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Allow custom cmdargs for lammps object #46

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merged 4 commits into from
Oct 14, 2022
Merged

Allow custom cmdargs for lammps object #46

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8c6d7b6
add cmdargs option
Leimeroth Oct 6, 2022
9c45db1
append pot instead of splitted list
Leimeroth Oct 13, 2022
027033f
update env
srmnitc Oct 14, 2022
20b4a19
fix version number for pylammpsmpi
srmnitc Oct 14, 2022
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4 changes: 2 additions & 2 deletions calphy/alchemy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def run_averaging(self):
Fix lattice option is not implemented at present.
At the end of the run, the averaged box dimensions are calculated.
"""
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

#set up structure
lmp = ph.create_structure(lmp, self.calc)
Expand Down Expand Up @@ -137,7 +137,7 @@ def run_integration(self, iteration=1):
"""

#create lammps object
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

# Adiabatic switching parameters.
lmp.command("variable li equal 1.0")
Expand Down
4 changes: 2 additions & 2 deletions calphy/helpers.py
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Expand Up @@ -32,7 +32,7 @@
from pyscal.trajectory import Trajectory


def create_object(cores, directory, timestep):
def create_object(cores, directory, timestep, cmdargs=None):
"""
Create LAMMPS object
Expand All @@ -52,7 +52,7 @@ def create_object(cores, directory, timestep):
lmp : LammpsLibrary object
"""
lmp = LammpsLibrary(mode="local", cores=cores,
working_directory=directory)
working_directory=directory, cmdargs=cmdargs)

lmp.units("metal")
lmp.boundary("p p p")
Expand Down
3 changes: 2 additions & 1 deletion calphy/input.py
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Expand Up @@ -186,6 +186,7 @@ def __init__(self):
self.md.n_cycles = 100
self.md.thermostat_damping = 0.1
self.md.barostat_damping = 0.1
self.md.cmdargs = None

self.nose_hoover = InputTemplate()
self.nose_hoover.thermostat_damping = 0.1
Expand Down Expand Up @@ -586,7 +587,7 @@ def fix_paths(self, potlist):
pcnew = " ".join([*pcraw[:2], filename, *pcraw[3:]])
fixedpots.append(pcnew)
else:
fixedpots.append(pcraw)
fixedpots.append(pot)
return fixedpots

def create_identifier(self):
Expand Down
4 changes: 2 additions & 2 deletions calphy/liquid.py
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Expand Up @@ -112,7 +112,7 @@ def run_averaging(self):
At the end of the run, the averaged box dimensions are calculated.
"""
#create lammps object
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

#set up structure
lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
Expand Down Expand Up @@ -171,7 +171,7 @@ def run_integration(self, iteration=1):
Run the integration routine where the initial and final systems are connected using
the lambda parameter. See algorithm 4 in publication.
"""
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

# Adiabatic switching parameters.
lmp.command("variable li equal 1.0")
Expand Down
6 changes: 3 additions & 3 deletions calphy/phase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -660,7 +660,7 @@ def reversible_scaling(self, iteration=1):
pf = lf*pi

#create lammps object
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

lmp.command("echo log")
lmp.command("variable li equal %f"%li)
Expand Down Expand Up @@ -835,7 +835,7 @@ def temperature_scaling(self, iteration=1):
pf = lf*p0

#create lammps object
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

lmp.command("echo log")
lmp.command("variable li equal %f"%li)
Expand Down Expand Up @@ -919,7 +919,7 @@ def pressure_scaling(self, iteration=1):
pf = self.calc._pressure_stop

#create lammps object
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

lmp.command("echo log")
lmp.command("variable li equal %f"%li)
Expand Down
4 changes: 2 additions & 2 deletions calphy/solid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ def run_averaging(self):
is calculated.
At the end of the run, the averaged box dimensions are calculated.
"""
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

#set up structure
lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
Expand Down Expand Up @@ -206,7 +206,7 @@ def run_integration(self, iteration=1):
Run the integration routine where the initial and final systems are connected using
the lambda parameter. See algorithm 4 in publication.
"""
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep)
lmp = ph.create_object(self.cores, self.simfolder, self.calc.md.timestep, self.calc.md.cmdargs)

#read in the conf file
conf = os.path.join(self.simfolder, "conf.equilibration.dump")
Expand Down