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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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349 changes: 110 additions & 239 deletions README.md
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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":
Expand Down
6 changes: 5 additions & 1 deletion dpti/hti.py
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Expand Up @@ -1331,7 +1331,11 @@ def compute_task(
print(print_format % (e1, de_err[0], de_err[1]))
elif free_energy_type == "gibbs":
if npt is not None:
npt_in = json.load(open(os.path.join(npt, "jdata.json")))
# Try jdata.json first, then equi_settings.json for compatibility
try:
npt_in = json.load(open(os.path.join(npt, "jdata.json")))
except FileNotFoundError:
npt_in = json.load(open(os.path.join(npt, "equi_settings.json")))
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🛠️ Refactor suggestion

Improve resource management while maintaining the fallback logic.

The fallback mechanism from jdata.json to equi_settings.json is a good improvement for compatibility. However, the file opening should use context managers to ensure proper resource cleanup.

Apply this diff to improve resource management:

-            # Try jdata.json first, then equi_settings.json for compatibility
-            try:
-                npt_in = json.load(open(os.path.join(npt, "jdata.json")))
-            except FileNotFoundError:
-                npt_in = json.load(open(os.path.join(npt, "equi_settings.json")))
+            # Try jdata.json first, then equi_settings.json for compatibility
+            try:
+                with open(os.path.join(npt, "jdata.json")) as f:
+                    npt_in = json.load(f)
+            except FileNotFoundError:
+                with open(os.path.join(npt, "equi_settings.json")) as f:
+                    npt_in = json.load(f)
📝 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
# Try jdata.json first, then equi_settings.json for compatibility
try:
npt_in = json.load(open(os.path.join(npt, "jdata.json")))
except FileNotFoundError:
npt_in = json.load(open(os.path.join(npt, "equi_settings.json")))
# Try jdata.json first, then equi_settings.json for compatibility
try:
with open(os.path.join(npt, "jdata.json")) as f:
npt_in = json.load(f)
except FileNotFoundError:
with open(os.path.join(npt, "equi_settings.json")) as f:
npt_in = json.load(f)
🧰 Tools
🪛 Pylint (3.3.7)

[refactor] 1336-1336: Consider using 'with' for resource-allocating operations

(R1732)

[refactor] 1338-1338: Consider using 'with' for resource-allocating operations

(R1732)

🤖 Prompt for AI Agents 
In dpti/hti.py around lines 1334 to 1338, the code opens JSON files without
using context managers, which can lead to resource leaks. Refactor the file
opening statements to use 'with' blocks for both 'jdata.json' and
'equi_settings.json' to ensure files are properly closed after reading, while
preserving the fallback logic from 'jdata.json' to 'equi_settings.json'.

npt_info = json.load(open(os.path.join(npt, "result.json")))
p = npt_in["pres"]
v = npt_info["v"]
Expand Down
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)
Expand Down
18 changes: 9 additions & 9 deletions dpti/hti_water.py
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Expand Up @@ -35,9 +35,9 @@ def _ff_angle_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["sigma_0_0"]
sigma_oh = sparam.get("sigma_oh", None) or sparam["sigma_0_1"]
sigma_hh = sparam.get("sigma_hh", None) or sparam["sigma_1_1"]
activation = sparam["activation"]
ret = ""
ret += f"variable EPSILON equal {epsilon:f}\n"
Expand All @@ -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"
Expand Down Expand Up @@ -94,9 +94,9 @@ def _ff_bond_angle_off(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["sigma_0_0"]
sigma_oh = sparam.get("sigma_oh", None) or sparam["sigma_0_1"]
sigma_hh = sparam.get("sigma_hh", None) or sparam["sigma_1_1"]
activation = sparam["activation"]
ret = ""
ret += "variable INV_LAMBDA equal 1-${LAMBDA}\n"
Expand Down
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"
Expand Down
19 changes: 19 additions & 0 deletions examples/Sn_High_Pressure/command.sh
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
# NPT
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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
3 changes: 3 additions & 0 deletions examples/download_models.sh
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@@ -0,0 +1,3 @@
wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb
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🛠️ Refactor suggestion

Add she-bang and fail-fast options for predictable execution

Without a she-bang the script’s interpreter is ambiguous (SC2148).
Insert a standard header and strict mode so any network/download failure aborts the script immediately.

