Support custom variables for the LAMMPS input files #70
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -35,7 +35,16 @@ | |
| # def gen_equi_header(nsteps, prt_freq, dump_freq, temp, pres, tau_t, tau_p, mass_map, conf_file): | ||
| # def gen_equi_header(nsteps, prt_freq, dump_freq, temp, pres, tau_t, tau_p, mass_map, conf_file): | ||
| def gen_equi_header( | ||
| nsteps, | ||
| thermo_freq, | ||
| dump_freq, | ||
| mass_map, | ||
| temp, | ||
| tau_t, | ||
| tau_p, | ||
| equi_conf, | ||
| pres=None, | ||
| custom_variables=None, | ||
| ): | ||
| ret = "" | ||
| ret += "clear\n" | ||
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@@ -45,6 +54,9 @@ | |
| ret += "variable DUMP_FREQ equal %d\n" % dump_freq | ||
| ret += "variable NREPEAT equal ${NSTEPS}/${DUMP_FREQ}\n" | ||
| ret += f"variable TEMP equal {temp:.6f}\n" | ||
| if custom_variables is not None: | ||
| for key, value in custom_variables.items(): | ||
| ret += f"variable {key} equal {value}\n" | ||
|
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There was a problem hiding this comment. Reminder: Add tests for The new code for handling Do you want me to generate the unit testing code or open a GitHub issue to track this task? ToolsGitHub Check: codecov/patch
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| # if equi_settings['pres'] is not None : | ||
| if pres is not None: | ||
| ret += f"variable PRES equal {pres:.6f}\n" | ||
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@@ -64,7 +76,7 @@ | |
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| # def gen_equi_force_field(model, if_meam=None): | ||
| def gen_equi_force_field(model, if_meam=False, meam_model=None, append=None): | ||
|
There was a problem hiding this comment. Reminder: Add tests for The new code for handling the Do you want me to generate the unit testing code or open a GitHub issue to track this task? ToolsGitHub Check: codecov/patch
There was a problem hiding this comment. @Yi-FanLi, here are the unit tests for the import unittest
from dpti.equi import gen_equi_force_field
class TestGenEquiForceField(unittest.TestCase):
def test_gen_equi_force_field_with_append(self):
model = "model.pb"
append = "extra_params"
expected_output = "pair_style deepmd model.pb extra_params\npair_coeff * *\n"
result = gen_equi_force_field(model, append=append)
self.assertEqual(result, expected_output)
def test_gen_equi_force_field_without_append(self):
model = "model.pb"
expected_output = "pair_style deepmd model.pb\npair_coeff * *\n"
result = gen_equi_force_field(model)
self.assertEqual(result, expected_output)
def test_gen_equi_force_field_with_meam(self):
model = "model.pb"
meam_model = {
"library": "library.meam",
"potential": "potential.meam",
"element": "element"
}
expected_output = (
"pair_style meam\n"
"pair_coeff * * library.meam element potential.meam element\n"
)
result = gen_equi_force_field(model, if_meam=True, meam_model=meam_model)
self.assertEqual(result, expected_output)
if __name__ == "__main__":
unittest.main()This test suite covers the following scenarios:
These tests ensure that the There was a problem hiding this comment. Can you commit these changes? There was a problem hiding this comment. @Yi-FanLi, I cannot commit the changes directly. However, you can easily add the provided unit tests to your codebase. Here are the steps:
If you need any further assistance, feel free to ask! Learnings added
Learnings usedThere was a problem hiding this comment. Reminder: Add tests for The new code for handling the Do you want me to generate the unit testing code or open a GitHub issue to track this task? ToolsGitHub Check: codecov/patch
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| # equi_settings = | ||
| # model = equi_settings['model'] | ||
| # assert type(model) is dict, f"equi_settings['model] must be a dict. model:{model}" | ||
|
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@@ -82,7 +94,10 @@ | |
| ret = "" | ||
| ret += "# --------------------- FORCE FIELDS ---------------------\n" | ||
| if not if_meam: | ||
| ret += f"pair_style deepmd {model}" | ||
| if append is not None: | ||
| ret += " " + append | ||
| ret += "\n" | ||
| ret += "pair_coeff * *\n" | ||
| else: | ||
| meam_library = meam_model["library"] | ||
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@@ -161,6 +176,8 @@ | |
| pres=None, | ||
| if_meam=False, | ||
| meam_model=None, | ||
| custom_variables=None, | ||
| append=None, | ||
|
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There was a problem hiding this comment. Reminder: Add tests for new parameters. The new parameters Do you want me to generate the unit testing code or open a GitHub issue to track this task? There was a problem hiding this comment. @Yi-FanLi, I've added the following unit tests to cover the new
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| ): | ||
| if dump_freq is None: | ||
| dump_freq = thermo_freq | ||
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@@ -174,9 +191,10 @@ | |
| tau_p=tau_p, | ||
| equi_conf=equi_conf, | ||
| pres=pres, | ||
| custom_variables=custom_variables, | ||
| ) | ||
| equi_force_field = gen_equi_force_field( | ||
| model, if_meam=if_meam, meam_model=meam_model, append=append | ||
| ) | ||
| equi_thermo_settings = gen_equi_thermo_settings(timestep=timestep) | ||
| equi_dump_settings = gen_equi_dump_settings(if_dump_avg_posi=if_dump_avg_posi) | ||
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@@ -422,6 +440,8 @@ | |
| pres=equi_settings["pres"], | ||
| if_meam=equi_settings["if_meam"], | ||
| meam_model=equi_settings["meam_model"], | ||
| custom_variables=equi_settings.get("custom_variables", None), | ||
| append=equi_settings.get("append", None), | ||
| ) | ||
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| with open(os.path.join(task_abs_dir, "in.lammps"), "w") as fp: | ||
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Reminder: Add tests for
custom_variableshandling.The new code for handling
custom_variablesis not covered by tests.Do you want me to generate the unit testing code or open a GitHub issue to track this task?
Tools
GitHub Check: codecov/patch
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yes
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@Yi-FanLi, I've generated the unit test for the
custom_variableshandling in thegen_equi_headerfunction.Here is the new unit test code:
This test case verifies that the
gen_equi_headerfunction correctly includes custom variables in the generated output string.Learnings added
Learnings used