def access_geometry(self, t, p=None, s=None, f=None):
"""
Access the equilibrium geometry of the corresponding configuration.
Parameters:
----------
- t (float): Temperature (compulsory)
- p (array): Pressure (optional)
- s (array): Strain (optional)
- f (array): Electric Field (optional)
Return:
----------
- A Geometry object for the corresponding configuration.
"""
# folder and file naming
folder, sim_name = self.get_location(t, p, s, f)
reference_file = os.path.join(folder, sim_name + "_FINAL.REF")
restart_file = os.path.join(folder, sim_name + "_EQUILIBRIUM.restart")
geo = Geometry(self.supercell, self.model["species"],
self.model["nats"])
geo.load_reference(reference_file)
geo.load_restart(restart_file)
return geo
sim = MCSimulation()
sim.setup("srtio3",
"srtio3_full_lat.xml",
SUPERCELL,
SPECIES,
NATS,
temp=TEMPERATURES,
strain=STRAINS,
stress=STRESSES,
field=FIELDS,
output_folder="output")
A, B, Ox, Oy, Oz = LABELS
# create an example starting geometry
start_geom = Geometry(SUPERCELL, SPECIES, NATS)
for x in range(SUPERCELL[0]):
for y in range(SUPERCELL[1]):
for z in range(SUPERCELL[2]):
start_geom.displacements[x, y, z, B, :] = [0., 0., 0.2]
# test independent simulation run
sim.change_output_folder("independent_output")
sim.independent_launch(start_geo=start_geom)
# test sequential simulation run
sim.change_output_folder("sequential_output")
sim.sequential_launch_by_temperature(start_geo=start_geom)
# test sequential simulation run (reverse order)
(0, 1, 2, 3, 4, 5, 6, 7, 8), # z axis rotation
# octahedral deformations
(1, 2, 4, 5), # x axis only
(0, 2, 3, 5), # y axis only
(0, 1, 3, 4), # z axis only
]
run = False # run the hessian calculation? (LONG)
pretty = True # print the pretty vectors or the original ones
ortho_check = False # print orthogonality check
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# ~~~~~~~~~~~~~~~~~~~~~~~ code starts here ~~~~~~~~~~~~~~~~~~~~~~~~ #
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
geo = Geometry(SUPERCELL, SPECIES, NATS)
# calculate or load the hessian
if run == True:
hessian = finite_hessian("srtio3_full_lat.xml", geo, MASSES)
with open("hessian.pickle", "wb") as f:
pickle.dump(hessian, f)
else:
with open("hessian.pickle", "rb") as f:
hessian = pickle.load(f)
# create mass matrix
M = []
for m in MASSES:
for _ in range(3):
M.append(m)
def sequential_launch_by_temperature(self,
start_geo=None,
inverse_order=False):
"""
Simulation run where the equilibrium geometry of the simulation for
the previous temperature is used as starting geometry of the next one.
Parameters:
----------
- start_geo (RestartGenerator): starting geometry of the first temperature.
"""
# check if setup() has been run
if self.SETUP != True:
raise ezSCUP.exceptions.MissingSetup(
"Run MCSimulation.setup() before launching any simulation.")
# check if somulation has already been carried out
if self.DONE == True:
return 0
print("\n ~ Sequential simulation run by temperature engaged. ~ ")
# checks restart file matches loaded geometry
if start_geo != None and isinstance(start_geo, Geometry):
print("\nApplying starting geometry...")
