(bool checked); - // Dialog - void on_OKButton_clicked(bool checked); - void on_CancelButton_clicked(bool checked); -}; diff --git a/src/gui/importCIFDialog.ui b/src/gui/importCIFDialog.ui deleted file mode 100644 index c85e18bbff..0000000000 --- a/src/gui/importCIFDialog.ui +++ /dev/null @@ -1,1375 +0,0 @@ - - - ImportCIFDialog - - - Qt::ApplicationModal - - - - 0 - 0 - 849 - 982 - - - - - 10 - - - - Import From CIF File - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - - 0 - 0 - - - - - 4 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Source CIF - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - - - - - - - :/general/icons/open.svg:/general/icons/open.svg - - - - - - - - - - Generation Control - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 0 - - - - - 0 - 0 - 292 - 639 - - - - - :/general/icons/data.svg:/general/icons/data.svg - - - CIF Data - - - - - - ID - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Spacegroup - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 0 - 0 - - - - - - - - - - - Chemical Formula - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Publication - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Authors - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - QAbstractItemView::NoEditTriggers - - - - - - - - - - Reference - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 2 - 0 - - - - ??? - - - true - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - 0 - 0 - 296 - 625 - - - - - :/general/icons/delete.svg:/general/icons/delete.svg - - - Structure Cleanup - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Tolerance distance at which atoms are considered to be overlapping and be removed - - - Overlap Removal Distance - - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Normal (0.1 Å) - - - true - - - - - - - Loose (0.5 Å) - - - - - - - - - - Moiety Removal - - - - - - Remove any lone (i.e. unbound) atoms - - - Remove unbound atoms - - - - - - - Remove any water molecules or coordinated oxygens without hydrogens - - - Remove water and coordinated oxygens - - - - - - - Remove atoms or fragments according to a NETA description - - - Remove by NETA - - - - - - - - - Qt::Horizontal - - - QSizePolicy::Fixed - - - - 20 - 20 - - - - - - - - 4 - - - - - - - false - - - NETA definition matching specific atoms whose encompassing moiety should be removed - - - ?O,nbonds=2,nh=2 - - - - - - - - 0 - 0 - - - - - 16 - 16 - - - - - - - true - - - - - - - - - false - - - If selected, fragments containing the matched atoms will be removed - - - Expand to bound fragments - - - - - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - - 0 - 0 - 276 - 93 - - - - - :/general/icons/calculateBonds.svg:/general/icons/calculateBonds.svg - - - Bonding - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Determine chemical bonds using overlap of defined elemental radii - - - Calculate - - - true - - - - - - - Use CIF definitions (from _geom_bond_*) - - - - - - - Qt::Horizontal - - - - - - - - 0 - 0 - - - - Don't add bonds between metallic elements - - - Prevent metallic bonds - - - true - - - - - - - Qt::Vertical - - - - 20 - 315 - - - - - - - - - - 0 - 0 - 96 - 78 - - - - - :/general/icons/selectedAtoms.svg:/general/icons/selectedAtoms.svg - - - Assemblies - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - Any defined disorder assemblies and groups will be listed here, including a Global assembly containing other (well-defined) atoms in the structure. - - - - - - - - - 0 - 0 - 96 - 78 - - - - - :/general/icons/threeSpecies.svg:/general/icons/threeSpecies.svg - - - Detected Species - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - - - - - 0 - 0 - 167 - 142 - - - - - :/general/icons/configuration.svg:/general/icons/configuration.svg - - - Supercell - - - - Qt::AlignRight|Qt::AlignTop|Qt::AlignTrailing - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - - 0 - 0 - - - - A - - - - - - - true - - - 1 - - - 10000 - - - - - - - - 0 - 0 - - - - B - - - - - - - 1 - - - 10000 - - - - - - - - 0 - 0 - - - - C - - - - - - - 1 - - - 10000 - - - - - - - - - - - - - - - - - - 1 - 0 - - - - - - - Preview - - - - 4 - - - 4 - - - 4 - - - 4 - - - 4 - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/configuration.svg:/general/icons/configuration.svg - - - true - - - - - - - - 0 - 0 - - - - - 10 - false - - - - Orthorhombic - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/density.svg:/general/icons/density.svg - - - - 14 - 14 - - - - true - - - - - - - - 0 - 0 - - - - - 10 - false - - - - 0.0 - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter - - - - - - - - - - - - - Number of molecules in the configuration - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/species.svg:/general/icons/species.svg - - - true - - - - - - - - 0 - 0 - - - - 0 - - - - - - - - - - Number of atoms in the configuration - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 4 - - - 2 - - - 2 - - - 2 - - - 2 - - - - - false - - - ... - - - - :/general/icons/spheres_on.svg:/general/icons/spheres_on.svg - - - true - - - - - - - - 0 - 0 - - - - 0 - - - - - - - - - - - - - 3 - 0 - - - - - 300 - 300 - - - - QFrame::StyledPanel - - - QFrame::Sunken - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - - 1 - 0 - - - - - - - - - - - - - - Output - - - - - - Create a single non-periodic species. Useful for generating "chunks" of crystal material. - - - Supermolecule - - - false - - - - - - - Create a single species with a periodic box and all atoms in the unit cell. Suitable for framework-style models. - - - Periodic Framework - - - true - - - - - - - Output a configuration containing individual molecules based on detected species - - - Molecular Species - - - - - - - - - - - - - - - Qt::Horizontal - - - - - - - 4 - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - - - - - 10 - true - - - - Cancel - - - - - - - - 10 - true - - - - OK - - - - - - - - - - ConfigurationViewerWidget - QWidget -
gui/configurationViewerWidget.h
- 1 - - - CheckIndicator - QLabel -
gui/widgets/checkIndicator.h
- - - - - - - diff --git a/src/gui/menu_species.cpp b/src/gui/menu_species.cpp index 3e6caa00d8..f7a66a853e 100644 --- a/src/gui/menu_species.cpp +++ b/src/gui/menu_species.cpp @@ -94,6 +94,7 @@ void DissolveWindow::on_SpeciesCreateFromExistingAction_triggered(bool checked) dissolve_.coreData().removeSpecies(newSpecies); } +/* DISSOLVE 2 TODO void DissolveWindow::on_SpeciesCreateGrapheneAction_triggered(bool checked) { CreateGrapheneSpeciesDialog createGrapheneSpeciesDialog(this, dissolve_); @@ -107,7 +108,7 @@ void DissolveWindow::on_SpeciesCreateGrapheneAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(dissolve_.coreData().species().back().get()); } } - +*/ void DissolveWindow::on_SpeciesImportFromDissolveAction_triggered(bool checked) { ImportSpeciesDialog importSpeciesDialog(this, dissolve_); @@ -172,7 +173,7 @@ void DissolveWindow::on_SpeciesImportLigParGenAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(dissolve_.coreData().species().back().get()); } } - +/* DISSOLVE 2 TODO void DissolveWindow::on_SpeciesImportFromCIFAction_triggered(bool checked) { ImportCIFDialog importCIFDialog(this, dissolve_); @@ -189,7 +190,7 @@ void DissolveWindow::on_SpeciesImportFromCIFAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(sp); } } - +*/ void DissolveWindow::on_SpeciesRenameAction_triggered(bool checked) { // Get the current tab - make sure it is a SpeciesTab, then call its rename() function diff --git a/src/gui/models/CMakeLists.txt b/src/gui/models/CMakeLists.txt index b17a107cf1..fd47cd0e0c 100644 --- a/src/gui/models/CMakeLists.txt +++ b/src/gui/models/CMakeLists.txt @@ -6,7 +6,6 @@ set(models_MOC_HDRS atomTypeModel.h braggReflectionFilterProxy.h braggReflectionModel.h - cifAssemblyModel.h configurationModel.h dataManagerSimulationModel.h dissolveModel.h @@ -63,7 +62,6 @@ set(models_SRCS atomTypeModel.cpp braggReflectionFilterProxy.cpp braggReflectionModel.cpp - cifAssemblyModel.cpp configurationModel.cpp dataManagerSimulationModel.cpp dissolveModel.cpp diff --git a/src/gui/models/cifAssemblyModel.cpp b/src/gui/models/cifAssemblyModel.cpp deleted file mode 100644 index faef2809d7..0000000000 --- a/src/gui/models/cifAssemblyModel.cpp +++ /dev/null @@ -1,149 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "gui/models/cifAssemblyModel.h" -#include "classes/empiricalFormula.h" - -CIFAssemblyModel::CIFAssemblyModel(std::vector &assemblies) : assemblies_(assemblies) {} - -int CIFAssemblyModel::rowCount(const QModelIndex &parent) const -{ - if (!parent.isValid()) - return assemblies_.size(); - return assemblies_[parent.row()].nGroups(); -} - -int CIFAssemblyModel::columnCount(const QModelIndex &parent) const { return 3; } - -QModelIndex CIFAssemblyModel::parent(const QModelIndex &index) const -{ - quintptr root = 0; - if (index.internalId() == 0) - return QModelIndex(); - return createIndex(index.internalId() - 1, 0, root); -} - -bool CIFAssemblyModel::hasChildren(const QModelIndex &parent) const { return !parent.internalId(); } - -QVariant CIFAssemblyModel::data(const QModelIndex &index, int role) const -{ - if (role != Qt::DisplayRole && role != Qt::UserRole && role != Qt::EditRole && role != Qt::CheckStateRole) - return QVariant(); - - // Assembly (root item) - if (!index.parent().isValid()) - { - if (index.row() > assemblies_.size()) - return QVariant(); - if (index.column() > 0) - return QVariant(); - auto &a = assemblies_[index.row()]; - switch (role) - { - case Qt::DisplayRole: - case Qt::EditRole: - return QString::fromStdString(std::string(a.name())); - case Qt::UserRole: - return QVariant::fromValue(a); - default: - return QVariant(); - } - } - - // Group (column 1) - auto &assembly = assemblies_[index.parent().row()]; - auto &groups = assembly.groups(); - if (index.row() > groups.size()) - return QVariant(); - if (index.column() > 2) - return QVariant(); - auto &g = groups[index.row()]; - switch (role) - { - case Qt::DisplayRole: - case Qt::EditRole: - switch (index.column()) - { - case 1: - return QString::fromStdString(std::string(g.name())); - case 2: - return QString::fromStdString(EmpiricalFormula::formula(g.atoms(), [](const auto &i) { return i.Z(); })); - default: - return QVariant(); - } - case Qt::CheckStateRole: - if (index.column() == 1) - return g.active() ? Qt::Checked : Qt::Unchecked; - else - return QVariant(); - case Qt::UserRole: - switch (index.column()) - { - case 1: - return QVariant::fromValue(g); - default: - return QVariant(); - } - default: - return QVariant(); - } -} - -QModelIndex CIFAssemblyModel::index(int row, int column, const QModelIndex &parent) const -{ - quintptr child; - if (!parent.isValid()) - child = 0; - else if (parent.internalId() == 0) - child = parent.row() + 1; - else - return QModelIndex(); - - return createIndex(row, column, child); -} - -QVariant CIFAssemblyModel::headerData(int section, Qt::Orientation orientation, int role) const -{ - if (role != Qt::DisplayRole) - return QVariant(); - switch (section) - { - case 0: - return "Assembly"; - case 1: - return "Group"; - case 2: - return "Chemical Formula"; - default: - return QVariant(); - } -} - -Qt::ItemFlags CIFAssemblyModel::flags(const QModelIndex &index) const -{ - // Assembly (root item) - if (!index.parent().isValid()) - return Qt::ItemIsSelectable | Qt::ItemIsEnabled; - else if (index.column() == 1) - return Qt::ItemIsSelectable | Qt::ItemIsEnabled | Qt::ItemIsUserCheckable; - - return Qt::ItemIsSelectable | Qt::ItemIsEnabled; -} - -bool CIFAssemblyModel::setData(const QModelIndex &index, const QVariant &value, int role) -{ - // Only editable data is the check state of groups (column 1) - if (!index.parent().isValid() || index.column() != 1 || role != Qt::CheckStateRole) - return false; - - // Get assembly and check for number of groups > 1 - auto &assembly = assemblies_[index.parent().row()]; - - // Get group being modified and set the active flag - auto &group = assembly.groups()[index.row()]; - group.setActive(value.value() == Qt::Checked); - - Q_EMIT(dataChanged(index, index)); - - return true; -} diff --git a/src/gui/models/cifAssemblyModel.h b/src/gui/models/cifAssemblyModel.h deleted file mode 100644 index 7ded24966d..0000000000 --- a/src/gui/models/cifAssemblyModel.h +++ /dev/null @@ -1,36 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "nodes/cif/io/cifContext.h" -#include -#include - -class CIFAssemblyModel : public QAbstractItemModel -{ - Q_OBJECT - private: - std::vector &assemblies_; - - public: - CIFAssemblyModel(std::vector &assemblies); - - QModelIndex parent(const QModelIndex &index) const override; - - QModelIndex index(int row, int column, const QModelIndex &parent = QModelIndex()) const override; - - bool hasChildren(const QModelIndex &parent) const override; - - int rowCount(const QModelIndex &parent = QModelIndex()) const override; - - int columnCount(const QModelIndex &parent = QModelIndex()) const override; - - QVariant data(const QModelIndex &index, int role = Qt::DisplayRole) const override; - - QVariant headerData(int section, Qt::Orientation orientation, int role = Qt::DisplayRole) const override; - - Qt::ItemFlags flags(const QModelIndex &index) const override; - - bool setData(const QModelIndex &index, const QVariant &value, int role = Qt::EditRole) override; -}; diff --git a/src/nodes/cif/io/cifContext.cpp b/src/nodes/cif/io/cifContext.cpp deleted file mode 100644 index c5eb9cac68..0000000000 --- a/src/nodes/cif/io/cifContext.cpp +++ /dev/null @@ -1,1363 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "nodes/cif/io/cifContext.h" -#include "CIFImportLexer.h" -#include "CIFImportParser.h" -#include "base/messenger.h" -#include "base/sysFunc.h" -#include "classes/coreData.h" -#include "classes/empiricalFormula.h" -#include "classes/species.h" -#include "generator/add.h" -#include "generator/box.h" -#include "generator/coordinateSets.h" -#include "neta/neta.h" -#include "nodes/cif/io/CIFImportErrorListeners.h" -#include "nodes/cif/io/CIFImportVisitor.h" -#include "templates/algorithms.h" - -CIFContext::CIFContext() -{ - unitCellConfiguration_.setName("Structural"); - unitCellSpecies_.setName("Crystal"); - cleanedUnitCellConfiguration_.setName("Cleaned"); - cleanedUnitCellSpecies_.setName("Crystal (Cleaned)"); - supercellConfiguration_.setName("Supercell"); - supercellSpecies_.setName("Crystal (Supercell)"); -} - -/* - * Raw Data - */ - -// Parse supplied file into the destination objects -bool CIFContext::parse(std::string_view filename, CIFContext::CIFTags &tags) const -{ - // Set up ANTLR input stream - std::ifstream cifFile(std::string(filename), std::ios::in | std::ios::binary); - if (!cifFile.is_open()) - return Messenger::error("Failed to open CIF file '{}.