Lammps template for MD+MC by wujing81 · Pull Request #1149 · deepmodeling/dpgen

wujing81 · 2023-03-09T01:56:19Z

Lammps template for MD+MC

for more information, see https://pre-commit.ci

Vibsteamer

The attatched param.json together with the template now dump-and-check in one loop_step:

50 MC snapshots from the last MD_snapshot in the last loop, many of them are repeated images as being not accepted by Metroplis criterion.
then, 100 MD snapshots from the last accepted MC_snapshot.

the sampling weights (then candidates and labelds) on physical structures could be correspondingly biased,

Please make sure this is of your expectation.

Vibsteamer · 2023-03-09T04:27:40Z

+
+# read in the potentia
+pair_style      deepmd ../graph.001.pb ../graph.000.pb ../graph.003.pb ../graph.002.pb  out_freq ${THERMO_FREQ} out_file model_devi.out
+pair_coeff


pair_coeff
--> pair coeff * *

to be compatible with the latest version of lammps

njzjz-bot

Verdict: Changes requested. The template contains a reproducible LAMMPS syntax error and cannot run. Previously reported issues involving pair_coeff and the sampling weight of repeated MC configurations are also unresolved. The branch is old and has no checks; I recommend rebuilding this example on the current template system with a smoke test.

Note: The Codex quota is about to reset, so I am using the remaining tokens to review all open PRs in this repository.

Coding agent: Codex
Codex version: codex-cli 0.144.6
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-10T14:21:55Z

+run             ${MC_NSTEPS}
+unfix           mc1
+
+velocity        all create ${TEMP_MD} ${RANDOM_SEED}"


[Blocking] The extra quote after the random seed makes LAMMPS fail immediately with Unmatched double quote in command; I reproduced this with LAMMPS 22 Jul 2025. Please change it to:

Suggested change

velocity all create ${TEMP_MD} ${RANDOM_SEED}"

velocity all create ${TEMP_MD} ${RANDOM_SEED}

The MC seed is also hard-coded to 500 and should be parameterized separately. In addition, dumping after rejected swaps produces repeated configurations, so the intended sampling weight should be documented or the frames should be deduplicated.

njzjz-bot

Independent review C

REQUEST_CHANGES. The added example is not runnable as written: its LAMMPS input contains an incomplete dump command and a malformed velocity command. These are direct syntax failures in the primary asset introduced by the PR.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:29:48Z

+# output observables
+thermo_style    custom step temp pe ke etotal press vol lx ly lz xy xz yz
+thermo          ${THERMO_FREQ}
+dump            dpgen_dump


This is not a valid LAMMPS dump command: after the dump ID, LAMMPS requires at least the group, style, frequency, and output file (plus style-specific fields). The example will stop while parsing this line, before either MC or MD runs. Please provide a complete trajectory dump compatible with DP-GEN frame collection.

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:29:48Z

+run             ${MC_NSTEPS}
+unfix           mc1
+
+velocity        all create ${TEMP_MD} ${RANDOM_SEED}"


The unmatched trailing quote becomes part of the random-seed token and makes the command invalid LAMMPS syntax.

Suggested change

velocity all create ${TEMP_MD} ${RANDOM_SEED}"

velocity all create ${TEMP_MD} ${RANDOM_SEED}

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot

Independent review A

Blocking LAMMPS syntax findings are attached inline. As committed, the example cannot reach its MC/MD loop.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:38:19Z

@@ -0,0 +1,55 @@
+variable        MD_NSTEPS         equal MD_NSTEPS


P1: The revision matrix replaces tokens such as ${MD_NSTEPS}, but these declarations use bare self-references (equal MD_NSTEPS, equal MC_NSTEPS, equal TEMP_MD, and so on). Those bare names remain after revise_by_keys and LAMMPS reports an invalid thermo keyword when the variable is evaluated. Use the same ${...} placeholders in each affected declaration (MD/MC steps, temperatures, random seed, element types, and loop count) so DP-GEN substitutes numeric values before execution.

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:38:19Z

+run             ${MC_NSTEPS}
+unfix           mc1
+
+velocity        all create ${TEMP_MD} ${RANDOM_SEED}"


P1: The unmatched trailing quote makes this velocity command invalid LAMMPS syntax.

