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And example CLI command and fix small bugs #91

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1fcd98d
fix unittests
felix5572 May 23, 2025
8eb9a7e
fix hti_water, support both old and newer version
felix5572 Jun 11, 2025
30e985f
add workflows module (mainly implement via prefect)
felix5572 Jun 11, 2025
c8abe54
update Sn example provide more concrete commands
felix5572 Jun 11, 2025
cffdc41
update graph.pb download link
felix5572 Jun 11, 2025
0deff46
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2025
effdd95
fix hti.py support both jdata.json and equi_settings.json
felix5572 Jul 6, 2025
fc61bcb
more clear instruction to download models
felix5572 Jul 6, 2025
3eaa6bc
update water SCAN model calculation example
felix5572 Jul 6, 2025
ccf268c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 6, 2025
e3943b3
update download example models script
felix5572 Jul 6, 2025
662f792
fix install; remove dependency of apache-airflow
felix5572 Jul 6, 2025
2b030ca
fix sigma_oo problem
felix5572 Jul 10, 2025
2887179
update README.md deprecated airflow related docs
felix5572 Jul 24, 2025
f8edc61
clean workflow dir
felix5572 Jul 24, 2025
c0d6eaa
fix lammps basic thermo_modify
felix5572 Jul 24, 2025
ebf7b9d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 24, 2025
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1 change: 1 addition & 0 deletions dpti/__init__.py
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Expand Up @@ -12,4 +12,5 @@
"ti",
"ti_water",
"lib",
"workflows",
]
2 changes: 1 addition & 1 deletion dpti/equi.py
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Expand Up @@ -131,7 +131,7 @@ def gen_equi_dump_settings(if_dump_avg_posi):
return ret


def gen_equi_ensemble_settings(ens, if_dump_avg_posi):
def gen_equi_ensemble_settings(ens, if_dump_avg_posi=False):
# ens = equi_settings['ens']
ret = ""
if ens == "nvt":
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2 changes: 1 addition & 1 deletion dpti/hti_liq.py
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Expand Up @@ -363,7 +363,7 @@ def make_tasks(iter_name, jdata, if_meam=None):
if model:
copied_model = os.path.join(os.path.abspath(iter_name), "graph.pb")
shutil.copyfile(model, copied_model)
jdata["model"] = copied_model
jdata["model"] = copied_model

cwd = os.getcwd()
os.chdir(iter_name)
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6 changes: 3 additions & 3 deletions dpti/hti_water.py
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Expand Up @@ -64,9 +64,9 @@ def _ff_deep_on(lamb, model, bparam, sparam):
alpha_lj = sparam["alpha_lj"]
rcut = sparam["rcut"]
epsilon = sparam["epsilon"]
sigma_oo = sparam["sigma_oo"]
sigma_oh = sparam["sigma_oh"]
sigma_hh = sparam["sigma_hh"]
sigma_oo = sparam.get("sigma_oo", None) or sparam.get("sigma_0_0")
sigma_oh = sparam.get("sigma_oh", None) or sparam.get("sigma_0_1")
sigma_hh = sparam.get("sigma_hh", None) or sparam.get("sigma_1_1")
activation = sparam["activation"]
ret = ""
ret += f"variable EPSILON equal {epsilon:f}\n"
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4 changes: 2 additions & 2 deletions dpti/ti.py
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Expand Up @@ -108,10 +108,10 @@ def _gen_lammps_input(
ret += "compute allmsd all msd\n"
if ens == "nvt":
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]\n"
ret += "thermo_modify format 4*8 %20.6f\n"
ret += "thermo_modify format float %20.6f\n"
elif "npt" in ens:
ret += "thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]\n"
ret += "thermo_modify format 4*8 %20.6f\n"
ret += "thermo_modify format float %20.6f\n"
else:
raise RuntimeError(f"unknow ensemble {ens}\n")
ret += "dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z\n"
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19 changes: 19 additions & 0 deletions examples/Sn_High_Pressure/command.sh
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@@ -0,0 +1,19 @@
# NPT
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@coderabbitai coderabbitai bot Jun 11, 2025

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🛠️ Refactor suggestion

Add a shebang and enable strict mode for portability and safety.