\n", filename); - - antlr4::ANTLRInputStream input(cifFile); - - // Create ANTLR lexer and set-up error listener - CIFImportLexer lexer(&input); - CIFImportLexerErrorListener lexerErrorListener; - lexer.removeErrorListeners(); - lexer.addErrorListener(&lexerErrorListener); - - // Generate tokens from input stream - antlr4::CommonTokenStream tokens(&lexer); - - // Create ANTLR parser and set-up error listeners - CIFImportParser parser(&tokens); - CIFImportParserErrorListener parserErrorListener; - parser.removeErrorListeners(); - parser.removeParseListeners(); - parser.addErrorListener(&lexerErrorListener); - parser.addErrorListener(&parserErrorListener); - - // Generate the AST - CIFImportParser::CifContext *tree = nullptr; - try - { - tree = parser.cif(); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - Messenger::error("{}", ex.what()); - return false; - } - - // Visit the nodes in the AST - CIFImportVisitor visitor(tags); - try - { - visitor.extract(tree); - } - catch (CIFImportExceptions::CIFImportSyntaxException &ex) - { - return Messenger::error("{}", ex.what()); - } - - return true; -} - -// Return whether the specified file parses correctly -bool CIFContext::validFile(std::string_view filename) const -{ - CIFTags tags; - return parse(filename, tags); -} - -// Read CIF data from specified file -bool CIFContext::read(std::string_view filename) -{ - assemblies_.clear(); - bondingPairs_.clear(); - tags_.clear(); - - if (!parse(filename, tags_)) - return Messenger::error("Failed to parse CIF file '{}'.\n", filename); - - /* - * Determine space group - the search order for tags is: - * - * 1. Hall symbol - * 2. Hermann-Mauginn name - * 3. Space group index - * - * In the case of 2 or 3 we also try to search for the origin choice. - * - * If a space group has already been set, don't try to overwrite it (it was probably forcibly set because the detection - * below fails). - */ - - // Check for Hall symbol - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_space_group_name_Hall")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_Hall")) - spaceGroup_ = SpaceGroups::findByHallSymbol(*getTagString("_symmetry_space_group_name_Hall")); - - if (spaceGroup_ == SpaceGroups::NoSpaceGroup) - { - // Might need the coordinate system code... - auto sgCode = getTagString("_space_group.IT_coordinate_system_code"); - - // Find a HM name - if (hasTag("_space_group_name_H-M_alt")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_space_group_name_H-M_alt"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_space_group_name_H-M")) - spaceGroup_ = - SpaceGroups::findByHermannMauginnSymbol(*getTagString("_symmetry_space_group_name_H-M"), sgCode.value_or("")); - - // Find a space group index? - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group_IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group_IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_space_group.IT_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_space_group.IT_number"), sgCode.value_or("")); - if (spaceGroup_ == SpaceGroups::NoSpaceGroup && hasTag("_symmetry_Int_Tables_number")) - spaceGroup_ = - SpaceGroups::findByInternationalTablesIndex(*getTagInt("_symmetry_Int_Tables_number"), sgCode.value_or("")); - } - - // Create symmetry-unique atoms list - auto atomSiteLabel = getTagStrings("_atom_site_label"); - auto atomSiteTypeSymbol = getTagStrings("_atom_site_type_symbol"); - auto atomSiteFractX = getTagDoubles("_atom_site_fract_x"); - auto atomSiteFractY = getTagDoubles("_atom_site_fract_y"); - auto atomSiteFractZ = getTagDoubles("_atom_site_fract_z"); - auto atomSiteOccupancy = getTagDoubles("_atom_site_occupancy"); - auto atomDisorderAssembly = getTagStrings("_atom_site_disorder_assembly"); - auto atomDisorderGroup = getTagStrings("_atom_site_disorder_group"); - if (atomSiteLabel.empty() && atomSiteTypeSymbol.empty()) - return Messenger::error( - "No suitable atom site names found (no '_atom_site_label' or '_atom_site_type_symbol' tags present in CIF).\n"); - if (atomSiteFractX.empty() || atomSiteFractY.empty() || atomSiteFractZ.empty()) - return Messenger::error("Atom site fractional positions are incomplete (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - if (!((atomSiteFractX.size() == atomSiteFractY.size()) && (atomSiteFractX.size() == atomSiteFractZ.size()))) - return Messenger::error("Atom site fractional positions have mismatched sizes (vector sizes are {}, {}, and {}).\n", - atomSiteFractX.size(), atomSiteFractY.size(), atomSiteFractZ.size()); - for (auto n = 0; n < atomSiteFractX.size(); ++n) - { - // Get standard information - auto label = n < atomSiteLabel.size() ? atomSiteLabel[n] : std::format("{}{}", atomSiteTypeSymbol[n], n); - auto Z = n < atomSiteTypeSymbol.size() - ? Elements::element(atomSiteTypeSymbol[n]) - : (n < atomSiteLabel.size() ? Elements::element(atomSiteLabel[n]) : Elements::Unknown); - auto occ = n < atomSiteOccupancy.size() ? atomSiteOccupancy[n] : 1.0; - Vector3 rFrac(atomSiteFractX[n], atomSiteFractY[n], atomSiteFractZ[n]); - - // Add the atom to an assembly - there are three possibilities regarding (disorder) grouping: - // 1) A group is defined, but no assembly - add the atom to the 'Disorder' assembly - // 2) An assembly and a group are defined - add it to that - // 3) No group or assembly are defined - add the atom to the 'Global' assembly under a 'Default' group - auto assemblyName = atomDisorderAssembly.empty() ? "." : atomDisorderAssembly[n]; - auto groupName = atomDisorderGroup.empty() ? "." : atomDisorderGroup[n]; - if (assemblyName == "." && groupName != ".") - assemblyName = "Disorder"; - else if (assemblyName == "." && groupName == ".") - assemblyName = "Global"; - - if (groupName == ".") - groupName = "Default"; - - // Get the assembly and group that we're adding the atom to - auto &assembly = getAssembly(assemblyName); - auto &group = assembly.getGroup(groupName); - group.setActive(groupName == "Default" || groupName == "1"); - group.addAtom({label, Z, rFrac, occ}); - } - - // Construct bonding pairs list - auto bondLabelsI = getTagStrings("_geom_bond_atom_site_label_1"); - auto bondLabelsJ = getTagStrings("_geom_bond_atom_site_label_2"); - auto bondDistances = getTagDoubles("_geom_bond_distance"); - if (bondLabelsI.size() == bondLabelsJ.size() && (bondLabelsI.size() == bondDistances.size())) - { - for (auto &&[i, j, r] : zip(bondLabelsI, bondLabelsJ, bondDistances)) - bondingPairs_.emplace_back(i, j, r); - } - else - Messenger::warn("Bonding pairs array sizes are mismatched, so no bonding information will be available."); - - return true; -} - -// Return if the specified tag exists -bool CIFContext::hasTag(std::string tag) const { return tags_.find(tag) != tags_.end(); } - -// Return tag data string (if it exists) assuming a single datum (first in the vector) -std::optional CIFContext::getTagString(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - return it->second.front(); -} - -// Return tag data strings (if it exists) -std::vector CIFContext::getTagStrings(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - return it->second; -} - -// Return tag data as double (if it exists) assuming a single datum (first in the vector) -std::optional CIFContext::getTagDouble(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - double result; - try - { - result = std::stod(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -// Return tag data doubles (if it exists) -std::vector CIFContext::getTagDoubles(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return {}; - - std::vector v; - for (const auto &s : it->second) - { - auto d = 0.0; - try - { - d = std::stod(s); - } - catch (...) - { - Messenger::warn("Data tag '{}' contains a value that can't be converted to a double ('{}').\n", tag, s); - } - v.push_back(d); - } - - return v; -} - -// Return tag data as integer (if it exists) assuming a single datum (first in the vector) -std::optional CIFContext::getTagInt(std::string tag) const -{ - auto it = tags_.find(tag); - if (it == tags_.end()) - return std::nullopt; - - // Check data vector size - if (it->second.size() != 1) - Messenger::warn("Returning first datum for tag '{}', but {} are available.\n", tag, it->second.size()); - - int result; - try - { - result = std::stoi(it->second.front()); - } - catch (...) - { - Messenger::error("Data tag '{}' contains a value that can't be converted to an integer ('{}').\n", tag, - it->second.front()); - return std::nullopt; - } - - return result; -} - -/* - * Processed Data - */ - -// Set space group from index -void CIFContext::setSpaceGroup(SpaceGroups::SpaceGroupId sgid) -{ - if (spaceGroup_ == sgid) - return; - - spaceGroup_ = sgid; - generate(); -} - -// Return space group information -SpaceGroups::SpaceGroupId CIFContext::spaceGroup() const { return spaceGroup_; } - -// Return cell lengths -std::optional CIFContext::getCellLengths() const -{ - auto a = getTagDouble("_cell_length_a"); - if (!a) - Messenger::error("Cell length A not defined in CIF.\n"); - auto b = getTagDouble("_cell_length_b"); - if (!b) - Messenger::error("Cell length B not defined in CIF.\n"); - auto c = getTagDouble("_cell_length_c"); - if (!c) - Messenger::error("Cell length C not defined in CIF.\n"); - - if (a && b && c) - return Vector3(a.value(), b.value(), c.value()); - else - return std::nullopt; -} - -// Return cell angles -std::optional CIFContext::getCellAngles() const -{ - auto alpha = getTagDouble("_cell_angle_alpha"); - if (!alpha) - Messenger::error("Cell angle alpha not defined in CIF.\n"); - auto beta = getTagDouble("_cell_angle_beta"); - if (!beta) - Messenger::error("Cell angle beta not defined in CIF.\n"); - auto gamma = getTagDouble("_cell_angle_gamma"); - if (!gamma) - Messenger::error("Cell angle gamma not defined in CIF.