if not np.all(self.generator.supercell == start_geo.supercell):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.nats != None and (start_geo.nats !=
self.model["nats"]):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.species != None and (set(
self.model["species"]) != set(self.model["species"])):
raise ezSCUP.exceptions.GeometryNotMatching()
# get a copy of the model file
copy(self.model["file"], "param_file.xml")
# parser to get equilibrium geometry
parser = MCSimulationParser(output_folder=self.output_folder)
# adjust temperature ordering
if inverse_order:
temp_sequence = list(reversed(list(self.temp)))
else:
temp_sequence = list(self.temp)
# simulation counters
total_counter = 0
# total number of simulations
nsims = self.temp.size * len(self.strain) * len(self.field) * len(
self.stress)
# starting time of the simulation process
main_start_time = time.time()
print("\nStarting calculations...\n")
for p in self.stress:
stress_counter = [np.array_equal(p, x)
for x in self.stress].index(True)
for s in self.strain:
strain_counter = [np.array_equal(s, x)
for x in self.strain].index(True)
for f in self.field:
field_counter = [np.array_equal(f, x)
for x in self.field].index(True)
# set starting geometry
if start_geo != None and isinstance(start_geo, Geometry):
self.generator.displacements = start_geo.displacements
tcount = 0
for t in temp_sequence:
temp_counter = np.where(self.temp == t)[0][0]
# update simulation counter
total_counter += 1
tcount += 1
# starting time of the current configuration
conf_start_time = time.time()
print("##############################")
print("Configuration " + str(total_counter) +
" out of " + str(nsims))
print("Temperature:", str(t), "K")
print("Stress:", str(p), "GPa")
print("Strain:", str(s), r"% change")
print("Electric Field:", str(f), "V/m")
print("##############################")
# file base name
sim_name = self.name + "T{:d}".format(int(t))
self.sim.settings["system_name"].value = sim_name
# configuration name
conf_name = "c{:02d}{:02d}{:02d}{:02d}".format(
temp_counter, stress_counter, strain_counter,
field_counter)
# subfolder name
subfolder_name = self.name + "." + conf_name
# modify target temperature
self.sim.settings["mc_temperature"].value = t
if self.stress != None: # modify target stress, if needed
self.sim.settings["external_stress"] = [p]
if self.strain != None: # set target strain, if needed
self.generator.strains = s
if self.field != None: # modify target field, if needed
self.sim.settings["static_electric_field"] = [f]
# define human output filename
output = sim_name + ".out"
# create restart file
self.sim.settings["geometry_restart"] = FDFSetting(
sim_name + ".restart")
self.generator.write_restart(sim_name + ".restart")
# simulate the current configuration
self.sim.launch(output_file=output)
# move all the output to its corresponding folder
configuration_folder = os.path.join(
self.main_output_folder, subfolder_name)
os.makedirs(configuration_folder)
files = os.listdir(self.current_path)
for fi in files:
if sim_name in fi:
move(fi, configuration_folder)
# finish time of the current conf
conf_finish_time = time.time()
conf_time = conf_finish_time - conf_start_time
print(
"\nConfiguration finished! (time elapsed: {:.3f}s)"
.format(conf_time))
# calculate equilibrium geometry
print("Calculating equilibrium geometry...")
partials = parser.find_partials(
t,
p=p,
s=s,
f=f,
min_step=self.mc_equilibration_steps)
aux_geo = Geometry(self.supercell,
self.model["species"],
self.model["nats"])
aux_geo.load_equilibrium_displacements(partials)
aux_geo.write_restart(
os.path.join(configuration_folder,
sim_name + "_EQUILIBRIUM.restart"))
# grab final geometry for next run if needed
if tcount < len(temp_sequence):
geo = parser.access_geometry(t, p=p, s=s, f=f)
self.generator.displacements = geo.displacements
print("All files stored in output/" + subfolder_name +
" succesfully.\n")
# remove the copy of the model
os.remove("param_file.xml")
self.generator.reset_geom()
main_finished_time = time.time()
main_time = main_finished_time - main_start_time
print("Simulation process complete!")
print("Total simulation time: {:.3f}s".format(main_time))
def setup(self,
system_name,
model,
supercell,
temp,
stress=None,
strain=None,
field=None,
output_folder="output"):
# TODO PARAMETER FILE, SPECIES, NATS
"""
Sets up everything
Parameters:
----------
- fdf (string): common fdf base file for all simulations.
- temp (list): list of temperatures, required.
- stress (list): list of stress vectors, if needed.
- strain (list): list of strain vectors, if needed.
- field (list): list of field vectors, if needed.
"""
# first and foremost, check if a valid
# ScaleUP executable has been configured.
if cfg.SCUP_EXEC == None or not os.path.exists(cfg.SCUP_EXEC):
print("""
WARNING: No valid executable detected
A path for a valid ScaleUP executable
must be provided before any simulations
are carried out.
In order to do this, include the lines
import ezSCUP.settings as cfg
cfg.SCUP_EXEC=[path_to_exec]
at the beginning of your script.
""")
raise ezSCUP.exceptions.NoSCUPExecutableDetected
self.name = system_name
self.model = model
self.supercell = supercell
self.sim = MC_SCUPHandler(self.name, "param_file.xml", cfg.SCUP_EXEC)
self.output_folder = output_folder # current output folder
self.temp = np.array(temp) # temperature vector, required
if stress == None: # stress vector, optional
self.stress = [np.zeros(6)]
else:
self.stress = [np.array(p, dtype=np.float64) for p in stress]
if strain == None: # strain vector list, optional
self.strain = [np.zeros(6)]
else:
self.strain = [np.array(s, dtype=np.float64) for s in strain]
if field == None: # electric field vector list, optional
self.field = [np.zeros(3)]
else:
self.field = [np.array(f, dtype=np.float64) for f in field]
# get the current path
self.current_path = os.getcwd()
# create output directory
try:
self.main_output_folder = os.path.join(self.current_path,
self.output_folder)
os.makedirs(self.main_output_folder)
self.DONE = False
except FileExistsError: # check whether directory already exists
if cfg.OVERWRITE:
print("""
Found already existing output
folder named "{}",
all its contents are now lost.
