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Merge pull request #46 from molssi-seamm/dev
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Dev
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@seamm
seamm authored Sep 6, 2023
2 parents 4bc3e90 + 76c377d commit e125790
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5 changes: 5 additions & 0 deletions HISTORY.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
=======
History
=======
2023.9.6 -- Corrected issues with final coordinates; added velocities
* There was a problem with getting the final coordinates from a dump file.
* Added saving and reusing velocities so now a second LAMMPS step will by default use
the velocities from the previous step, which is what you would expect.

2023.8.31 -- Bugfix: not reading structure correctly after dynamics

2023.8.27 -- Added support for tabulated angle potentials.
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159 changes: 114 additions & 45 deletions lammps_step/lammps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -594,16 +594,22 @@ def run(self):
base = "lammps"

restart = base + ".restart.*"
dump = base + ".dump.*"
dump = base + ".dump"
input_file = base + ".dat"
new_input_data = []
new_input_data.append("run 0")
new_input_data.append(f"write_restart {restart}")

new_input_data.append(
f"write_dump all custom {dump} id "
"xu yu zu modify flush yes sort id"
)
if configuration.periodicity == 0:
new_input_data.append(
f"write_dump all custom {dump} id xu yu zu vx vy vz"
" modify flush yes sort id"
)
else:
new_input_data.append(
f"write_dump all custom {dump} id xsu ysu zsu vx vy vz"
" modify flush yes sort id"
)
new_input_data.append("")
new_input_data.append("info computes fixes dumps log out")

Expand Down Expand Up @@ -632,9 +638,10 @@ def run(self):

self._trajectory = []

if "dump" in files:
dump_file = Path(self.directory) / "final.dump"
if dump_file.exists:
try:
self.read_dump(os.path.join(self.directory, files["dump"]["filename"]))
self.read_dump(dump_file)
except Exception as e:
printer.normal("Warning: unable to read the LAMMPS dumpfile")
logger.warning(f"The was a problem reading the LAMMPS dumpfile: {e}")
Expand Down Expand Up @@ -670,6 +677,7 @@ def _execute_single_sim(self, files, np=1, return_files=None):
"trajectory_*.seamm_trj",
"*.trj",
"*.restart.*",
"*.dump",
"*.dump.*",
"*.log",
"*.dat",
Expand Down Expand Up @@ -833,11 +841,11 @@ def _execute_single_sim(self, files, np=1, return_files=None):
else:
if "ngpus" in batch:
printer.important(
f" LAMMPS using MPI with {np} processes and "
f" LAMMPS using MPI with {np} processes and "
f"{batch['ngpus']} gpus.\n"
)
else:
printer.important(f" LAMMPS using MPI with {np} processes")
printer.important(f" LAMMPS using MPI with {np} processes")

result = local.run(
cmd=cmd,
Expand Down Expand Up @@ -868,13 +876,6 @@ def _execute_single_sim(self, files, np=1, return_files=None):
else:
self._add_lammps_citations(result["stdout"])

# base = os.path.basename(files["input"]["filename"][0:-4])
# dump_file = base + ".dump.0"

# files["dump"] = {}
# files["dump"]["filename"] = dump_file
# files["dump"]["data"] = None

files["input"] = {}
files["input"]["filename"] = None
initialization_header, eex = self._get_node_input(
Expand All @@ -898,6 +899,7 @@ def _prepare_input(
write_restart=False,
extras=None,
):
_, configuration = self.get_system_configuration()
python_script = None
postscript = None
if isinstance(nodes, list) is False:
Expand All @@ -921,11 +923,7 @@ def _prepare_input(
python_script = todo["python script"]

# base = "lammps_substep_%s_iter_%d" % ("_".join(node_ids), iteration)
base = "lammps"

input_file = base + ".dat"
# restart = base + ".restart.*"
dump = base + ".dump.*"

# if read_restart:
# new_input_data.insert(
Expand All @@ -936,29 +934,37 @@ def _prepare_input(
# new_input_data.append(f"write_restart {restart}")

if postscript is None:
new_input_data.append("reset_timestep 0")
new_input_data.append("run 0")
new_input_data.append(
f"write_dump all custom {dump} id xu yu zu "
"modify flush yes sort id"
)
if configuration.periodicity == 0:
new_input_data.append(
"write_dump all custom final.dump id xu yu zu vx vy vz"
" modify flush yes sort id"
)
else:
new_input_data.append(
"write_dump all custom final.dump id xsu ysu zsu vx vy vz"
" modify flush yes sort id"
)
new_input_data.append("")
new_input_data.append("")
new_input_data.append("info computes fixes dumps out log")

files["input"]["data"] += new_input_data

files["input"]["filename"] = input_file
files["input"]["filename"] = "input.dat"
files["input"]["data"] = "\n".join(files["input"]["data"])
self.logger.debug(files["input"]["filename"] + ":\n" + files["input"]["data"])

if postscript is not None:
postscript.append("reset_timestep 0")
postscript.append("run 0")
postscript.append(
f"write_dump all custom {dump} id xu yu zu "
"modify flush yes sort id"
)
if configuration.periodicity == 0:
postscript.append(
"write_dump all custom final.dump id xu yu zu vx vy vz"
" modify flush yes sort id"
)
else:
postscript.append(
"write_dump all custom final.dump id xsu ysu zsu vx vy vz"
" modify flush yes sort id"
)
postscript.append("")
postscript.append("info computes fixes dumps out log")
files["postscript"] = {
Expand Down Expand Up @@ -1092,6 +1098,17 @@ def structure_data(self, eex, triclinic=False):
x, y, z, index = xyz_index
lines.append(f"{i+1:6d} {index:6d} {x:12.7f} {y:12.7f} {z:12.7f}")