\n"); - - if (alpha && beta && gamma) - return Vector3(alpha.value(), beta.value(), gamma.value()); - else - return std::nullopt; -} - -// Return chemical formula -std::string CIFContext::chemicalFormula() const -{ - auto it = tags_.find("_chemical_formula_sum"); - return (it != tags_.end() ? it->second.front() : "Unknown"); -} - -// Get (add or retrieve) named assembly -CIFAssembly &CIFContext::getAssembly(std::string_view name) -{ - auto it = std::find_if(assemblies_.begin(), assemblies_.end(), [name](const auto &a) { return a.name() == name; }); - if (it != assemblies_.end()) - return *it; - - return assemblies_.emplace_back(name); -} - -// Return atom assemblies -std::vector &CIFContext::assemblies() { return assemblies_; } - -const std::vector &CIFContext::assemblies() const { return assemblies_; } - -// Return whether any bond distances are defined -bool CIFContext::hasBondDistances() const { return !bondingPairs_.empty(); } - -// Return whether a bond distance is defined for the specified label pair -std::optional CIFContext::bondDistance(std::string_view labelI, std::string_view labelJ) const -{ - auto it = std::find_if( - bondingPairs_.begin(), bondingPairs_.end(), [labelI, labelJ](const auto &bp) - { return (bp.labelI() == labelI && bp.labelJ() == labelJ) || (bp.labelI() == labelJ && bp.labelJ() == labelI); }); - if (it != bondingPairs_.end()) - return it->r(); - return std::nullopt; -} - -/* - * Creation - */ - -// Create basic unit cell -bool CIFContext::createBasicUnitCell() -{ - unitCellConfiguration_.empty(); - unitCellSpecies_.clear(); - atomLabelTypes_.clear(); - - // Create temporary atom types corresponding to the unique atom labels - for (auto &a : assemblies_) - { - for (auto &g : a.groups()) - { - if (!g.active()) - continue; - - for (auto &i : g.atoms()) - { - if (std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [i](const auto &at) { return i.label() == at->name(); }) == atomLabelTypes_.end()) - { - atomLabelTypes_.emplace_back(std::make_shared(i.Z(), i.label())); - } - } - } - } - - // Configure the unit cell "species" - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - unitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - auto *box = unitCellSpecies_.box(); - - // Configuration - Messenger::setQuiet(true); - unitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - // -- Generate atoms - auto symmetryGenerators = SpaceGroups::symmetryOperators(spaceGroup_); - for (const auto &generator : symmetryGenerators) - for (auto &a : assemblies_) - for (auto &g : a.groups()) - if (g.active()) - for (auto &unique : g.atoms()) - { - // Generate folded atomic position in real space - auto r = generator * unique.rFrac(); - box->toReal(r); - r = box->fold(r); - - // If this atom overlaps with another in the box, don't add it as it's a symmetry-related copy - if (std::any_of(unitCellSpecies_.atoms().begin(), unitCellSpecies_.atoms().end(), - [&, r, box](const auto &j) - { return box->minimumDistance(r, j.r()) < overlapTolerance_; })) - continue; - - // Create the new atom - auto atIt = std::find_if(atomLabelTypes_.begin(), atomLabelTypes_.end(), - [&unique](const auto at) { return unique.label() == at->name(); }); - unitCellSpecies_.addAtom(unique.Z(), r, 0.0, atIt != atomLabelTypes_.end() ? atIt->get() : nullptr); - } - - // Check that we actually generated some atoms... - if (unitCellSpecies_.nAtoms() == 0) - return false; - - // Bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&unitCellSpecies_, preventMetallicBonds_); - else - unitCellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - unitCellConfiguration_.addMolecule(&unitCellSpecies_); - unitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created basic crystal unit cell - {} non-overlapping atoms.\n", unitCellSpecies_.nAtoms()); - - createStructure(); - - return true; -} - -// Create structure from basic unit cell atoms and connectivity -bool CIFContext::createStructure() -{ - // Create box for structure - auto box = unitCellConfiguration_.box(); - structure_.createBox(box->axisLengths(), box->axisAngles(), box->type() == Box::BoxType::NonPeriodic); - - // Add structural atoms - std::map structureAtomLookUp; - const auto &atoms = unitCellSpecies_.atoms(); - for (const auto &atom : atoms) - structureAtomLookUp.insert_or_assign(&atom, structure_.addAtom(atom.Z(), atom.r(), atom.q())); - - // Iterate over newly added structure atom pairs, adding any existing bonds between them if not already present - for (const auto &atom : atoms) - for (const auto &bond : atom.bonds()) - { - auto i = structureAtomLookUp[bond.get().i()]; - auto j = structureAtomLookUp[bond.get().j()]; - if (!structure_.hasBond(i, j)) - structure_.addBond(i, j); - } - - Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", - structure_.nAtoms(), structure_.bonds().size()); - - return true; -} - -// Create the cleaned unit cell -bool CIFContext::createCleanedUnitCell() -{ - cleanedUnitCellConfiguration_.empty(); - cleanedUnitCellSpecies_.clear(); - - // Configure the species - cleanedUnitCellSpecies_.copyBasic(&unitCellSpecies_, true); - auto cellLengths = getCellLengths(); - if (!cellLengths) - return false; - auto cellAngles = getCellAngles(); - if (!cellAngles) - return false; - cleanedUnitCellSpecies_.createBox(cellLengths.value(), cellAngles.value()); - - // Configuration - Messenger::setQuiet(true); - cleanedUnitCellConfiguration_.createBoxAndCells(cellLengths.value(), cellAngles.value(), false); - Messenger::setQuiet(false); - - if (removeAtomics_) - { - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (i.nBonds() == 0) - indicesToRemove.push_back(i.index()); - Messenger::print("Atomic removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeWaterAndCoordinateOxygens_) - { - NETADefinition waterVacuum("?O,nbonds=1,nh<=1|?O,nbonds>=2,-H(nbonds=1,-O)"); - if (!waterVacuum.isValid()) - { - Messenger::error("NETA definition for water removal is invalid.\n"); - return false; - } - - std::vector indicesToRemove; - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - if (waterVacuum.matches(&i)) - indicesToRemove.push_back(i.index()); - Messenger::print("Water removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - if (removeNETA_ && moietyRemovalNETA_.isValid()) - { - // Select all atoms that are in moieties where one of its atoms matches our NETA definition - std::vector indicesToRemove; - for (auto &i : cleanedUnitCellSpecies_.atoms()) - if (moietyRemovalNETA_.matches(&i)) - { - // Select all atoms that are part of the same moiety? - if (removeNETAByFragment_) - { - cleanedUnitCellSpecies_.clearAtomSelection(); - auto selection = cleanedUnitCellSpecies_.fragment(i.index()); - std::copy(selection.begin(), selection.end(), std::back_inserter(indicesToRemove)); - } - else - indicesToRemove.push_back(i.index()); - } - Messenger::print("Moiety removal deleted {} atoms.\n", indicesToRemove.size()); - - // Remove selected atoms - cleanedUnitCellSpecies_.removeAtoms(indicesToRemove); - } - - cleanedUnitCellConfiguration_.addMolecule(&cleanedUnitCellSpecies_); - cleanedUnitCellConfiguration_.updateObjectRelationships(); - - Messenger::print("Created cleaned crystal unit cell - {} atoms after removal(s).\n", cleanedUnitCellSpecies_.nAtoms()); - - return true; -} - -// Try to detect molecules in the cell contents -bool CIFContext::detectMolecules() -{ - molecularSpecies_.clear(); - - // Try selecting within the species from the first atom - if this captures all atoms we have a bound framework... - if (cleanedUnitCellSpecies_.fragment(0).size() == cleanedUnitCellSpecies_.nAtoms()) - { - Messenger::print( - "Can't create molecular definitions since this unit cell appears to be a continuous framework/network. Consider " - "adjusting the bonding options in order to generate molecular fragments.\n"); - return false; - } - - std::vector atomMask(cleanedUnitCellSpecies_.nAtoms(), false); - - // Find all molecular species, and their instances - auto indexIterator = atomMask.begin(); - while (indexIterator != atomMask.end()) - { - // Select a fragment from the next available index - auto atomIndex = indexIterator - atomMask.begin(); - auto fragmentIndices = cleanedUnitCellSpecies_.fragment(atomIndex); - - // Create a new CIF molecular species from the fragment - auto &cifSp = molecularSpecies_.emplace_back(); - auto *sp = cifSp.species().get(); - // -- Copy selected atoms - for (auto fragAtomIndex : fragmentIndices) - { - const auto &unitCellAtom = cleanedUnitCellSpecies_.atom(fragAtomIndex); - sp->addAtom(unitCellAtom.Z(), unitCellAtom.r(), 0.0, unitCellAtom.atomType()); - } - - // Give the species a temporary unit cell so we can calculate / apply bonding - if (!preventAllBonds_) - sp->createBox(cleanedUnitCellSpecies_.box()->axisLengths(), cleanedUnitCellSpecies_.box()->axisAngles()); - if (useCIFBondingDefinitions_) - applyCIFBonding(sp, preventMetallicBonds_); - else - sp->addMissingBonds(bondingTolerance_, preventMetallicBonds_); - sp->removeBox(); - - // Set up a temporary molecule to unfold the species - LocalMolecule tempMol(sp); - tempMol.unFold(cleanedUnitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(tempMol.localAtoms(), sp->atoms())) - spAtom.setR(molAtom.r()); - - // Give the species a name - sp->setName(EmpiricalFormula::formula(sp->atoms(), [&](const auto &at) { return at.Z(); })); - - // Find instances of this fragment. For large fragments that represent > 50% of the remaining atoms we don't even - // attempt to create a NETA definition etc. For cases such as framework species this will speed up detection no end. - std::vector instances; - if (fragmentIndices.size() * 2 > cleanedUnitCellSpecies_.nAtoms()) - { - // Create an instance of the current fragment - auto &mol = instances.emplace_back(sp); - for (auto i = 0; i < sp->nAtoms(); ++i) - atomMask[fragmentIndices[i]] = true; - } - else - { - // Determine the best NETA definition describing the fragment - auto &&[bestNETA, rootAtoms] = bestNETADefinition(sp); - if (rootAtoms.empty()) - return Messenger::error( - "Couldn't generate molecular partitioning for CIF - no suitable NETA definition for the " - "fragment {} could be determined.\n", - sp->name()); - - // Find instances of this fragment - instances = getSpeciesInstances(sp, atomMask, bestNETA, rootAtoms); - if (instances.empty()) - { - molecularSpecies_.clear(); - return Messenger::error("Failed to find species instances for fragment '{}'.\n", sp->name()); - } - } - - // Store the instances - cifSp.instances() = instances; - - // Search for the next valid starting index - indexIterator = std::find(std::next(indexIterator), atomMask.end(), false); - } - - Messenger::print("Partitioned unit cell into {} distinct molecular species:\n\n", molecularSpecies_.size()); - Messenger::print(" ID N Species Formula\n"); - auto count = 1; - for (const auto &cifMol : molecularSpecies_) - Messenger::print(" {:3d} {:4d} {}\n", count++, cifMol.instances().size(), - EmpiricalFormula::formula(cifMol.species()->atoms(), [](const auto &i) { return i.Z(); })); - Messenger::print(""); - - return true; -} - -// Create supercell species -bool CIFContext::createSupercell() -{ - supercellConfiguration_.empty(); - supercellSpecies_.clear(); - - // Configure the species - auto supercellLengths = cleanedUnitCellSpecies_.box()->axisLengths(); - supercellLengths.multiply(supercellRepeat_.x, supercellRepeat_.y, supercellRepeat_.z); - supercellSpecies_.createBox(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - - // Set up configuration - Messenger::setQuiet(true); - supercellConfiguration_.createBoxAndCells(supercellLengths, cleanedUnitCellSpecies_.box()->axisAngles(), false); - Messenger::setQuiet(false); - - // Copy atoms from the Crystal species - we'll do the bonding afterwards - if (molecularSpecies_.empty()) - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - Vector3 deltaR = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - for (const auto &i : cleanedUnitCellSpecies_.atoms()) - supercellSpecies_.addAtom(i.Z(), i.r() + deltaR, 0.0, i.atomType()); - } - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&supercellSpecies_, preventMetallicBonds_); - else - supercellSpecies_.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Add the structural species to the configuration - supercellConfiguration_.addMolecule(&supercellSpecies_); - supercellConfiguration_.updateObjectRelationships(); - } - else - { - supercellSpecies_.atoms().reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * - cleanedUnitCellSpecies_.nAtoms()); - - // Create images of all molecular unit cell species - for (auto &molecularSpecies : molecularSpecies_) - { - const auto *sp = molecularSpecies.species().get(); - const auto &coreInstances = molecularSpecies.instances(); - std::vector supercellInstances; - supercellInstances.reserve(supercellRepeat_.x * supercellRepeat_.y * supercellRepeat_.z * coreInstances.size()); - - // Loop over cell images - for (auto ix = 0; ix < supercellRepeat_.x; ++ix) - { - for (auto iy = 0; iy < supercellRepeat_.y; ++iy) - { - for (auto iz = 0; iz < supercellRepeat_.z; ++iz) - { - // Skip origin cell - if (ix == 0 && iy == 0 && iz == 0) - continue; - - // Set translation vector - auto tVec = cleanedUnitCellSpecies_.box()->axes() * Vector3(ix, iy, iz); - - // Create images of core molecule instances - for (auto &instance : coreInstances) - { - auto &mol = supercellInstances.emplace_back(); - mol.setSpecies(sp); - - for (auto &&[coreAtom, instanceAtom] : zip(instance.localAtoms(), mol.localAtoms())) - instanceAtom.setR(coreAtom.r() + tVec); - } - } - } - } - - // Append the new instances to our existing ones for the unit cell - molecularSpecies.appendInstances(supercellInstances); - - // Add the molecules to our configuration - for (const auto &instance : molecularSpecies.instances()) - { - auto mol = supercellConfiguration_.addMolecule(sp); - for (auto &&[molAtom, instanceAtom] : zip(mol->atoms(), instance.localAtoms())) - molAtom->setR(instanceAtom.r()); - } - } - - supercellConfiguration_.updateObjectRelationships(); - } - - Messenger::print("Created ({}, {}, {}) supercell - {} atoms total.