+#!/usr/bin/env bash
+# Download compressed DeepPot models required by example workflows
+set -euo pipefail
+
 wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb
📝 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
wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb
#!/usr/bin/env bash
# Download compressed DeepPot models required by example workflows
set -euo pipefail
wget https://huggingface.co/Felix5572/Sn-SCAN-Compressed/resolve/main/graph.pb -O Sn_SCAN_compressed.pb
🧰 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/download_models.sh at line 1, add a she-bang line (e.g.,
#!/bin/bash) at the top to specify the script interpreter explicitly. Also,
enable fail-fast behavior by adding set -e to the script so it exits immediately
on any command failure, ensuring predictable execution and proper error handling
during the download process.


wget https://huggingface.co/Felix5572/Water-Ice-SCAN-Phase-Dirgram/resolve/main/graph.pb -O H2O-Phase-Diagram-model_compressed.pb
1 change: 1 addition & 0 deletions examples/water_SCAN/H2O-Phase-Diagram-model_compressed.pb
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../H2O-Phase-Diagram-model_compressed.pb
37 changes: 37 additions & 0 deletions examples/water_SCAN/ice04/command.sh
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@@ -0,0 +1,37 @@
# docker pull yfb222333/dpti-lammps-fep:latest
# docker run -it --gpus all dpti-lammps-fep:latest
# all in /opt/
# all files in /opt/dpti/examples/water_SCAN/ice04/

Comment on lines +1 to +5
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🛠️ Refactor suggestion

Add shebang line for proper shell script execution.

The workflow documentation is excellent and provides clear guidance for users. However, the script should include a shebang line to specify the shell interpreter.

Add this line at the beginning of the file:

+#!/bin/bash
 # docker pull yfb222333/dpti-lammps-fep:latest
 #  docker run -it --gpus all dpti-lammps-fep:latest
 # all in /opt/
 # all files in /opt/dpti/examples/water_SCAN/ice04/
📝 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
# docker pull yfb222333/dpti-lammps-fep:latest
# docker run -it --gpus all dpti-lammps-fep:latest
# all in /opt/
# all files in /opt/dpti/examples/water_SCAN/ice04/
#!/bin/bash
# docker pull yfb222333/dpti-lammps-fep:latest
# docker run -it --gpus all dpti-lammps-fep:latest
# all in /opt/
# all files in /opt/dpti/examples/water_SCAN/ice04/
🧰 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/water_SCAN/ice04/command.sh at the beginning of the file, add a
shebang line such as #!/bin/bash to specify the shell interpreter for proper
script execution.

#NPT
dpti equi gen npt.json -o npt/

# submit jobs `lmp -i in.lammps` for npt/

dpti equi extract ./npt/ -o npt_avg.lmp # extract average

# NVT
dpti equi gen nvt.json -o nvt/

# submit jobs `lmp -i in.lammps` for nvt/

dpti equi extract ./nvt/ -o nvt_last_dump.lmp # extract average

## HTI (hti,hti_liq, hti_water, hti_ice) module
dpti hti_ice gen hti_ice.json -s three-step -o hti/

# submit jobs `lmp -i in.lammps` for subdirs like `hti/0*/task*/`

dpti hti_ice compute ./hti/ -t gibbs --npt ./npt/ # note use NPT simulation usually longer steps, and the P*V value is more accurate

# result txt in ./hti/result

## TI (ti, ti_water) module

dpti ti_water gen path-t.json -o ti_path_t/

# submit jobs `lmp -i in.lammps` for subdirs like `ti_path_t/task*/`

dpti ti_water compute ./ti_path_t/ --hti ./hti/ # HTI simulation (starting point, gibbs free energy value)

# final result for a ti-line txt in ./ti_path_t/result
1 change: 1 addition & 0 deletions examples/water_SCAN/ice04/conf.lmp
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ice04.lmp
1 change: 1 addition & 0 deletions examples/water_SCAN/ice04/graph.pb
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../H2O-Phase-Diagram-model_compressed.pb
52 changes: 52 additions & 0 deletions examples/water_SCAN/ice04/hti_ice.json
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{
"equi_conf": "nvt_last_dump.lmp",
"ncopies": [
1,
1,
1
],
"lambda_lj_on": [
"0.000:0.100:0.0125",
"0.100:0.200:0.025",
"0.200:1.000:0.2",
"1"
],
"lambda_deep_on": [
"0.0:0.1:0.025",
"0.1:1.0:0.1125",
"1"
],
"lambda_spring_off": [
"0.000:0.750:0.125",
"0.750:0.875:0.0625",
"0.875:1.000:0.03125",
"1"
],
"protect_eps": 1e-08,
"model": "graph.pb",
"model_mass_map": [
16,
2
],
"spring_k": 0.5,
"soft_param": {
"epsilon": 0.02,
"sigma_oo": 3.15,
"sigma_oh": 0.987,
"sigma_hh": 0.987,
"activation": 0.5,
"n": 1.0,
"alpha_lj": 0.5,
"rcut": 6.0,
"_comment": "that's all"
},
"crystal": "frenkel",
"langevin": true,
"nsteps": 200000,
"dt": 0.0005,
"stat_freq": 10,
"stat_skip": 10000,
"stat_bsize": 2000,
"temp": 150.000000,
"_comment": "that's all"
}
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