_, configuration = self.get_system_configuration()
if configuration.atoms.have_velocities:
lines.append("")
lines.append("Velocities")
lines.append("")
for i, vxyz in enumerate(
configuration.atoms.get_velocities(fractionals=False), start=1
):
vx, vy, vz = vxyz
lines.append(f"{i:6d} {vx:12.7f} {vy:12.7f} {vz:12.7f}")

lines.append("")
lines.append("Masses")
lines.append("")
Expand Down Expand Up @@ -1826,6 +1843,8 @@ def analyze_trajectory(
}

# Process the trajectory data
# temporary until we sort out multiple runs
self._trajectory = []
with path.open() as fd:
file_data = pandas.read_csv(
fd,
Expand Down Expand Up @@ -2303,9 +2322,6 @@ def read_dump(self, dumpfile):

section = ""
section_lines = []
xs = []
ys = []
zs = []
with open(dumpfile, "r") as fd:
lineno = 0
for line in fd:
Expand Down Expand Up @@ -2369,28 +2385,81 @@ def read_dump(self, dumpfile):
)
)
elif "ATOMS" in section:
for tmp in section_lines:
id, x, y, z = tmp.split()
xs.append(float(x))
ys.append(float(y))
zs.append(float(z))
xyz = []
vxyz = []
keys = section.split()[1:]
if keys[1:4] == ["x", "y", "z"] or keys[1:4] == [
"xu",
"yu",
"zu",
]:
fractional = False
elif keys[1:4] == ["xs", "ys", "zs"] or keys[1:4] == [
"xsu",
"ysu",
"zsu",
]:
fractional = True
else:
logger.error(f"Can't handle dump file, {keys=}")
if len(keys) >= 7 and keys[4:7] == ["vx", "vy", "vz"]:
have_velocities = True
factor = lammps_step.from_lammps_units(1, "fs").magnitude
factor = 1 / factor
for tmp in section_lines:
x, y, z, vx, vy, vz = tmp.split()[1:7]
xyz.append([float(x), float(y), float(z)])
vxyz.append(
[
factor * float(vx),
factor * float(vy),
factor * float(vz),
]
)
else:
have_velocities = False
for tmp in section_lines:
x, y, z = tmp.split()[1:4]
xyz.append([float(x), float(y), float(z)])
section = line[6:].strip()
section_lines = []
else:
section_lines.append(line)

# Clean up the last section
xyz = []
vxyz = []
if "ATOMS" in section:
self.logger.debug(" processing section '{}'".format(section))
self.logger.debug(" handling the atoms")
for tmp in section_lines:
id, x, y, z = tmp.split()
xyz.append([float(x), float(y), float(z)])
keys = section.split()[1:]
if keys[1:4] == ["x", "y", "z"] or keys[1:4] == ["xu", "yu", "zu"]:
fractional = False
elif keys[1:4] == ["xs", "ys", "zs"] or keys[1:4] == ["xsu", "ysu", "zsu"]:
fractional = True
else:
logger.error(f"Can't handle dump file, {keys=}")
if len(keys) >= 7 and keys[4:7] == ["vx", "vy", "vz"]:
have_velocities = True
factor = 1.0 / lammps_step.from_lammps_units(1, "fs").magnitude
for tmp in section_lines:
x, y, z, vx, vy, vz = tmp.split()[1:7]
xyz.append([float(x), float(y), float(z)])
vxyz.append(
[factor * float(vx), factor * float(vy), factor * float(vz)]
)
else:
have_velocities = False
for tmp in section_lines:
x, y, z = tmp.split()[1:4]
xyz.append([float(x), float(y), float(z)])

if periodicity == 3:
configuration.cell.parameters = cell
configuration.atoms.set_coordinates(xyz, fractionals=False)
configuration.atoms.set_coordinates(xyz, fractionals=fractional)
if have_velocities:
# LAMMPS only has Cartesian velocities
configuration.atoms.set_velocities(vxyz, fractionals=False)

def _add_lammps_citations(self, text, cite=None):
"""Add the two main citations for LAMMPS, getting the version from stdout
Expand Down
2 changes: 1 addition & 1 deletion lammps_step/tk_velocities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def reset_dialog(self, widget=None):
widgets.append(self[key])
row += 1

if "scaling" in method:
if "scaling" not in method:
self["seed"].grid(row=row, column=0, sticky=tk.EW)
widgets.append(self["seed"])
row += 1
Expand Down

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