\n", supercellRepeat_.x, supercellRepeat_.y, - supercellRepeat_.z, supercellConfiguration_.nAtoms()); - - return true; -} - -// Set overlap tolerance -void CIFContext::setOverlapTolerance(double tol) -{ - overlapTolerance_ = tol; - - generate(CIFGenerationStage::CreateBasicUnitCell); -} - -// Set whether to use CIF bonding definitions -void CIFContext::setUseCIFBondingDefinitions(bool b) -{ - if (useCIFBondingDefinitions_ == b) - return; - - useCIFBondingDefinitions_ = b; - - generate(); -} - -// Set bonding tolerance -void CIFContext::setBondingTolerance(double tol) -{ - bondingTolerance_ = tol; - - if (!useCIFBondingDefinitions_) - generate(); -} - -// Whether to ignore all bonds -void CIFContext::setPreventAllBonds(bool b) -{ - if (preventAllBonds_ == b) - return; - - preventAllBonds_ = b; - - generate(); -} - -// Set whether to prevent metallic bonding -void CIFContext::setPreventMetallicBonds(bool b) -{ - if (preventMetallicBonds_ == b) - return; - - preventMetallicBonds_ = b; - - generate(); -} - -// Set whether to remove free atomic moieties in clean-up -void CIFContext::setRemoveAtomics(bool b) -{ - if (removeAtomics_ == b) - return; - - removeAtomics_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove water and coordinated oxygen atoms in clean-up -void CIFContext::setRemoveWaterAndCoordinateOxygens(bool b) -{ - if (removeWaterAndCoordinateOxygens_ == b) - return; - - removeWaterAndCoordinateOxygens_ = b; - - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set whether to remove by NETA definition in clean-up -void CIFContext::setRemoveNETA(bool b, bool byFragment) -{ - if (removeNETA_ == b && removeNETAByFragment_ == byFragment) - return; - - removeNETA_ = b; - removeNETAByFragment_ = byFragment; - - if (moietyRemovalNETA_.isValid()) - generate(CIFGenerationStage::CreateCleanedUnitCell); -} - -// Set NETA for moiety removal -bool CIFContext::setMoietyRemovalNETA(std::string_view netaDefinition) { return moietyRemovalNETA_.create(netaDefinition); } - -// Set supercell repeat -void CIFContext::setSupercellRepeat(const Vector3i &repeat) -{ - supercellRepeat_ = repeat; - - generate(CIFGenerationStage::CreateSupercell); -} - -// Recreate the data -bool CIFContext::generate(CIFGenerationStage fromStage) -{ - // Generate data starting from the specified stage, falling through to subsequent stages in the switch - - switch (fromStage) - { - case (CIFGenerationStage::CreateBasicUnitCell): - if (!createBasicUnitCell()) - return false; - case (CIFGenerationStage::CreateCleanedUnitCell): - if (!createCleanedUnitCell()) - return false; - case (CIFGenerationStage::DetectMolecules): - detectMolecules(); - case (CIFGenerationStage::CreateSupercell): - if (!createSupercell()) - return false; - } - - return true; -} - -// Return whether the generated data is valid -bool CIFContext::isValid() const -{ - return !molecularSpecies_.empty() || supercellSpecies_.fragment(0).size() != supercellSpecies_.nAtoms(); -} - -// Return supercell species -const Species &CIFContext::supercellSpecies() const { return supercellSpecies_; } - -// Return cleaned unit cell species -const Species &CIFContext::cleanedUnitCellSpecies() const { return cleanedUnitCellSpecies_; } - -// Return the detected molecular species -const std::vector &CIFContext::molecularSpecies() const { return molecularSpecies_; } - -// Return the generated configuration -Configuration *CIFContext::generatedConfiguration() { return &supercellConfiguration_; } - -// Return the basic unit cell configuration -Structure *CIFContext::structure() { return &structure_; } - -// Finalise, copying the required species and resulting configuration to the target CoreData -void CIFContext::finalise(CoreData &coreData, const Flags &flags) const -{ - Configuration *configuration; - - if (flags.isSet(OutputFlags::OutputMolecularSpecies)) - { - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - for (auto &cifMolecularSp : molecularSpecies_) - { - // Add the species - auto *sp = coreData.copySpecies(cifMolecularSp.species().get()); - - // Determine a unique suffix - auto base = sp->name(); - std::string uniqueSuffix{base}; - if (!generator.nodes().empty()) - { - // Start from the last root node - auto root = generator.nodes().back(); - auto suffix = 0; - - while (generator.rootSequence().nodeInScope(root, std::format("SymmetryCopies_{}", uniqueSuffix)) != - nullptr) - uniqueSuffix = std::format("{}_{:02d}", base, ++suffix); - } - - // We use 'CoordinateSets' here, because in this instance we are working with (CoordinateSet, Add) pairs - - // CoordinateSets - auto coordsNode = - generator.createRootNode(std::format("SymmetryCopies_{}", uniqueSuffix), sp); - coordsNode->keywords().setEnumeration("Source", CoordinateSetsGeneratorNode::CoordinateSetSource::File); - coordsNode->setSets(cifMolecularSp.allInstanceCoordinates()); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", uniqueSuffix), coordsNode); - addNode->keywords().set("Population", NodeValueProxy(int(cifMolecularSp.instances().size()))); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } - else - { - for (auto &cifMolecularSp : molecularSpecies_) - { - coreData.copySpecies(cifMolecularSp.species().get()); - } - } - } - else - { - auto *sp = coreData.addSpecies(); - sp->copyBasic(&supercellSpecies_); - if (flags.isSet(OutputFlags::OutputSupermolecule)) - { - sp->removePeriodicBonds(); - sp->removeBox(); - } - else - sp->createBox(supercellSpecies_.box()->axisLengths(), supercellSpecies_.box()->axisAngles()); - - sp->updateIntramolecularTerms(); - - if (flags.isSet(OutputFlags::OutputConfiguration)) - { - configuration = coreData.addConfiguration(); - configuration->setName(chemicalFormula()); - - // Grab the generator - auto &generator = configuration->generator(); - - // Add Box - auto boxNode = generator.createRootNode({}); - auto cellLengths = supercellConfiguration_.box()->axisLengths(); - auto cellAngles = supercellConfiguration_.box()->axisAngles(); - boxNode->keywords().set("Lengths", Vector3NodeValue(cellLengths.get(0), cellLengths.get(1), cellLengths.get(2))); - boxNode->keywords().set("Angles", Vector3NodeValue(cellAngles.get(0), cellAngles.get(1), cellAngles.get(2))); - - // Add - auto addNode = generator.createRootNode(std::format("Add_{}", sp->name()), sp); - addNode->keywords().set("Population", NodeValueProxy(1)); - addNode->keywords().setEnumeration("Positioning", AddGeneratorNode::PositioningType::Current); - addNode->keywords().set("Rotate", false); - addNode->keywords().setEnumeration("BoxAction", AddGeneratorNode::BoxActionStyle::None); - } - } -} - -/* - * Helpers - */ - -// Apply CIF bonding to a given species -void CIFContext::applyCIFBonding(Species *sp, bool preventMetallicBonding) -{ - if (!hasBondDistances()) - return; - - auto *box = sp->box(); - auto pairs = PairIterator(sp->nAtoms()); - for (auto pair : pairs) - { - // Grab indices and atom references - auto [indexI, indexJ] = pair; - if (indexI == indexJ) - continue; - - auto &i = sp->atom(indexI); - auto &j = sp->atom(indexJ); - - // Prevent metallic bonding? - if (preventMetallicBonding && Elements::isMetallic(i.Z()) && Elements::isMetallic(j.Z())) - continue; - - // Retrieve distance - auto r = bondDistance(i.atomType()->name(), j.atomType()->name()); - if (!r) - continue; - else if (fabs(box->minimumDistance(i.r(), j.r()) - r.value()) < 1.0e-2) - sp->addBond(&i, &j); - } -} - -// Determine the best NETA definition for the supplied species -std::tuple> CIFContext::bestNETADefinition(Species *sp) -{ - // Set up the return value and bind its contents - std::tuple> result{NETADefinition(), {}}; - auto &&[bestNETA, rootAtoms] = result; - - // Maintain a set of atoms matched by any NETA description we generate - std::set alreadyMatched; - - // Loop over species atoms - for (auto &i : sp->atoms()) - { - // Skip this atom? - if (alreadyMatched.find(&i) != alreadyMatched.end()) - continue; - - // Create a NETA definition with this atom as the root - NETADefinition neta; - neta.create(&i, std::nullopt, - Flags(NETADefinition::NETACreationFlags::ExplicitHydrogens, - NETADefinition::NETACreationFlags::IncludeRootElement)); - - // Apply this match over the whole species - std::vector currentRootAtoms; - for (auto &j : sp->atoms()) - { - if (neta.matches(&j)) - { - currentRootAtoms.push_back(&j); - alreadyMatched.insert(&j); - } - } - - // Is this a better description? - auto better = false; - if (rootAtoms.empty() || currentRootAtoms.size() < rootAtoms.size()) - better = true; - else if (currentRootAtoms.size() == rootAtoms.size()) - { - // Replace the current match if there are more bonds on the current atom. - if (i.nBonds() > rootAtoms.front()->nBonds()) - better = true; - } - - if (better) - { - bestNETA = neta; - rootAtoms = currentRootAtoms; - } - } - - return result; -} - -// Get instances for the supplied species from the cleaned unit cell -std::vector CIFContext::getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms) -{ - if (referenceRootAtoms.empty() || !neta.isValid()) - return {}; - - // Loop over atoms in the unit cell - we'll mark any that we select as an instance so we speed things up and avoid - // duplicates - const auto &unitCellAtoms = cleanedUnitCellSpecies_.atoms(); - std::vector instances; - auto atomIndexIterator = std::find(atomMask.begin(), atomMask.end(), false); - while (atomIndexIterator != atomMask.end()) - { - // Try to match this atom / fragment - const auto atomIndex = atomIndexIterator - atomMask.begin(); - auto &atom = unitCellAtoms[atomIndex]; - auto matchedUnitCellAtoms = neta.matchedPath(&atom).set(); - if (matchedUnitCellAtoms.empty()) - { - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - continue; - } - - // Found a fragment that matches the NETA description - we now create a temporary instance Species which will contain - // the selected fragment atoms, reassembled into a molecule (i.e. unfolded) and with bonding applied / calculated. - // We need to copy the unit cell from the crystal so we detect bonds properly. - Species instanceSpecies; - instanceSpecies.createBox(unitCellSpecies_.box()->axisLengths(), unitCellSpecies_.box()->axisAngles()); - auto rootAtomLocalIndex = -1; - // -- Create species atoms from those matched in the unit cell by the NETA description. - for (auto &matchedAtom : matchedUnitCellAtoms) - { - auto idx = instanceSpecies.addAtom(matchedAtom->Z(), matchedAtom->r(), 0.0, matchedAtom->atomType()); - - // Store the index of the root atom in match in our instance species when we find it - if (matchedAtom == &atom) - rootAtomLocalIndex = idx; - } - // -- Store the local root atom so we can access its coordinates for the origin translation - auto &instanceSpeciesRootAtom = instanceSpecies.atom(rootAtomLocalIndex); - // -- Calculate / apply bonding - if (!preventAllBonds_) - if (useCIFBondingDefinitions_) - applyCIFBonding(&instanceSpecies, preventMetallicBonds_); - else - instanceSpecies.addMissingBonds(bondingTolerance_, preventMetallicBonds_); - - // Create a LocalMolecule as a working area for folding, translation, and rotation of the instance coordinates. - LocalMolecule instanceMolecule; - instanceMolecule.setSpecies(&instanceSpecies); - // -- Copy the coordinates off the matched unit cell atoms to our molecule and flag them as complete - auto count = 0; - for (auto &&[matchedAtom, instanceMolAtom] : zip(matchedUnitCellAtoms, instanceMolecule.localAtoms())) - { - instanceMolAtom.setR(matchedAtom->r()); - atomMask[matchedAtom->index()] = true; - } - auto &instanceMoleculeRootAtom = instanceMolecule.localAtoms()[rootAtomLocalIndex]; - - // Unfold the molecule and store the unfolded molecule coordinates back into the instance Species. - // This represents our full instance coordinates we will be storing (but not their final order) - instanceMolecule.unFold(unitCellSpecies_.box()); - for (auto &&[molAtom, spAtom] : zip(instanceMolecule.localAtoms(), instanceSpecies.atoms())) - spAtom.setR(molAtom.r()); - - /* - * Now, we have a root match atom on the current instance and a vector of possible matching sites on the reference - * species (in referenceRootAtoms). For each of the referenceRootAtoms, try to incrementally select along bonds using - * basic NETA connectivity. - */ - - // Generate basic NETA descriptions for each atom in the reference and candidate species - std::map referenceAtomNETA; - for (auto &spAtom : referenceSpecies->atoms()) - referenceAtomNETA[&spAtom] = NETADefinition(&spAtom, 1, {NETADefinition::NETACreationFlags::IncludeRootElement}); - - std::map matchMap; - for (const auto *referenceRootAtom : referenceRootAtoms) - { - // The root atom is the starting point - matchMap = matchAtom(referenceRootAtom, &instanceSpeciesRootAtom, referenceAtomNETA, {}); - if (!matchMap.empty()) - break; - } - - // Result? - if (matchMap.empty()) - { - Messenger::error("Failed to match connectivity of an instance to the reference molecule.\n"); - return {}; - } - else if (matchMap.size() != referenceSpecies->nAtoms()) - { - Messenger::error( - "Internal error - failed to match connectivity of all atoms within an instance to the reference molecule.