Reason: OVERWRITE set to True.""".format(self.output_folder))
rmtree(self.main_output_folder)
os.makedirs(self.main_output_folder)
self.DONE = False
print("")
pass
else:
print("""
Found already existing output
folder named "{}",
skipping simulation process.
Reason: OVERWRITE set to False.""".format(self.output_folder))
self.SETUP = True
self.DONE = True
return 0
# adjust the supercell as needed
self.sim.settings["supercell"] = [list(self.supercell)]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# record current settings from ezSCUP.settings
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
self.mc_steps = int(cfg.MC_STEPS)
self.mc_step_interval = int(cfg.MC_STEP_INTERVAL)
self.mc_equilibration_steps = int(cfg.MC_EQUILIBRATION_STEPS)
self.mc_max_jump = float(cfg.MC_MAX_JUMP)
self.lat_output_interval = int(cfg.LATTICE_OUTPUT_INTERVAL)
self.fixed_strain_components = cfg.FIXED_STRAIN_COMPONENTS
self.mc_annealing_rate = cfg.MC_ANNEALING_RATE
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# setup restart file generator
self.generator = Geometry(self.supercell, model["species"],
model["nats"])
# print common simulation settings
if cfg.PRINT_CONF_SETTINGS:
print("Starting FDF settings:")
self.sim.print()
print("")
# save simulation setup file
print("Saving simulation setup file... ")
setup = {
"name": self.name,
"model": self.model,
"supercell": self.supercell,
"temp": self.temp,
"strain": self.strain,
"stress": self.stress,
"field": self.field,
"mc_steps": self.mc_steps,
"mc_step_interval": self.mc_step_interval,
"mc_equilibration_steps": self.mc_equilibration_steps,
"mc_annealing_rate": self.mc_annealing_rate,
"mc_max_jump": self.mc_max_jump,
"lat_output_interval": self.lat_output_interval,
"fixed_strain_components": self.fixed_strain_components,
}
simulation_setup_file = os.path.join(self.main_output_folder,
cfg.SIMULATION_SETUP_FILE)
with open(simulation_setup_file, "wb") as f:
pickle.dump(setup, f)
print("\nSimulation run has been properly configured.")
print("You may now proceed to launch it.")
self.SETUP = True # simulation run setup nicely
pass
class MCSimulation:
"""
Executes Monte Carlo simulations with the given parameters.
# BASIC USAGE #
Creates an output folder in the current directory.
All the simulation data for each configuration is
conveniently stored in subfolders within it:
output / [scale-up system_name].c[n]
where n is the configuration number. That is, an 8 digit
integer that specifies the index for each parameter in the
given simulation, with two digits each in the following order:
n = [temp][stress][strain][field]
for example, in a simulation with temp=[20,40,60,80] all confs
simulated at 40K will be stored in folders named
output / [scale-up system_name].c01******
and so on. The information about the parameters for the simulation
run is stored in the file:
output / simulation.info # formated as a pickle file
In order to access all the simulation output for any given
configuration, refer to the class MCSimulationParser in this
same module.
# SIMULATION PARAMETER SPECIFICATION #
- Temperature (temp):
List of temperatures, in K
i.e:temp = np.linspace(20,100,5)
temp = [27, 45, 36]
- External Stress (stress):
List of stress vectors in Voigt notation, in GPa
i.e:stress = [
[10., 0., 0., 0., 0., 0.],
[0., 10., 0., 0., 0., 0.],
[0., 0., 10., 0., 0., 0.]
] # 10 GPa strains in each direction
- Strains (strain):
List of strain vectors in Voigt notation, in percentual change
i.e:strain = [
[+0.02, +0.02, 0., 0., 0., 0.],
[+0.00, +0.00, 0., 0., 0., 0.],
[-0.02, -0.02, 0., 0., 0., 0.]
] # +-2% and 0% cell strain in the x and y direction
- Static Electric Field (field):
List of electric field vectors, in V/m
i.e:field = [
[1e9, 0., 0.]
] # 1e9 V/m = 1V/nm in the x direction
Attributes:
----------
- fdf (string): base fdf file name
- name (string): default fdf's system_name
- temp (array): temperature vectors (K)
- stress (array): stress vectors (Gpa)
- strain (array): strain vectors (% change)
- field (array): electric field vectors (V/m)
"""
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
def setup(self,
system_name,
model,
supercell,
temp,
stress=None,
strain=None,
field=None,
output_folder="output"):
# TODO PARAMETER FILE, SPECIES, NATS
"""
Sets up everything
Parameters:
----------
- fdf (string): common fdf base file for all simulations.