Without a shebang, the script may run under an unexpected shell. Enabling strict mode (-euo pipefail) ensures early failure on errors and prevents silent bugs.

Apply this diff:

+#!/usr/bin/env bash
+set -euo pipefail
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
# NPT
#!/usr/bin/env bash
set -euo pipefail
# NPT
🧰 Tools
🪛 Shellcheck (0.10.0)

[error] 1-1: Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.

(SC2148)

🤖 Prompt for AI Agents 
In examples/Sn_High_Pressure/command.sh at line 1, add a shebang line (e.g.,
#!/bin/bash) at the very top of the script to specify the shell interpreter.
Immediately after the shebang, enable strict mode by adding set -euo pipefail to
ensure the script exits on errors, treats unset variables as errors, and fails
on pipeline errors for better safety and portability.

dpti equi gen npt.json -e npt-xy -t 200 -p 20000 -o NPT_sim/
# cd NPT_sim/new_job/
dpti equi extract ./ -o npt_avg.lmp

# NVT
dpti equi gen equi_settings.json --ensemble nvt -t 200 -p 20000 --conf-npt ./NPT_sim/new_job/ -o NVT_sim/
# cd NVT_sim/new_job/
dpti equi extract ./ -o nvt_last_dump.lmp

# HTI
dpti hti gen hti.json -s three-step -o HTI_sim/
# dpti hti_water gen hti_water.json -o HTI_water/
# dpti hti_ice gen hti_ice.json -s three-step -o HTI_ice/
dpti hti compute ./new_job/ -t gibbs --npt ../NPT_sim/new_job/

# TI
dpti ti gen ti_settings.json -o TI_sim/
dpti ti compute ./TI_sim/new_job/ --hti ../HTI_sim/new_job/
1 change: 1 addition & 0 deletions examples/Sn_High_Pressure/conf.lmp
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@@ -0,0 +1 @@
beta.lmp
2 changes: 1 addition & 1 deletion examples/Sn_High_Pressure/hti.json
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@@ -1,5 +1,5 @@
{
"equi_conf": null,
"equi_conf": "nvt_last_dump.lmp",
"ncopies": [
1,
1,
Expand Down
2 changes: 1 addition & 1 deletion tests/benchmark_gdi/deepmd/0/in.lammps
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Expand Up @@ -25,7 +25,7 @@ timestep 0.002
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify format 4*8 %20.6f
thermo_modify format float %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}
fix mzero all momentum 10 linear 1 1 1
Expand Down
2 changes: 1 addition & 1 deletion tests/benchmark_ti/path-p/in.lammps
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Expand Up @@ -26,7 +26,7 @@ timestep 0.002
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify 4*8 format %20.6f
thermo_modify float format %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy
fix mzero all momentum 10 linear 1 1 1
Expand Down
2 changes: 1 addition & 1 deletion tests/benchmark_ti/path-p/task.000006/in.lammps
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Expand Up @@ -26,7 +26,7 @@ timestep 0.002
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify format 4*8 %20.6f
thermo_modify format float %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy
fix mzero all momentum 10 linear 1 1 1
Expand Down
2 changes: 1 addition & 1 deletion tests/benchmark_ti/path-t/task.000006/in.lammps
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Expand Up @@ -25,7 +25,7 @@ timestep 0.002
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify 4*8 format %20.6f
thermo_modify float format %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} aniso ${PRES} ${PRES} ${TAU_P} couple xy
fix mzero all momentum 10 linear 1 1 1
Expand Down
2 changes: 1 addition & 1 deletion tests/benchmark_ti_water/new_job/task.000003/in.lammps
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Expand Up @@ -27,7 +27,7 @@ timestep 0.0005
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify format 4*8 %20.6f
thermo_modify format float %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}
fix mzero all momentum 10 linear 1 1 1
Expand Down
15 changes: 15 additions & 0 deletions tests/conftest.py
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@@ -0,0 +1,15 @@
import os
import sys

from _pytest.config import Config # type: ignore

project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
sys.path.insert(0, project_root)