\n"); - return {}; - } - - // Create the final instance - auto &instance = instances.emplace_back(); - instance.setSpecies(referenceSpecies); - for (const auto &[refSpeciesAtom, instanceSpeciesAtom] : matchMap) - { - instance.localAtom(refSpeciesAtom->index()).setR(instanceSpeciesAtom->r()); - } - - // Find the next available atom - atomIndexIterator = std::find(std::next(atomIndexIterator), atomMask.end(), false); - } - - return instances; -} - -// Recursively check NETA description matches between the supplied atoms -std::map -CIFContext::matchAtom(const SpeciesAtom *referenceAtom, const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map) -{ - // If the reference atom NETA doesn't match the instance atom we cannot proceed - if (!refNETA.at(referenceAtom).matches(instanceAtom)) - return {}; - - // Check the map to see if we have already associated the reference atom to an instance atom, or if the instance atom - // is already associated to a different reference atom. - for (auto &&[mappedRefAtom, mappedInstanceAtom] : map) - { - // Found it - double-check to ensure that the current association matches our instance atom. If it does we can return - // the map as it currently stands. If not we return an empty map to indicate failure. - if (mappedRefAtom == referenceAtom) - { - if (mappedInstanceAtom == instanceAtom) - { - return map; - } - else - { - return {}; - } - } - else if (mappedInstanceAtom == instanceAtom) - { - return {}; - } - } - - // Copy the current map, associate our initial pair of atoms and try to extend it - auto newMap = map; - newMap[referenceAtom] = instanceAtom; - - // Cycle over bonds on the reference atom and find - for (const auto &referenceBond : referenceAtom->bonds()) - { - // Get the reference bond partner - auto *referenceBondPartner = referenceBond.get().partner(referenceAtom); - - // Try to find a match over bonds on the instance atom - std::map bondResult; - for (const auto &instanceBond : instanceAtom->bonds()) - { - // Get the instance bond partner - auto *instanceBondPartner = instanceBond.get().partner(instanceAtom); - - // Recurse - bondResult = matchAtom(referenceBondPartner, instanceBondPartner, refNETA, newMap); - if (!bondResult.empty()) - break; - } - - // If we found a suitable match recursing into the bond, store the result into newMap and continue to the next bond. - // If we didn't find a good match, we return now. - if (bondResult.empty()) - { - return {}; - } - else - { - newMap = bondResult; - } - } - - // If we get to here then we succeeded, so return the new map - return newMap; -} - -// Calculate difference metric between the supplied species and local molecule -std::pair> CIFContext::differenceMetric(const Species *species, const LocalMolecule &molecule) -{ - auto difference = 0.0; - std::vector atomIndexMap(species->nAtoms(), -1); - auto nBadAtoms = 0; - for (auto spI = 0; spI < species->nAtoms(); ++spI) - { - auto &spAtom = species->atom(spI); - - // For this species atom find the closest atom in the molecule - auto distanceSq = 1.0e6; - for (auto molI = 0; molI < molecule.nAtoms(); ++molI) - { - auto rABSq = (spAtom.r() - molecule.localAtoms()[molI].r()).magnitudeSq(); - if (rABSq < distanceSq) - { - distanceSq = rABSq; - atomIndexMap[spI] = molI; - } - } - - if (distanceSq > 0.1) - ++nBadAtoms; - - // Update the difference score - const auto &closestMolSpAtom = molecule.species()->atom(atomIndexMap[spI]); - difference += distanceSq; - if (spAtom.Z() != closestMolSpAtom.Z()) - difference += std::max(int(spAtom.Z()), int(closestMolSpAtom.Z())) * 10.0; - } - - return {difference, atomIndexMap}; -} diff --git a/src/nodes/cif/io/cifContext.h b/src/nodes/cif/io/cifContext.h deleted file mode 100644 index 3f168a292f..0000000000 --- a/src/nodes/cif/io/cifContext.h +++ /dev/null @@ -1,220 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#pragma once - -#include "classes/configuration.h" -#include "classes/coreData.h" -#include "classes/species.h" -#include "classes/structure.h" -#include "data/spaceGroups.h" -#include "math/matrix4.h" -#include "neta/neta.h" -#include "nodes/cif/io/cifClasses.h" -#include "templates/flags.h" -#include - -// Forward Declarations -class Box; - -// CIF Handler -class CIFContext -{ - public: - CIFContext(); - ~CIFContext() = default; - - /* - * Raw Data - */ - public: - // Data Types - using CIFTags = std::map>; - - private: - // Vector of enumerated data items - CIFTags tags_; - - private: - // Parse supplied file into the destination objects - bool parse(std::string_view filename, CIFTags &tags) const; - - public: - // Return whether the specified file parses correctly - bool validFile(std::string_view filename) const; - // Read CIF data from specified file - bool read(std::string_view filename); - // Return if the specified tag exists - bool hasTag(std::string tag) const; - // Return tag data string (if it exists) assuming a single datum (first in the vector) - std::optional getTagString(std::string tag) const; - // Return tag data strings (if it exists) - std::vector getTagStrings(std::string tag) const; - // Return tag data as double (if it exists) assuming a single datum (first in the vector) - std::optional getTagDouble(std::string tag) const; - // Return tag data doubles (if it exists) - std::vector getTagDoubles(std::string tag) const; - // Return tag data as integer (if it exists) assuming a single datum (first in the vector) - std::optional getTagInt(std::string tag) const; - - /* - * Processed Data - */ - private: - // Space group - SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::NoSpaceGroup}; - // Atom assemblies - std::vector assemblies_; - // Bond information - std::vector bondingPairs_; - - public: - // Set space group from index - void setSpaceGroup(SpaceGroups::SpaceGroupId sgid); - // Return space group - SpaceGroups::SpaceGroupId spaceGroup() const; - // Return cell lengths - std::optional getCellLengths() const; - // Return cell angles - std::optional getCellAngles() const; - // Return chemical formula - std::string chemicalFormula() const; - // Get (add or retrieve) named assembly - CIFAssembly &getAssembly(std::string_view name); - // Return atom assemblies - std::vector &assemblies(); - const std::vector &assemblies() const; - // Return whether any bond distances are defined - bool hasBondDistances() const; - // Return whether a bond distance is defined for the specified label pair - std::optional bondDistance(std::string_view labelI, std::string_view labelJ) const; - - /* - * Creation - */ - public: - // CIF Generation Stages - enum class CIFGenerationStage - { - CreateBasicUnitCell, - CreateCleanedUnitCell, - DetectMolecules, - CreateSupercell - }; - // CIF Species Output Flags - enum OutputFlags - { - OutputConfiguration, /* Output a Configuration */ - OutputMolecularSpecies, /* Partitioning - output molecular species */ - OutputFramework, /* Partitioning - output a framework species */ - OutputSupermolecule /* Partitioning - output a supermolecule */ - }; - - private: - // Temporary atom types used for unique atom labels - std::vector> atomLabelTypes_; - // Tolerance for removal of overlapping atoms - double overlapTolerance_{0.1}; - // Whether to use CIF bonding definitions - bool useCIFBondingDefinitions_{false}; - // Bonding tolerance, if calculating bonding rather than using CIF definitions - double bondingTolerance_{1.1}; - // Whether to ignore all bonds - bool preventAllBonds_{false}; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; - // Whether to remove free atomic moieties in clean-up - bool removeAtomics_{false}; - // Whether to remove water and coordinated oxygen atoms in clean-up - bool removeWaterAndCoordinateOxygens_{false}; - // Whether to remove by NETA definition in clean-up - bool removeNETA_{false}; - // Whether to expand NETA matches to fragments when removing in clean-up - bool removeNETAByFragment_{false}; - // NETA for moiety removal, if specified - NETADefinition moietyRemovalNETA_; - // Supercell repeat - Vector3i supercellRepeat_{1, 1, 1}; - // Basic unit cell - Species unitCellSpecies_; - Configuration unitCellConfiguration_; - Structure structure_; - // Cleaned unit cell - Species cleanedUnitCellSpecies_; - Configuration cleanedUnitCellConfiguration_; - // Molecular definition of unit cell (if possible) - std::vector molecularSpecies_; - // Final generated result (supercell) - Species supercellSpecies_; - Configuration supercellConfiguration_; - - private: - // Create basic unit cell - bool createBasicUnitCell(); - // Create structure from basic unit cell atoms and connectivity - bool createStructure(); - // Create the cleaned unit cell - bool createCleanedUnitCell(); - // Try to detect molecules in the cell contents - bool detectMolecules(); - // Create supercell species - bool createSupercell(); - - public: - // Set overlap tolerance - void setOverlapTolerance(double tol); - // Set whether to use CIF bonding definitions - void setUseCIFBondingDefinitions(bool b); - // Set bonding tolerance - void setBondingTolerance(double tol); - // Whether to ignore all bonds - void setPreventAllBonds(bool b); - // Set whether to prevent metallic bonding - void setPreventMetallicBonds(bool b); - // Set whether to remove free atomic moieties in clean-up - void setRemoveAtomics(bool b); - // Set whether to remove water and coordinated oxygen atoms in clean-up - void setRemoveWaterAndCoordinateOxygens(bool b); - // Set whether to remove by NETA definition in clean-up - void setRemoveNETA(bool b, bool byFragment); - // Set NETA for moiety removal - bool setMoietyRemovalNETA(std::string_view netaDefinition); - // Set supercell repeat - void setSupercellRepeat(const Vector3i &repeat); - // Recreate the data - bool generate(CIFGenerationStage fromStage = CIFGenerationStage::CreateBasicUnitCell); - // Return whether the generated data is valid - bool isValid() const; - // Return supercell species - const Species &supercellSpecies() const; - // Return cleaned unit cell species - const Species &cleanedUnitCellSpecies() const; - // Return the detected molecular species - const std::vector &molecularSpecies() const; - // Return the generated configuration - Configuration *generatedConfiguration(); - // Return the basic crystal structure - Structure *structure(); - // Finalise, copying the required species and resulting configuration to the target CoreData - void finalise(CoreData &coreData, const Flags &flags = {}) const; - - /* - * Helpers - */ - private: - // Apply CIF bonding to a given species - void applyCIFBonding(Species *sp, bool preventMetallicBonding); - // Determine the best NETA definition for the supplied species - std::tuple> bestNETADefinition(Species *sp); - // Get instances of species molecules from the supplied NETA definition - std::vector getSpeciesInstances(const Species *referenceSpecies, std::vector &atomMask, - const NETADefinition &neta, - const std::vector &referenceRootAtoms); - // Calculate difference metric between the supplied species and local molecule - static std::pair> differenceMetric(const Species *species, const LocalMolecule &molecule); - // Recursively check NETA description matches between the supplied atoms - std::map matchAtom(const SpeciesAtom *referenceAtom, - const SpeciesAtom *instanceAtom, - const std::map &refNETA, - const std::map &map); -}; diff --git a/tests/io/CMakeLists.txt b/tests/io/CMakeLists.txt index 182e81dac2..6ab8d5340d 100644 --- a/tests/io/CMakeLists.txt +++ b/tests/io/CMakeLists.txt @@ -1,4 +1,3 @@ dissolve_add_test(SRC cbor.cpp) -dissolve_add_test(SRC cif.cpp) dissolve_add_test(SRC intraParameterParse.cpp) dissolve_add_test(SRC version.cpp) diff --git a/tests/io/cif.cpp b/tests/io/cif.cpp deleted file mode 100644 index 82031fe6a3..0000000000 --- a/tests/io/cif.cpp +++ /dev/null @@ -1,212 +0,0 @@ -// SPDX-License-Identifier: GPL-3.0-or-later -// Copyright (c) 2026 Team Dissolve and contributors - -#include "classes/empiricalFormula.h" -#include "io/import/species.h" -#include "nodes/cif/io/cifContext.h" -#include "tests/testData.h" -#include - -namespace UnitTest -{ -class ImportCIFTest : public ::testing::Test -{ - public: - // Molecular species information - using MolecularSpeciesInfo = std::tuple; - // Test Box definition - void testBox(const Configuration *cfg, const Vector3 &lengths, const Vector3 &angles, int nAtoms) - { - ASSERT_TRUE(cfg); - EXPECT_EQ(cfg->nAtoms(), nAtoms); - EXPECT_NEAR(cfg->box()->axisLengths().x, lengths.x, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisLengths().y, lengths.y, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisLengths().z, lengths.z, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().x, angles.x, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().y, angles.y, 1.0e-6); - EXPECT_NEAR(cfg->box()->axisAngles().z, angles.z, 1.0e-6); - } - // Test molecular species information provided - void testMolecularSpecies(const CIFMolecularSpecies &molSp, const MolecularSpeciesInfo &info) - { - EXPECT_EQ(molSp.species()->name(), std::get<0>(info)); - EXPECT_EQ(molSp.instances().size(), std::get<1>(info)); - EXPECT_EQ(molSp.species()->nAtoms(), std::get<2>(info)); - } - // Check instance consistency with reference coordinates - void testInstanceConsistency(const CIFMolecularSpecies &molSp, const Species &referenceCoordinates) - { - // Get the box from the reference species - const auto *box = referenceCoordinates.box(); - - // Loop over instances and ensure their stored atoms overlap exactly with one in the reference system - for (const auto &instance : molSp.instances()) - { - for (auto &&[instanceAtom, speciesAtom] : zip(instance.localAtoms(), molSp.species()->atoms())) - { - // Locate the atom in the reference system at the instance atom coordinates - auto instanceR = instanceAtom.r(); - auto spAtomIt = std::find_if(referenceCoordinates.atoms().begin(), referenceCoordinates.atoms().end(), - [box, instanceR](const