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docs: explain LAMMPS exploration extra files #393

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3 changes: 3 additions & 0 deletions docs/input.md
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Original file line number Diff line number Diff line change
Expand Up @@ -99,6 +99,7 @@ This section defines how the configuration space is explored.
"_comment" : "stage 0, task group 0",
"type" : "lmp-md",
"ensemble": "nvt", "nsteps": 50, "temps": [50, 100], "trj_freq": 10,
"input_extra_files": ["assets/dp/SiC_ZBL.txt"],
"conf_idx": [0], "n_sample" : 3
},
{
Expand Down Expand Up @@ -131,6 +132,8 @@ The {dargs:argument}`"stages"<explore[lmp]/stages>` defines the exploration stag

The {dargs:argument}`"n_sample"<task_group[lmp-md]/n_sample>` tells the number of confgiruations randomly sampled from the set picked by {dargs:argument}`"conf_idx"<task_group[lmp-md]/conf_idx>` from {dargs:argument}`"configurations"<explore[lmp]/configurations>` for each exploration task. All configurations has the equal possibility to be sampled. The default value of `"n_sample"` is `null`, in this case all picked configurations are sampled. In the example, we have 3 samples for stage 0 task group 0 and 2 thermodynamic states (NVT, T=50 and 100K), then the task group has 3x2=6 NVT DPMD tasks.

The {dargs:argument}`"input_extra_files"<task_group[lmp-md]/input_extra_files>` list copies each named file into every exploration task directory. The file is available there by its basename. For example, a DP-ZBL model using `use_srtab` should list its ZBL table here and reference `SiC_ZBL.txt` from the model configuration.


### FP

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19 changes: 19 additions & 0 deletions tests/exploration/test_make_task_group_from_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,8 @@

class TestMakeLmpTaskGroupFromConfig(unittest.TestCase):
def setUp(self):
self.extra_file = Path("SiC_ZBL.txt")
self.extra_file.write_text("ZBL table content\n")
self.config_npt = {
"type": "lmp-md",
"Ts": [100],
Expand All @@ -51,13 +53,30 @@ def setUp(self):

def tearDown(self):
os.remove(self.config_template["lmp_template_fname"])
self.extra_file.unlink()

def test_npt(self):
tgroup = make_lmp_task_group_from_config(
self.numb_models, self.mass_map, self.config_npt
)
self.assertTrue(isinstance(tgroup, NPTTaskGroup))

def test_npt_copies_input_extra_files_to_each_task(self):
config = {
**self.config_npt,
"input_extra_files": [str(self.extra_file)],
}
tgroup = make_lmp_task_group_from_config(
self.numb_models, self.mass_map, config
)
tgroup.set_conf(["LAMMPS configuration"])
tgroup.make_task()

self.assertEqual(
tgroup[0].files()[self.extra_file.name],
"ZBL table content\n",
)

def test_template(self):
tgroup = make_lmp_task_group_from_config(
self.numb_models, self.mass_map, self.config_template
Expand Down