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fix restart #298

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Merged
jan-janssen merged 5 commits into from
Jan 24, 2026
Merged

fix restart #298

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c701f9e
fix restart
jan-janssen Jan 24, 2026
0d4ce14
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 24, 2026
0758883
add test
jan-janssen Jan 24, 2026
3eff0ea
add restart file
jan-janssen Jan 24, 2026
1f19646
fix space
jan-janssen Jan 24, 2026
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43 changes: 34 additions & 9 deletions src/pyiron_lammps/compatibility/file.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import os
import shutil
import subprocess
from typing import Optional

Expand Down Expand Up @@ -26,6 +27,9 @@ def lammps_file_interface_function(
lmp_command: str = "mpiexec -n 1 --oversubscribe lmp_mpi -in lmp.in",
resource_path: Optional[str] = None,
input_control_file: Optional[dict] = None,
write_restart_file: bool = False,
read_restart_file: bool = False,
restart_file: str = "restart.out",
):
"""
A single function to execute a LAMMPS calculation based on the LAMMPS job implemented in pyiron
Expand Down Expand Up @@ -94,7 +98,12 @@ def lammps_file_interface_function(

lmp_str_lst = []
atom_type = "atomic"
for l in lammps_file_initialization(structure=structure):
for l in lammps_file_initialization(
structure=structure,
units=units,
read_restart_file=read_restart_file,
restart_file=restart_file,
):
if l.startswith("units") and "units" in potential_replace:
lmp_str_lst.append(potential_replace["units"])
elif l.startswith("atom_style") and "atom_style" in potential_replace:
Expand Down Expand Up @@ -136,12 +145,16 @@ def lammps_file_interface_function(
n_ionic_steps = int(calc_kwargs.pop("n_ionic_steps"))
else:
n_ionic_steps = 1
if read_restart_file:
calc_kwargs["initial_temperature"] = 0.0
calc_kwargs["units"] = units
lmp_str_lst += calc_md(**calc_kwargs)
lmp_str_lst = _modify_input_dict(
input_control_file=input_control_file,
lmp_str_lst=lmp_str_lst,
)
if read_restart_file:
lmp_str_lst += ["reset_timestep 0"]
lmp_str_lst += ["run {} ".format(n_ionic_steps)]
elif calc_mode == "minimize":
calc_kwargs["units"] = units
Expand All @@ -161,6 +174,13 @@ def lammps_file_interface_function(
raise ValueError(
f"calc_mode must be one of: static, md or minimize, not {calc_mode}"
)
if read_restart_file:
shutil.copyfile(
os.path.abspath(restart_file),
os.path.join(working_directory, os.path.basename(restart_file)),
)
if write_restart_file:
lmp_str_lst.append(f"write_restart {os.path.basename(restart_file)}")

with open(os.path.join(working_directory, "lmp.in"), "w") as f:
f.writelines([l + "\n" for l in lmp_str_lst])
Expand Down Expand Up @@ -195,15 +215,20 @@ def lammps_file_interface_function(
return shell, output, False


def lammps_file_initialization(structure, dimension=3, units="metal"):
def lammps_file_initialization(
structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
):
init_commands = ["units " + units]
boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
init_commands = [
"units " + units,
"dimension " + str(dimension),
"boundary " + boundary + "",
"atom_style atomic",
"read_data lammps.data",
]
if read_restart_file:
init_commands.append(f"read_restart {os.path.basename(restart_file)}")
Comment on lines +218 to +224
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@coderabbitai coderabbitai bot Jan 24, 2026

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⚠️ Potential issue | 🟡 Minor

Potential TypeError if restart_file is None when read_restart_file=True.

The default restart_file=None combined with read_restart_file=True will cause os.path.basename(None) to raise a TypeError. While the main function always passes a value, this function could be called directly by external code.

Consider either validating the parameter combination or changing the default to match the main function.