auto &refAtom) - { return box->minimumDistance(refAtom.r(), instanceR) < 0.01; }); - std::cout << std::format("{} {} {} {}", Elements::symbol(speciesAtom.Z()), instanceAtom.r().x, - instanceAtom.r().y, instanceAtom.r().z) - << std::endl; - ASSERT_NE(spAtomIt, referenceCoordinates.atoms().end()); - EXPECT_EQ(spAtomIt->Z(), speciesAtom.Z()); - } - } - } -}; - -TEST_F(ImportCIFTest, Parse) -{ - // Test files - auto cifPath = "cif/"; - std::vector cifs = {"1557470.cif", "1557599.cif", "7705246.cif", "9000004.cif", "9000095.cif", "9000418.cif"}; - - for (auto &cif : cifs) - { - CIFContext cifContext; - ASSERT_TRUE(cifContext.read(cifPath + cif)); - } -} - -TEST_F(ImportCIFTest, NaCl) -{ - CIFContext cifContext; - ASSERT_TRUE(cifContext.read("cif/NaCl-1000041.cif")); - EXPECT_TRUE(cifContext.generate()); - - // Check basic info - EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_225); - constexpr double A = 5.62; - testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 8); - - // Calculating bonding is the default, but this gives a continuous framework... - EXPECT_EQ(cifContext.molecularSpecies().size(), 0); - - // Get molecular species - cifContext.setUseCIFBondingDefinitions(true); - EXPECT_EQ(cifContext.molecularSpecies().size(), 2); - testMolecularSpecies(cifContext.molecularSpecies()[0], {"Na", 4, 1}); - std::vector R = {{0.0, 0.0, 0.0}, {0.0, A / 2, A / 2}, {A / 2, 0.0, A / 2}, {A / 2, A / 2, 0.0}}; - for (auto &&[instance, r2] : zip(cifContext.molecularSpecies()[0].instances(), R)) - DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), r2); - testMolecularSpecies(cifContext.molecularSpecies()[1], {"Cl", 4, 1}); - for (auto &&[instance, r2] : zip(cifContext.molecularSpecies()[1].instances(), R)) - DissolveSystemTest::checkVec3(instance.localAtoms()[0].r(), (r2 - A / 2).abs()); - - // 2x2x2 supercell - cifContext.setSupercellRepeat({2, 2, 2}); - EXPECT_TRUE(cifContext.generate()); - testBox(cifContext.generatedConfiguration(), {A * 2, A * 2, A * 2}, {90, 90, 90}, 8 * 8); -} - -TEST_F(ImportCIFTest, NaClO3) -{ - CIFContext cifContext; - ASSERT_TRUE(cifContext.read("cif/NaClO3-1010057.cif")); - EXPECT_TRUE(cifContext.generate()); - - // Check basic info - EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_198); - constexpr double A = 6.55; - testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 20); - - // Turn off automatic bond calculation - there are no bonding defs in the CIF, so we expect species for each atomic - // component (4 Na, 4 Cl, and 12 O) - cifContext.setUseCIFBondingDefinitions(true); - auto &cifMols = cifContext.molecularSpecies(); - ASSERT_EQ(cifMols.size(), 3); - testMolecularSpecies(cifMols[0], {"Na", 4, 1}); - testMolecularSpecies(cifMols[1], {"Cl", 4, 1}); - testMolecularSpecies(cifMols[2], {"O", 12, 1}); - - // Calculate bonding ourselves to get the correct species - cifContext.setUseCIFBondingDefinitions(false); - ASSERT_EQ(cifMols.size(), 2); - testMolecularSpecies(cifMols[0], {"Na", 4, 1}); - testMolecularSpecies(cifMols[1], {"ClO3", 4, 4}); -} - -TEST_F(ImportCIFTest, CuBTC) -{ - CIFContext cifContext; - ASSERT_TRUE(cifContext.read("cif/CuBTC-7108574.cif")); - EXPECT_TRUE(cifContext.generate()); - - // Check basic info - EXPECT_EQ(cifContext.spaceGroup(), SpaceGroups::SpaceGroup_225); - constexpr auto A = 26.3336; - testBox(cifContext.generatedConfiguration(), {A, A, A}, {90, 90, 90}, 672); - - // 16 basic formula units per unit cell - constexpr auto N = 16; - - // Check basic formula (which includes bound water oxygens - with no H - at this point) and using O group - EmpiricalFormula::EmpiricalFormulaMap cellFormulaH = { - {Elements::Cu, 3 * N}, {Elements::C, 18 * N}, {Elements::H, 6 * N}, {Elements::O, 15 * N}}; - EXPECT_EQ(EmpiricalFormula::formula(cifContext.generatedConfiguration()->atoms(), - [](const auto &i) { return i.speciesAtom()->Z(); }), - EmpiricalFormula::formula(cellFormulaH)); - EXPECT_EQ(cifContext.molecularSpecies().size(), 2); - - // Change active assemblies to get amine-substituted structure - EmpiricalFormula::EmpiricalFormulaMap cellFormulaNH2 = cellFormulaH; - cellFormulaNH2[Elements::N] = 6 * N; - cellFormulaNH2[Elements::H] *= 2; - cifContext.getAssembly("A").getGroup("1").setActive(false); - cifContext.getAssembly("B").getGroup("2").setActive(true); - cifContext.getAssembly("C").getGroup("2").setActive(true); - EXPECT_TRUE(cifContext.generate()); - EXPECT_EQ(EmpiricalFormula::formula(cifContext.generatedConfiguration()->atoms(), - [](const auto &i) { return i.speciesAtom()->Z(); }), - EmpiricalFormula::formula(cellFormulaNH2)); - - // Remove those free oxygens so we just have a framework - cifContext.setRemoveAtomics(true); - EXPECT_EQ(cifContext.molecularSpecies().size(), 0); -} - -TEST_F(ImportCIFTest, MoleculeOrdering) -{ - CIFContext cifContext; - const auto cifFiles = {"cif/molecule-test-simple-ordered.cif", "cif/molecule-test-simple-unordered.cif", - "cif/molecule-test-simple-unordered-rotated.cif"}; - for (auto cifFile : cifFiles) - { - // Load the CIF file - ASSERT_TRUE(cifContext.read(cifFile)); - EXPECT_TRUE(cifContext.generate()); - - EXPECT_EQ(cifContext.molecularSpecies().size(), 1); - - auto &cifMolecule = cifContext.molecularSpecies().front(); - EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = { - {Elements::Cl, 1}, {Elements::O, 1}, {Elements::C, 1}, {Elements::H, 3}}; - testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 6, 6}); - - testInstanceConsistency(cifMolecule, cifContext.cleanedUnitCellSpecies()); - } -} - -TEST_F(ImportCIFTest, BigMoleculeOrdering) -{ - CIFContext cifContext; - const auto cifFile = "cif/Bisphen_n_arenes_1517789.cif"; - - // Load the CIF file - ASSERT_TRUE(cifContext.read(cifFile)); - EXPECT_TRUE(cifContext.generate()); - - EXPECT_EQ(cifContext.molecularSpecies().size(), 1); - - auto &cifMolecule = cifContext.molecularSpecies().front(); - EmpiricalFormula::EmpiricalFormulaMap moleculeFormula = {{Elements::O, 6}, {Elements::C, 51}, {Elements::H, 54}}; - testMolecularSpecies(cifMolecule, {EmpiricalFormula::formula(moleculeFormula), 4, 111}); - - testInstanceConsistency(cifMolecule, cifContext.cleanedUnitCellSpecies()); -} - -} // namespace UnitTest From 18fe0f905c58ac556042de1da18d2d74a81fd42e Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Fri, 8 May 2026 13:33:25 +0100 Subject: [PATCH 14/22] clear structure at process --- src/nodes/cif/importCIFStructure.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index ff85a594cf..02da725b86 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -40,6 +40,8 @@ std::string_view ImportCIFStructureNode::summary() const // Run main processing NodeConstants::ProcessResult ImportCIFStructureNode::process() { + structure_.clear(); + // Read contents of CIF file if (read(filePath_)) { From 655090dcd323a89dfe2d5be62499ff0fd1f7100d Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 10:01:58 +0100 Subject: [PATCH 15/22] remove neta header --- src/nodes/cif/importCIFStructure.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index 02da725b86..5771f115c1 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -11,7 +11,6 @@ #include "generator/add.h" #include "generator/box.h" #include "generator/coordinateSets.h" -#include "neta/neta.h" #include "nodes/cif/io/CIFImportErrorListeners.h" #include "nodes/cif/io/CIFImportVisitor.h" #include "templates/algorithms.h" From a2556b01682d7280669f5727a0a371832da40809 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 10:04:04 +0100 Subject: [PATCH 16/22] edit descriptive comments --- src/nodes/cif/importCIFStructure.cpp | 6 +----- src/nodes/cif/importCIFStructure.h | 6 +----- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index 5771f115c1..c8c1b7f608 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -58,7 +58,7 @@ NodeConstants::ProcessResult ImportCIFStructureNode::process() */ /* - * Raw Data + * Basic CIF Data */ // Parse supplied file into the destination objects @@ -535,10 +535,6 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou return true; } -/* - * End CIF I/O - */ - /* * Getters */ diff --git a/src/nodes/cif/importCIFStructure.h b/src/nodes/cif/importCIFStructure.h index 9efaea9deb..9a604b9b03 100644 --- a/src/nodes/cif/importCIFStructure.h +++ b/src/nodes/cif/importCIFStructure.h @@ -41,7 +41,7 @@ class ImportCIFStructureNode : public Node */ /* - * Raw Data + * Basic CIF Data */ private: // Vector of enumerated data items @@ -116,10 +116,6 @@ class ImportCIFStructureNode : public Node // Set overlap tolerance void setOverlapTolerance(double tol); - /* - * End CIF I/O - */ - /* * Processing */ From bd8cac712a2f4215f87e73cb9e2d3203fc21e7b6 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 10:08:09 +0100 Subject: [PATCH 17/22] no metallic bonding option --- src/nodes/cif/importCIFStructure.cpp | 3 +-- src/nodes/cif/importCIFStructure.h | 2 -- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index c8c1b7f608..c1bf0e87d4 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -25,7 +25,6 @@ ImportCIFStructureNode::ImportCIFStructureNode(Graph *parentGraph) : Node(parent // Option addOption("FilePath", "File path", filePath_); - addOption("PreventMetallicBonds", "Whether to prevent metallic bonding", preventMetallicBonds_); addOption("SpaceGroupID", "Set space group from index", spaceGroup_); } @@ -517,7 +516,7 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou auto j = structure_.atomAt(indexJ); // Prevent metallic bonding? - if (preventMetallicBonds_ && Elements::isMetallic(i->Z()) && Elements::isMetallic(j->Z())) + if (Elements::isMetallic(i->Z()) && Elements::isMetallic(j->Z())) continue; // Retrieve distance diff --git a/src/nodes/cif/importCIFStructure.h b/src/nodes/cif/importCIFStructure.h index 9a604b9b03..fc039bff78 100644 --- a/src/nodes/cif/importCIFStructure.h +++ b/src/nodes/cif/importCIFStructure.h @@ -33,8 +33,6 @@ class ImportCIFStructureNode : public Node SpaceGroups::SpaceGroupId spaceGroup_{SpaceGroups::SpaceGroupId::NoSpaceGroup}; // CIF filepath std::string filePath_; - // Whether to prevent metallic bonding - bool preventMetallicBonds_{true}; /* * CIF I/O From 397db674496e346abac8b1fcfd12ff072d8c4613 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 10:24:55 +0100 Subject: [PATCH 18/22] replace deprecated std library strstream to fix non-linux compiler error --- src/nodes/exportDLPolyConfiguration.h | 2 +- src/nodes/exportXYZConfiguration.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/nodes/exportDLPolyConfiguration.h b/src/nodes/exportDLPolyConfiguration.h index dd81493130..224d204383 100644 --- a/src/nodes/exportDLPolyConfiguration.h +++ b/src/nodes/exportDLPolyConfiguration.h @@ -5,7 +5,7 @@ #include "nodes/node.h" #include -#include +#include // Forward Declarations class Configuration; diff --git a/src/nodes/exportXYZConfiguration.h b/src/nodes/exportXYZConfiguration.h index fc3821d5dc..d22c6859be 100644 --- a/src/nodes/exportXYZConfiguration.h +++ b/src/nodes/exportXYZConfiguration.h @@ -5,7 +5,7 @@ #include "nodes/node.h" #include -#include +#include // Forward Declarations class Configuration; From 97455878e31698796b30fe524a1a3984e6f6547d Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 15:38:38 +0100 Subject: [PATCH 19/22] graphene species dialog is back! --- src/gui/createGrapheneSpeciesDialog.cpp | 521 ++++++++++++ src/gui/createGrapheneSpeciesDialog.h | 112 +++ src/gui/createGrapheneSpeciesDialog.ui | 1014 +++++++++++++++++++++++ src/gui/gui.h | 2 +- src/gui/menu_species.cpp | 3 +- 5 files changed, 1649 insertions(+), 3 deletions(-) create mode 100644 src/gui/createGrapheneSpeciesDialog.cpp create mode 100644 src/gui/createGrapheneSpeciesDialog.h create mode 100644 src/gui/createGrapheneSpeciesDialog.ui diff --git a/src/gui/createGrapheneSpeciesDialog.cpp b/src/gui/createGrapheneSpeciesDialog.cpp new file mode 100644 index 0000000000..3287bdcb22 --- /dev/null +++ b/src/gui/createGrapheneSpeciesDialog.cpp @@ -0,0 +1,521 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#include "gui/createGrapheneSpeciesDialog.h" +#include "classes/empiricalFormula.h" +#include "gui/helpers/comboPopulator.h" +#include "math/mathFunc.h" +#include + +// Useful constants +const auto root3 = sqrt(3.0); +const auto oneSixthPi = M_PI / 6.0; // == 30 degrees + +CreateGrapheneSpeciesDialog::CreateGrapheneSpeciesDialog(QWidget *parent, Dissolve &dissolve) + : QDialog(parent), selectElementDialog_(this), dissolve_(dissolve) +{ + ui_.setupUi(this); + + Locker refreshLock(widgetsUpdating_); + + ui_.ElementAButton->setText(QString::fromStdString(std::string(Elements::symbol(zA_)))); + ui_.ElementBButton->setText(QString::fromStdString(std::string(Elements::symbol(zB_)))); + ui_.TerminateElementButton->setText(QString::fromStdString(std::string(Elements::symbol(zTerminate_)))); + + ui_.MSpin->setMaximum(ui_.NSpin->value()); + + // Set display configuration + ui_.StructureViewer->setSpecies(&species_); + + refreshLock.unlock(); + + calculateParameters(); + + regenerate(); +} + +/* + * Data + */ + +// Calculate parameters +void CreateGrapheneSpeciesDialog::calculateParameters() +{ + /* + * Procedure based on "Determination