def pytest_configure(config: Config) -> None:
"""Print paths information before any test collection starts."""
print("\n" + "=" * 50)
print(f"Running tests from: {os.path.abspath(__file__)}")
print(f"Project root: {project_root}")
print("=" * 50 + "\n")
1 change: 1 addition & 0 deletions tests/graph.pb
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Expand Up @@ -2,3 +2,4 @@
# origin file Sn SCAN functional label:continue-2/000 by yfb222333@gmail.com; github:felix5572
# model version 1.2: wget https://deepmd-kit.oss-cn-beijing.aliyuncs.com/graph.pb
# model version 2.0: wget https://deepmd-kit.oss-cn-beijing.aliyuncs.com/graph_Sn_convert_from_1.2_to_2.0.pb
# compressed model: wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb
31 changes: 15 additions & 16 deletions tests/test_hti_ff_spring.py
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Expand Up @@ -50,22 +50,21 @@ def test_spring_multiple_element(self):
ret2 = dpti.hti._ff_spring(**input)
self.assertEqual(ret1, ret2)


def test_spring_var_spring_multiple_element(self):
input = {"lamb": 0.20, "m_spring_k": [118.71, 207.2], "var_spring": False}
ret1 = textwrap.dedent(
"""\
group type_1 type 1
group type_2 type 2
fix l_spring_1 type_1 spring/self 9.4968000000e+01
fix_modify l_spring_1 energy yes
fix l_spring_2 type_2 spring/self 1.6576000000e+02
fix_modify l_spring_2 energy yes
variable l_spring equal f_l_spring_1+f_l_spring_2
"""
)
ret2 = dpti.hti._ff_spring(**input)
self.assertEqual(ret1, ret2)
def test_spring_var_spring_multiple_element(self):
input = {"lamb": 0.20, "m_spring_k": [118.71, 207.2], "var_spring": False}
ret1 = textwrap.dedent(
"""\
group type_1 type 1
group type_2 type 2
fix l_spring_1 type_1 spring/self 1.1871000000e+02
fix_modify l_spring_1 energy yes
fix l_spring_2 type_2 spring/self 2.0720000000e+02
fix_modify l_spring_2 energy yes
variable l_spring equal f_l_spring_1+f_l_spring_2
"""
)
ret2 = dpti.hti._ff_spring(**input)
self.assertEqual(ret1, ret2)
Comment on lines +53 to +67
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@coderabbitai coderabbitai bot Jun 11, 2025

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🛠️ Refactor suggestion

Duplicate scenario & misleading test name

test_spring_var_spring_multiple_element sets var_spring=False, so it exercises the same code path already covered by test_spring_multiple_element.
Either:

  1. Rename to reflect it is a non-varying spring with a different λ, or
  2. Change var_spring to True and update expected constants to k*(1-λ) so the varying-spring branch for multiple elements is actually tested.

Removing redundancy will keep the suite fast and intention-revealing.

🤖 Prompt for AI Agents 
In tests/test_hti_ff_spring.py around lines 53 to 67, the test named
test_spring_var_spring_multiple_element sets var_spring to False, duplicating
the code path of test_spring_multiple_element. To fix this, either rename the
test to indicate it tests a non-varying spring with a different lambda value or
change var_spring to True and update the expected output constants to reflect
k*(1-lambda), ensuring the varying spring branch for multiple elements is
actually tested and removing redundancy.



if __name__ == "__main__":
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4 changes: 2 additions & 2 deletions tests/test_ti_gen_lammps_input.py
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Expand Up @@ -62,7 +62,7 @@ def test_deepmd(self, patch_random):
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify format 4*8 %20.6f
thermo_modify format float %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}
fix mzero all momentum 10 linear 1 1 1
Expand Down Expand Up @@ -128,7 +128,7 @@ def test_meam(self, patch_random):
thermo ${THERMO_FREQ}
compute allmsd all msd
thermo_style custom step ke pe etotal enthalpy temp press vol c_allmsd[*]
thermo_modify format 4*8 %20.6f
thermo_modify format float %20.6f
dump 1 all custom ${DUMP_FREQ} traj.dump id type x y z
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRES} ${PRES} ${TAU_P}
fix mzero all momentum 10 linear 1 1 1
Expand Down
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