🐛 Option 1: Add validation 
 def lammps_file_initialization(
     structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
 ):
     init_commands = ["units " + units]
     boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
     if read_restart_file:
+        if restart_file is None:
+            raise ValueError("restart_file must be specified when read_restart_file=True")
         init_commands.append(f"read_restart {os.path.basename(restart_file)}")
♻️ Option 2: Use consistent default 
 def lammps_file_initialization(
-    structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
+    structure, dimension=3, units="metal", read_restart_file=False, restart_file="restart.out"
 ):
📝 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
def lammps_file_initialization(
structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
):
init_commands = ["units " + units]
boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
init_commands = [
"units " + units,
"dimension " + str(dimension),
"boundary " + boundary + "",
"atom_style atomic",
"read_data lammps.data",
]
if read_restart_file:
init_commands.append(f"read_restart {os.path.basename(restart_file)}")
def lammps_file_initialization(
structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
):
init_commands = ["units " + units]
boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
if read_restart_file:
if restart_file is None:
raise ValueError("restart_file must be specified when read_restart_file=True")
init_commands.append(f"read_restart {os.path.basename(restart_file)}")
Suggested change
def lammps_file_initialization(
structure, dimension=3, units="metal", read_restart_file=False, restart_file=None
):
init_commands = ["units " + units]
boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
init_commands = [
"units " + units,
"dimension " + str(dimension),
"boundary " + boundary + "",
"atom_style atomic",
"read_data lammps.data",
]
if read_restart_file:
init_commands.append(f"read_restart {os.path.basename(restart_file)}")
def lammps_file_initialization(
structure, dimension=3, units="metal", read_restart_file=False, restart_file="restart.out"
):
init_commands = ["units " + units]
boundary = " ".join(["p" if coord else "f" for coord in structure.pbc])
if read_restart_file:
init_commands.append(f"read_restart {os.path.basename(restart_file)}")
🤖 Prompt for AI Agents 
In `@src/pyiron_lammps/compatibility/file.py` around lines 218 - 224, The
lammps_file_initialization function can raise TypeError because
os.path.basename(restart_file) is called even when restart_file is None while
read_restart_file=True; update lammps_file_initialization to validate the
parameter combination (e.g., if read_restart_file: require restart_file is not
None and raise a clear ValueError mentioning restart_file) or guard the append
(only call os.path.basename and append the read_restart command when
restart_file is a non-empty string); reference the symbols
lammps_file_initialization, read_restart_file, restart_file, and
os.path.basename when making the change.

else:
init_commands += [
"dimension " + str(dimension),
"boundary " + boundary + "",
"atom_style atomic",
"read_data lammps.data",
]
return init_commands


Expand Down
Empty file added tests/static/restart/restart.out
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Empty file.
42 changes: 42 additions & 0 deletions tests/test_compatibility_file.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,48 @@ def test_calc_md_nvt(self):
for line in content_expected:
self.assertIn(line, content)

def test_calc_md_nvt_restart(self):
calc_kwargs = {"temperature": 500.0, "n_print": 100}
shell_output, parsed_output, job_crashed = lammps_file_interface_function(
working_directory=self.working_dir,
structure=self.structure,
potential=self.potential,
calc_mode="md",
calc_kwargs=calc_kwargs,
units=self.units,
lmp_command="cp "
+ str(os.path.join(self.static_path, "compatibility_output"))
+ "/* .",
resource_path=os.path.join(self.static_path, "potential"),
restart_file=os.path.join(self.static_path, "restart", "restart.out"),
write_restart_file=True,
read_restart_file=True,
)
self.assertFalse(job_crashed)
for key in self.keys:
self.assertIn(key, parsed_output["generic"])
with open(self.working_dir + "/lmp.in", "r") as f:
content = f.readlines()
content_expected = [
"units metal\n",
"read_restart restart.out\n",
"pair_style eam/alloy\n",
"variable dumptime equal 100 \n",
"dump 1 all custom ${dumptime} dump.out id type xsu ysu zsu fx fy fz vx vy vz\n",
'dump_modify 1 sort id format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g"\n',
"fix ensemble all nvt temp 500.0 500.0 0.1\n",
"variable thermotime equal 100 \n",
"timestep 0.001\n",
"thermo_style custom step temp pe etotal pxx pxy pxz pyy pyz pzz vol\n",
"thermo_modify format float %20.15g\n",
"thermo ${thermotime}\n",
"reset_timestep 0\n",
"run 1 \n",
"write_restart restart.out\n",
]
for line in content_expected:
self.assertIn(line, content)

def test_calc_md_nvt_langevin(self):
calc_kwargs = {"temperature": 500.0, "n_print": 100, "langevin": True}
shell_output, parsed_output, job_crashed = lammps_file_interface_function(
Expand Down
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