Suggested change

velocity all create ${TEMP_MD} ${RANDOM_SEED}"

velocity all create ${TEMP_MD} ${RANDOM_SEED}

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot

Independent review B

Requesting changes because the template placeholders are not substituted and a generated LAMMPS command has an unmatched quote.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:39:05Z

+variable        MD_NSTEPS         equal MD_NSTEPS
+variable        MC_NSTEPS         equal MC_NSTEPS
+variable        THERMO_FREQ       equal 10
+variable        TEMP_MD           equal TEMP_MD
+variable        TEMP_MC           equal TEMP_MC
+variable        PRES              equal press
+variable        TAU_T             equal 0.100000
+variable        TAU_P             equal 0.500000
+variable        RANDOM_SEED       equal RANDOM_SEED
+variable        ELEMENT_TYPE_1    equal ELEMENT_TYPE_1
+variable        ELEMENT_TYPE_2    equal ELEMENT_TYPE_2
+variable        N_LOOP            equal N_LOOP


rev_mat searches for the literal ${...} keys configured in param.json, but most variables in this block omit that syntax. They remain self-referential expressions such as equal MD_NSTEPS and fail when LAMMPS evaluates them. Use the configured placeholders throughout.\n\nsuggestion\nvariable MD_NSTEPS equal ${MD_NSTEPS}\nvariable MC_NSTEPS equal ${MC_NSTEPS}\nvariable THERMO_FREQ equal 10\nvariable TEMP_MD equal ${TEMP_MD}\nvariable TEMP_MC equal ${TEMP_MC}\nvariable PRES equal ${PRES}\nvariable TAU_T equal 0.100000\nvariable TAU_P equal 0.500000\nvariable RANDOM_SEED equal ${RANDOM_SEED}\nvariable ELEMENT_TYPE_1 equal ${ELEMENT_TYPE_1}\nvariable ELEMENT_TYPE_2 equal ${ELEMENT_TYPE_2}\nvariable N_LOOP equal ${N_LOOP}\n

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot · 2026-08-29T15:39:05Z

+run             ${MC_NSTEPS}
+unfix           mc1
+
+velocity        all create ${TEMP_MD} ${RANDOM_SEED}"


The trailing quote is unmatched, so this generated LAMMPS input cannot be parsed.\n\nsuggestion\nvelocity all create ${TEMP_MD} ${RANDOM_SEED}\n

Fixed in a2129ad by using revision-matrix placeholders consistently, completing the trajectory dump, and removing the unmatched quote. Pre-commit follow-up f759dc4 retains the fix. Validation: the MC+MD example regression test passed.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

Coding-Agent: Codex Codex-Version: codex-cli 0.151.0 Model: gpt-5.6-sol Reasoning-Effort: xhigh

for more information, see https://pre-commit.ci

njzjz-bot

The LAMMPS template findings were addressed in a2129ad and retained by pre-commit follow-up f759dc4. Placeholder substitution, dump syntax, and velocity syntax are covered by a passing regression test; pre-commit passes.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot

Independent re-review C

No blocking issues found; the LAMMPS dump and velocity commands are now syntactically complete.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot

Independent re-review B

Reviewed the parameter file and LAMMPS template against the current revision-matrix path, strict DP-GEN argument validation, model-file substitution behavior, and the regression test. I found no blocking correctness issue in the example and approve this head.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

njzjz-bot

Independent re-review A

Approved at f759dc4. I checked the revision-matrix placeholders, LAMMPS variable expansion, atom/swap syntax, dump command, JSON structure, and regression test.

Coding agent: Codex
Codex version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

wujing81 and others added 2 commits March 8, 2023 10:49

Lammps template for MD+MC

7b2beda

[pre-commit.ci] auto fixes from pre-commit.com hooks

2ae7756

for more information, see https://pre-commit.ci

wanghan-iapcm requested a review from Vibsteamer March 9, 2023 03:01

Vibsteamer suggested changes Mar 9, 2023

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njzjz-bot suggested changes Aug 10, 2026

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njzjz-bot suggested changes Aug 29, 2026

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njzjz-bot and others added 2 commits August 30, 2026 00:21

fix: make MC and MD LAMMPS template runnable

a2129ad

Coding-Agent: Codex Codex-Version: codex-cli 0.151.0 Model: gpt-5.6-sol Reasoning-Effort: xhigh

[pre-commit.ci] auto fixes from pre-commit.com hooks

f759dc4

for more information, see https://pre-commit.ci

njzjz-bot approved these changes Aug 29, 2026

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	velocity all create ${TEMP_MD} ${RANDOM_SEED}"
	velocity all create ${TEMP_MD} ${RANDOM_SEED}

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