of the chiral indices (n,m) of carbon nanotubes by electron diffraction", + * Lu-Chan Qin, Phys. Chem. Chem. Phys. 2007, *9*, 31-48. https://doi.org/10.1039/B614121H + */ + + // Get n,m values for tube + n_ = ui_.NSpin->value(); + m_ = ui_.MSpin->value(); + + // Determine a0, the principal unit length of the structure, from the specified bond distance. See Figure 1a, noting that + // a1 == a2 == a0. + const auto r = ui_.BondLengthSpin->value(); + a0_ = r * root3; + + // Set principal vectors for reference + va1_ = Vector3(a0_, 0.0, 0.0); + va2_ = Vector3(a0_ * sin(oneSixthPi), a0_ * cos(oneSixthPi), 0.0); + + // Calculate repeat dimensions of the (n,m) sheet + // -- A is magnitude of vecA (equation 1) and represents our X dimension + A_ = a0_ * sqrt(n_ * n_ + m_ * m_ + n_ * m_); + // -- c is the magnitude of the vector perpendicular to vecA, along the tube axis, and represents our Y dimension + const auto M = std::gcd(2 * n_ + m_, n_ + 2 * m_); + c_ = sqrt(3.0) * A_ / M; + + // Determine angle alpha, describing the tilt of the sheet away from va1 (equation 3) + alpha_ = atan((sqrt(3.0) * m_) / (2 * n_ + m_)); + + // The radius of the tube is then the circumference (== A) divided by 2PI + radius_ = A_ / (2.0 * M_PI); + + dy_ = va2_.y / cos(alpha_); + H_ = round(c_ / dy_); +} + +// Find dangling atoms, defined as those which have two bonds spanning PBC of the box +std::map> CreateGrapheneSpeciesDialog::findDanglingAtoms(double localCutoff) +{ + std::map> atoms; + for (auto &i : species_.atoms()) + { + // Find all bound partners which are across the unit cell + std::vector pbcJ; + for (auto &b : i.bonds()) + { + auto *j = b.get().partner(&i); + if ((i.r() - j->r()).magnitude() > localCutoff) + pbcJ.push_back(j); + } + + if (pbcJ.size() == 2) + atoms[&i] = pbcJ; + } + + return atoms; +} + +// Get vector of atom keys from atom/neighbour map, sorted by position along indicated direction +std::vector +CreateGrapheneSpeciesDialog::getSortedByY(const std::map> &atoms) const +{ + std::vector sorted; + for (auto &&[i, _] : atoms) + sorted.push_back(i); + + std::sort(sorted.begin(), sorted.end(), [](const SpeciesAtom *a, const SpeciesAtom *b) { return a->r().y < b->r().y; }); + + return sorted; +} + +// Recursive branch function +void CreateGrapheneSpeciesDialog::extendBranch(SpeciesAtom *i, const Box *box, Vector3 &vFrac, + std::vector &branch, double localCutoff) const +{ + // Get PBC and non-PBC (local) bond partners for this atom and see what type of atom we have... + std::vector pbcJ, localJ; + for (auto &b : i->bonds()) + { + auto j = b.get().partner(i); + if ((i->r() - j->r()).magnitude() > localCutoff) + pbcJ.push_back(j); + else if (std::find(branch.begin(), branch.end(), j) == branch.end()) + localJ.push_back(j); + } + + // If all atoms are local this is a completely internally-bound atom, and we are done here. + if (pbcJ.size() == 0) + return; + + // Add ourselves to the branch + branch.push_back(i); + + // For all pbc atoms, increment the fractional direction + for (auto j : pbcJ) + vFrac += (box->getFractional(j->r()) - box->getFractional(i->r())); + + // For local atoms, recurse into them if we haven't visited them already + for (auto j : localJ) + extendBranch(j, box, vFrac, branch, localCutoff); +} + +// Regenerate species +void CreateGrapheneSpeciesDialog::regenerate() +{ + species_.clear(); + + const auto roll = ui_.RollUpCheck->isChecked(); + const auto cFactor = ui_.CFactorSpin->value(); + + // Determine a suitable periodic box for the species - we will always create one so that we get proper folding. + auto offset = Vector3(), cellLengths = Vector3(); + if (roll) + { + // Create some extra space and set an offset so the tube is central in XZ + cellLengths = {radius_ * 3, c_ * cFactor, radius_ * 3}; + offset = Vector3(radius_ * 1.5, 0.0, radius_ * 1.5); + } + else + { + cellLengths = {A_, c_ * cFactor, sheetZ_}; + offset = Vector3(0.0, 0.0, sheetZ_ * 0.5); + } + species_.createBox(cellLengths, {90, 90, 90}); + + /* + * Generate the full coordinates of the sheet. This process is based on equations 7 - 9, but does not follow it precisely. + * Specifically, the innermost loop to translate the primary helix pair is originally stated to run over j (here 'i') from + * 0 - (m-1) inclusive, but this does not generate the correct number of copies for most cases. Instead, the number of + * required helix copies 'H' is calculated from c and the rotated y component of va2 (see earlier). + */ + for (auto j = 0; j < n_ + m_; ++j) + { + // Primary helix atoms (equation 7) + auto x1j = j * a0_ * cos(alpha_); + auto y1j = -j * a0_ * sin(alpha_); + + // Secondary helix atoms (equation 8) + auto x2j = x1j - (a0_ / sqrt(3.0)) * cos(oneSixthPi - alpha_); + auto y2j = y1j - (a0_ / sqrt(3.0)) * sin(oneSixthPi - alpha_); + + // Create H copies of the helix pairs, multiplied by the extension factor along C + for (auto i = 0; i < H_ * cFactor; ++i) + { + // Generate translation vector for this copy (equation 9) + auto delta = Vector3(-i * a0_ * sin(oneSixthPi - alpha_), i * a0_ * cos(oneSixthPi - alpha_), 0.0); + auto r1 = delta + Vector3(x1j, y1j, 0.0); + auto r2 = delta + Vector3(x2j, y2j, 0.0); + + // Get new helix pair coordinates + Vector3 p1, p2; + if (roll) + { + // Wrap the X coordinate (== real position on circumference) onto a tube of radius 'radius', applying the + // offset we set earlier when creating the periodic box so as to put it in the centre of XZ. + p1 = species_.box()->fold( + offset + Vector3(radius_ * sin(2.0 * M_PI * r1.x / A_), r1.y, radius_ * cos(2.0 * M_PI * r1.x / A_))); + p2 = species_.box()->fold( + offset + Vector3(radius_ * sin(2.0 * M_PI * r2.x / A_), r2.y, radius_ * cos(2.0 * M_PI * r2.x / A_))); + } + else + { + p1 = species_.box()->fold(r1); + p2 = species_.box()->fold(r2); + } + + // Check for overlaps with existing atoms - easier and more efficient to do this now as we go. + auto add1 = true, add2 = true; + for (auto &existing : species_.atoms()) + { + if (add1) + add1 = (p1 - existing.r()).magnitude() > 0.1; + if (add2) + add2 = (p2 - existing.r()).magnitude() > 0.1; + if (!add1 && !add2) + break; + } + if (add1) + species_.addAtom(zA_, p1); + if (add2) + species_.addAtom(zB_, p2); + } + } + + // Finalise the species + if (ui_.PeriodicRadio->isChecked()) + { + species_.recalculateIntermolecularTerms(1.1); + } + else if (ui_.NonPeriodicRadio->isChecked()) + { + species_.recalculateIntermolecularTerms(1.1); + + if (ui_.TidyEndsCheck->isChecked()) + { + // Find all atoms which have two bonds spanning PBC of the box + auto localCutoff = ui_.BondLengthSpin->value() * 1.01; + const auto atoms = findDanglingAtoms(localCutoff); + auto sorted = getSortedByY(atoms); + + // Pass 1 - Move all atoms along the PBC bond vectors + while (!sorted.empty()) + { + auto i = sorted.back(); + auto &pbcJ = atoms.at(i); + + // Determine the fractional average vector to the pbc atoms + Vector3 vFrac; + for (auto j : pbcJ) + vFrac += species_.box()->getFractional(j->r()) - species_.box()->getFractional(i->r()); + + // Make this a sensible translation vector - divide elements by their abs value to make unitary and round + for (auto n = 0; n < 3; ++n) + vFrac[n] = fabs(vFrac[n]) < 0.5 ? 0.0 : round(vFrac[n] / fabs(vFrac[n])); + vFrac.multiply(cellLengths); + + // Translate the atom + i->setCoordinates(i->r() + vFrac); + + // Remove this atom from the vector, along with any that were in its pbc neighbour lists + for (auto j : pbcJ) + { + auto it = std::ranges::find(sorted, j); + if (it != sorted.end()) + sorted.erase(it); + } + + sorted.pop_back(); + } + + // Pass 2 - We may have generated some "branches" inadvertently, so rebond, find any singly-bound atoms and check + auto branchEnd = findDanglingAtoms(localCutoff); + std::vector indicesToRemove; + for (auto &&[i, _] : branchEnd) + { + // For this atom we will step along bonds until we find an atom with three non-PBC bonds - this marks a fully + // "internal" atom which does not need (and should not be) translated, and the end of the linear branch we're + // interested in. Along the way we maintain a fractional translation vector based on all PBC bonds we encounter + // which will inform the direction we might want to move the branch. Or we could just remove it. + + Vector3 vFrac; + std::vector branch; + extendBranch(i, species_.box(), vFrac, branch, localCutoff); + auto maxEl = vFrac.absMaxElement(); + Vector3 tVec; + tVec.set(maxEl, round(vFrac.get(maxEl) / fabs(vFrac.get(maxEl)))); + tVec.multiply(cellLengths); + ; + + // Translate or remove the branch? + for (auto j : branch) + if (ui_.RemoveBranchesCheck->isChecked()) + indicesToRemove.push_back(j->index()); + else + j->setCoordinates(j->r() + tVec); + } + + // Final tidy-up - remove any branch atoms if required + species_.removeAtoms(indicesToRemove); + } + + species_.removeBox(); + species_.recalculateIntermolecularTerms(1.1); + + // Terminate? + if (ui_.TerminateCheck->isChecked()) + { + auto rT = ui_.TerminateBondLengthSpin->value(); + auto excludeA = !ui_.TerminateACheck->isChecked(); + auto excludeB = !ui_.TerminateBCheck->isChecked(); + + // Any atom with just two bonds can be terminated + for (auto &i : species_.atoms()) + { + if ((i.nBonds() != 2) || (excludeA && i.Z() == zA_) || (excludeB && i.Z() == zB_)) + continue; + + // Get average bond vector + auto v = (i.r() - i.bond(0).partner(&i)->r()) + (i.r() - i.bond(1).partner(&i)->r()); + v.normalise(); + + species_.addAtom(zTerminate_, i.r() + v * rT); + } + + species_.recalculateIntermolecularTerms(1.1); + } + } + else + { + species_.recalculateIntermolecularTerms(1.1); + species_.removeBox(); + } +} + +/* + * UI + */ + +// Update all controls +void CreateGrapheneSpeciesDialog::updateWidgets() +{ + Locker updateLock(widgetsUpdating_); + + // Sheet properties + ui_.ALabel->setText(QString("%1 \u212B").arg(A_, 0, 'f', 3)); + ui_.CLabel->setText(QString("%1 (%2) \u212B").arg(c_, 0, 'f', 3).arg(c_ * ui_.CFactorSpin->value(), 0, 'f', 3)); + ui_.AlphaLabel->setText(QString("%1\u00B0").arg(DissolveMath::toDegrees(alpha_), 0, 'f', 3)); + ui_.HLabel->setText(QString("%1 (%2)").arg(H_).arg(H_ * ui_.CFactorSpin->value())); + ui_.RadiusLabel->setText(QString("%1 \u212B").arg(radius_, 0, 'f', 3)); + + // Final cell properties + ui_.CellALabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().x, 0, 'f', 3)); + ui_.CellBLabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().y, 0, 'f', 3)); + ui_.CellCLabel->setText(QString("%1 \u212B").arg(species_.box()->axisLengths().z, 0, 'f', 3)); + + // Configuration information + const auto *box = species_.box(); + ui_.CurrentBoxTypeLabel->setText(QString::fromStdString(std::string(Box::boxTypes().keyword(box->type())))); + QString boxInfo = QString("A: %1 Å
").arg(box->axisLengths().x); + boxInfo += QString("B: %1 Å
").arg(box->axisLengths().y); + boxInfo += QString("C: %1 Å
").arg(box->axisLengths().z); + boxInfo += QString("α: %1°
").arg(box->axisAngles().x); + boxInfo += QString("β: %1°
").arg(box->axisAngles().y); + boxInfo += QString("γ: %1°").arg(box->axisAngles().z); + ui_.CurrentBoxFrame->setToolTip(boxInfo); + + ui_.AtomPopulationLabel->setText(QString::number(species_.nAtoms())); + + // Structure + ui_.StructureViewer->postRedisplay(); +} + +void CreateGrapheneSpeciesDialog::on_NSpin_valueChanged(int value) +{ + if (widgetsUpdating_.isLocked()) + return; + + // MSpin's upper value is our current value + ui_.MSpin->setMaximum(value); + + calculateParameters(); + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_MSpin_valueChanged(int value) +{ + calculateParameters(); + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_ElementAButton_clicked(bool checked) +{ + auto Z = selectElementDialog_.selectElement(zA_); + if (Z == Elements::Unknown) + return; + zA_ = Z; + ui_.ElementAButton->setText(QString::fromStdString(std::string(Elements::symbol(zA_)))); + + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_ElementBButton_clicked(bool checked) +{ + auto Z = selectElementDialog_.selectElement(zB_); + if (Z == Elements::Unknown) + return; + zB_ = Z; + ui_.ElementBButton->setText(QString::fromStdString(std::string(Elements::symbol(zB_)))); + + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_BondLengthSpin_valueChanged(double value) +{ + calculateParameters(); + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_CFactorSpin_valueChanged(int value) +{ + calculateParameters(); + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_RollUpCheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_PeriodicRadio_clicked(bool checked) +{ + if (widgetsUpdating_) + return; + + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_PseudoPeriodicRadio_clicked(bool checked) +{ + if (widgetsUpdating_) + return; + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_NonPeriodicRadio_clicked(bool checked) +{ + if (widgetsUpdating_) + return; + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TidyEndsCheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_RemoveBranchesCheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TerminateCheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TerminateElementButton_clicked(bool checked) +{ + auto Z = selectElementDialog_.selectElement(zB_); + if (Z == Elements::Unknown) + return; + zTerminate_ = Z; + ui_.TerminateElementButton->setText(QString::fromStdString(std::string(Elements::symbol(zTerminate_)))); + + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TerminateBondLengthSpin_valueChanged(double value) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TerminateACheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_TerminateBCheck_clicked(bool checked) +{ + regenerate(); + updateWidgets(); +} + +void CreateGrapheneSpeciesDialog::on_OKButton_clicked(bool checked) +{ + // Copy the species to the main Dissolve instance and set its new name + auto *sp = dissolve_.coreData().copySpecies(&species_); + sp->setName(std::format("Nanotube-({},{})", ui_.NSpin->value(), ui_.MSpin->value())); + + accept(); +} + +void CreateGrapheneSpeciesDialog::on_CancelButton_clicked(bool checked) { reject(); } \ No newline at end of file diff --git a/src/gui/createGrapheneSpeciesDialog.h b/src/gui/createGrapheneSpeciesDialog.h new file mode 100644 index 0000000000..49de0954c4 --- /dev/null +++ b/src/gui/createGrapheneSpeciesDialog.h @@ -0,0 +1,112 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// Copyright (c) 2026 Team Dissolve and contributors + +#pragma once + +#include "base/lock.h" +#include "gui/models/cifAssemblyModel.h" +#include "gui/selectElementDialog.h" +#include "gui/ui_createGrapheneSpeciesDialog.h" +#include "gui/wizard.h" +#include "main/dissolve.h" +#include + +// Forward Declarations +class Dissolve; +class Species; + +// Create Graphene Species Dialog +class CreateGrapheneSpeciesDialog : public QDialog +{ + Q_OBJECT + + public: + CreateGrapheneSpeciesDialog(QWidget *parent, Dissolve &dissolve); + ~CreateGrapheneSpeciesDialog() = default; + + private: + // Main form declaration + Ui::CreateGrapheneSpeciesDialog ui_; + // Temporary core data + CoreData temporaryCoreData_; + + /* + * Data + */ + private: + // Main Dissolve object + Dissolve &dissolve_; + // Elements in nanotube + Elements::Element zA_{Elements::Element::C}, zB_{Elements::Element::N}, zTerminate_{Elements::H}; + // Generated nanotube species + Species species_; + // Chirality parameters + int n_{0}, m_{0}; + // Sheet width (A) and height (c) + double A_{0.0}, c_{0.0}; + // Representative unit length + double a0_{0.0}; + // Principal vectors + Vector3 va1_, va2_; + // Angle between principal vector va1 and the sheet vector + double alpha_{0.0}; + // Radius of resulting tube + double radius_{0.0}; + // Delta along y between helices + double dy_{0.0}; + // Number of helices required + int H_{0}; + // Default size of unit cell for sheet + const double sheetZ_{10.0}; + + private: + // Calculate parameters + void calculateParameters(); + // Find dangling atoms, defined as those which have two bonds spanning PBC of the box + std::map> findDanglingAtoms(double localCutoff); + // Get vector of atom keys from atom/neighbour map, sorted by position along y + std::vector getSortedByY(const std::map> &atoms) const; + // Recursive branch function + void extendBranch(SpeciesAtom *i, const Box *box, Vector3 &vFrac, std::vector &branch, + double localCutoff) const; + // Regenerate species + void regenerate(); + + /* + * UI + */ + private: + // Widget update lock + Lock widgetsUpdating_; + // Element selection dialog + SelectElementDialog selectElementDialog_; + + private: + // Update all controls + void updateWidgets(); + + private Q_SLOTS: + // Sheet Definition + void on_NSpin_valueChanged(int value); + void on_MSpin_valueChanged(int value); + void on_ElementAButton_clicked(bool checked); + void on_ElementBButton_clicked(bool checked); + void on_BondLengthSpin_valueChanged(double value); + // Sheet Transforms + void on_CFactorSpin_valueChanged(int value); + void on_RollUpCheck_clicked(bool checked); + // Output Options + void on_PeriodicRadio_clicked(bool checked); + void on_PseudoPeriodicRadio_clicked(bool checked); + void on_NonPeriodicRadio_clicked(bool checked); + void on_TidyEndsCheck_clicked(bool checked); + void on_RemoveBranchesCheck_clicked(bool checked); + void on_TerminateCheck_clicked(bool checked); + void on_TerminateElementButton_clicked(bool checked); + void on_TerminateBondLengthSpin_valueChanged(double value); + void on_TerminateACheck_clicked(bool checked); + void on_TerminateBCheck_clicked(bool checked); + // Dialog + void on_OKButton_clicked(bool checked); + void on_CancelButton_clicked(bool checked); +}; \ No newline at end of file diff --git a/src/gui/createGrapheneSpeciesDialog.ui b/src/gui/createGrapheneSpeciesDialog.ui new file mode 100644 index 0000000000..8cea452017 --- /dev/null +++ b/src/gui/createGrapheneSpeciesDialog.ui @@ -0,0 +1,1014 @@ + + + CreateGrapheneSpeciesDialog + + + Qt::ApplicationModal + + + + 0 + 0 + 1227 + 835 + + + + + 10 + + + + Create Graphene Species + + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + + + 4 + + + + + + 0 + 0 + + + + + 4 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Sheet Definition + + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + + + N + + + + + + + 1 + + + 1000 + + + 5 + + + + + + + M + + + + + + + 0 + + + 1000 + + + 0 + + + + + + + Element A + + + + + + + ElementA + + + + + + + Element B + + + + + + + ElementB + + + + + + + Bond Length + + + + + + + 3 + + + 0.100000000000000 + + + 0.010000000000000 + + + 1.420000000000000 + + + + + + + Qt::Horizontal + + + + + + + + 10 + true + + + + Sheet repeat dimension along x, or circumference if rolled into a tube + + + A + + + + + + + Sheet repeat dimension along x, or circumference if rolled into a tube + + + 0 + + + + + + + + 10 + true + + + + Axial length of sheet along the y direction + + + c + + + + + + + Axial length of sheet along the y direction + + + 0 + + + + + + + + 10 + true + + + + Angle alpha between principal vector a1 and the x axis of the repeat unit cell + + + ɑ + + + + + + + Angle alpha between principal vector a1 and the x axis of the repeat unit cell + + + 0 + + + + + + + + 10 + true + + + + Number of repeated translations of the primary helix required (adjusted value in brackets) + + + H + + + + + + + Number of repeated translations of the primary helix required (adjusted value in brackets) + + + 0 + + + + + + + + + + Sheet Transforms + + + + 4 + + + 4 + + + 4 + + + 4 + + + + + Whether to roll up the sheet about the y axis to form a nanotube + + + Roll + + + + + + + + 10 + true + + + + Radius, if rolled into a nanotube + + + Radius + + + + + + + Radius, if rolled into a nanotube + + + 0 + + + + + + + Multiplier for the sheet along the c axis + + + c Factor + + + + + + + Multiplier for the sheet along the c axis + + + 1 + + + 100 + + + + + + + + + + + 0 + 0 + + + + Cell Properties + + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + + + + 0 + 0 + + + + + 10 + true + + + + A + + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + + + + + + + + 0 + 0 + + + + + 10 + true + + + + B + + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + + + + + + + + 0 + 0 + + + + + 10 + true + + + + C + + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + + + + + + + 0.0 + + + + + + + 0.0 + + + + + + + 0.0 + + + + + + + + + + Output Options + + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + + + Periodic + + + true + + + + + + + Pseudo-periodic + + + + + + + Non-periodic + + + false + + + + + + + + + Qt::Horizontal + + + QSizePolicy::Fixed + + + + 20 + 20 + + + + + + + + 4 + + + + + Tidy the ends of non-periodic sheets, moving dangling atoms to leave complete rings + + + Tidy Ends + + + true + + + + + + + Whether to remove any remaining branches rather than try to translate them into a meaningful position (requires Tidy Ends) + + + Remove branches + + + + + + + Terminate? + + + + + + + + + Qt::Horizontal + + + QSizePolicy::Fixed + + + + 20 + 20 + + + + + + + + + + Element + + + + + + + ElementA + + + + + + + Bond Length + + + + + + + 3 + + + 0.100000000000000 + + + 0.010000000000000 + + + 1.000000000000000 + + + + + + + Terminate A + + + true + + + + + + + Terminate B + + + true + + + + + + + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + 1 + 0 + + + + + + + Preview + + + + 4 + + + 4 + + + 4 + + + 4 + + + 4 + + + + + 4 + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + QFrame::StyledPanel + + + QFrame::Sunken + + + + 4 + + + 2 + + + 2 + + + 2 + + + 2 + + + + + false + + + ... + + + + :/general/icons/configuration.svg:/general/icons/configuration.svg + + + true + + + + + + + + 0 + 0 + + + + + 10 + false + + + + Orthorhombic + + + Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter + + + + + + + + + + Number of atoms in the configuration + + + QFrame::StyledPanel + + + QFrame::Sunken + + + + 4 + + + 2 + + + 2 + + + 2 + + + 2 + + + + + false + + + ... + + + + :/general/icons/spheres_on.svg:/general/icons/spheres_on.svg + + + true + + + + + + + + 0 + 0 + + + + 0 + + + + + + + + + + + + + 3 + 0 + + + + + 300 + 300 + + + + QFrame::StyledPanel + + + QFrame::Sunken + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + 1 + 0 + + + + + + + + + + + + + + + + + + + Qt::Horizontal + + + + + + + 4 + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + 10 + true + + + + Cancel + + + + + + + + 10 + true + + + + OK + + + + + + + + + + SpeciesViewer + QWidget +
gui/speciesViewer.h
+ 1 + + + + NSpin + MSpin + ElementAButton + ElementBButton + BondLengthSpin + CancelButton + OKButton + CurrentBoxToolButton + AtomPopulationToolButton + + + + + + \ No newline at end of file diff --git a/src/gui/gui.h b/src/gui/gui.h index 451d55d26a..37ae3b6a2b 100644 --- a/src/gui/gui.h +++ b/src/gui/gui.h @@ -166,7 +166,7 @@ class DissolveWindow : public QMainWindow void on_SpeciesCreateAtomicAction_triggered(bool checked); void on_SpeciesCreateDrawAction_triggered(bool checked); void on_SpeciesCreateFromExistingAction_triggered(bool checked); - // void on_SpeciesCreateGrapheneAction_triggered(bool checked); + void on_SpeciesCreateGrapheneAction_triggered(bool checked); void on_SpeciesImportFromDissolveAction_triggered(bool checked); void on_SpeciesImportFromXYZAction_triggered(bool checked); void on_SpeciesImportLigParGenAction_triggered(bool checked); diff --git a/src/gui/menu_species.cpp b/src/gui/menu_species.cpp index f7a66a853e..bf77faf085 100644 --- a/src/gui/menu_species.cpp +++ b/src/gui/menu_species.cpp @@ -94,7 +94,6 @@ void DissolveWindow::on_SpeciesCreateFromExistingAction_triggered(bool checked) dissolve_.coreData().removeSpecies(newSpecies); } -/* DISSOLVE 2 TODO void DissolveWindow::on_SpeciesCreateGrapheneAction_triggered(bool checked) { CreateGrapheneSpeciesDialog createGrapheneSpeciesDialog(this, dissolve_); @@ -108,7 +107,7 @@ void DissolveWindow::on_SpeciesCreateGrapheneAction_triggered(bool checked) ui_.MainTabs->setCurrentTab(dissolve_.coreData().species().back().get()); } } -*/ + void DissolveWindow::on_SpeciesImportFromDissolveAction_triggered(bool checked) { ImportSpeciesDialog importSpeciesDialog(this, dissolve_); From d94b877d6cbf3a0b97e212edf9c78aae4f6e8cfd Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Mon, 11 May 2026 16:42:22 +0100 Subject: [PATCH 20/22] use message --- src/nodes/cif/importCIFStructure.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index c1bf0e87d4..e551d24ee1 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -529,7 +529,7 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou structure_.addBond(i, j); } - Messenger::print("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", + message("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", structure_.nAtoms(), structure_.bonds().size()); return true; } From e456cbe9430356410780b606bd646af46ad4e93d Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Tue, 12 May 2026 09:13:51 +0100 Subject: [PATCH 21/22] clang format --- src/nodes/cif/importCIFStructure.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index e551d24ee1..ba189cdfdd 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -530,7 +530,7 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou } message("Created basic structure - {} structure atoms, {} structure bonds found whle parsing the CIF.\n", - structure_.nAtoms(), structure_.bonds().size()); + structure_.nAtoms(), structure_.bonds().size()); return true; } From d2616d3155554e532256488efaf5d3f91f662af0 Mon Sep 17 00:00:00 2001 From: RobBuchanan Date: Wed, 13 May 2026 16:46:50 +0100 Subject: [PATCH 22/22] remove prevent metallic bonding --- src/nodes/cif/importCIFStructure.cpp | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/nodes/cif/importCIFStructure.cpp b/src/nodes/cif/importCIFStructure.cpp index ba189cdfdd..a20c8ef049 100644 --- a/src/nodes/cif/importCIFStructure.cpp +++ b/src/nodes/cif/importCIFStructure.cpp @@ -515,10 +515,6 @@ bool ImportCIFStructureNode::createStructure(SpaceGroups::SpaceGroupId sgid, dou auto i = structure_.atomAt(indexI); auto j = structure_.atomAt(indexJ); - // Prevent metallic bonding? - if (Elements::isMetallic(i->Z()) && Elements::isMetallic(j->Z())) - continue; - // Retrieve distance auto atomTypeIdxI = i->atomTypeIndex(); auto atomTypeIdxJ = j->atomTypeIndex();