- temp (list): list of temperatures, required.
- stress (list): list of stress vectors, if needed.
- strain (list): list of strain vectors, if needed.
- field (list): list of field vectors, if needed.
"""
# first and foremost, check if a valid
# ScaleUP executable has been configured.
if cfg.SCUP_EXEC == None or not os.path.exists(cfg.SCUP_EXEC):
print("""
WARNING: No valid executable detected
A path for a valid ScaleUP executable
must be provided before any simulations
are carried out.
In order to do this, include the lines
import ezSCUP.settings as cfg
cfg.SCUP_EXEC=[path_to_exec]
at the beginning of your script.
""")
raise ezSCUP.exceptions.NoSCUPExecutableDetected
self.name = system_name
self.model = model
self.supercell = supercell
self.sim = MC_SCUPHandler(self.name, "param_file.xml", cfg.SCUP_EXEC)
self.output_folder = output_folder # current output folder
self.temp = np.array(temp) # temperature vector, required
if stress == None: # stress vector, optional
self.stress = [np.zeros(6)]
else:
self.stress = [np.array(p, dtype=np.float64) for p in stress]
if strain == None: # strain vector list, optional
self.strain = [np.zeros(6)]
else:
self.strain = [np.array(s, dtype=np.float64) for s in strain]
if field == None: # electric field vector list, optional
self.field = [np.zeros(3)]
else:
self.field = [np.array(f, dtype=np.float64) for f in field]
# get the current path
self.current_path = os.getcwd()
# create output directory
try:
self.main_output_folder = os.path.join(self.current_path,
self.output_folder)
os.makedirs(self.main_output_folder)
self.DONE = False
except FileExistsError: # check whether directory already exists
if cfg.OVERWRITE:
print("""
Found already existing output
folder named "{}",
all its contents are now lost.
Reason: OVERWRITE set to True.""".format(self.output_folder))
rmtree(self.main_output_folder)
os.makedirs(self.main_output_folder)
self.DONE = False
print("")
pass
else:
print("""
Found already existing output
folder named "{}",
skipping simulation process.
Reason: OVERWRITE set to False.""".format(self.output_folder))
self.SETUP = True
self.DONE = True
return 0
# adjust the supercell as needed
self.sim.settings["supercell"] = [list(self.supercell)]
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# record current settings from ezSCUP.settings
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
self.mc_steps = int(cfg.MC_STEPS)
self.mc_step_interval = int(cfg.MC_STEP_INTERVAL)
self.mc_equilibration_steps = int(cfg.MC_EQUILIBRATION_STEPS)
self.mc_max_jump = float(cfg.MC_MAX_JUMP)
self.lat_output_interval = int(cfg.LATTICE_OUTPUT_INTERVAL)
self.fixed_strain_components = cfg.FIXED_STRAIN_COMPONENTS
self.mc_annealing_rate = cfg.MC_ANNEALING_RATE
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
# setup restart file generator
self.generator = Geometry(self.supercell, model["species"],
model["nats"])
# print common simulation settings
if cfg.PRINT_CONF_SETTINGS:
print("Starting FDF settings:")
self.sim.print()
print("")
# save simulation setup file
print("Saving simulation setup file... ")
setup = {
"name": self.name,
"model": self.model,
"supercell": self.supercell,
"temp": self.temp,
"strain": self.strain,
"stress": self.stress,
"field": self.field,
"mc_steps": self.mc_steps,
"mc_step_interval": self.mc_step_interval,
"mc_equilibration_steps": self.mc_equilibration_steps,
"mc_annealing_rate": self.mc_annealing_rate,
"mc_max_jump": self.mc_max_jump,
"lat_output_interval": self.lat_output_interval,
"fixed_strain_components": self.fixed_strain_components,
}
simulation_setup_file = os.path.join(self.main_output_folder,
cfg.SIMULATION_SETUP_FILE)
with open(simulation_setup_file, "wb") as f:
pickle.dump(setup, f)
print("\nSimulation run has been properly configured.")
print("You may now proceed to launch it.")
self.SETUP = True # simulation run setup nicely
pass
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
def change_output_folder(self, new_output_folder):
# get the current path
self.current_path = os.getcwd()
previous = self.output_folder
# create output directory
print("\nCreating new output folder...")
try:
main_output_folder = os.path.join(self.current_path,
new_output_folder)
os.makedirs(main_output_folder)
self.output_folder = new_output_folder
self.main_output_folder = main_output_folder
self.DONE = False
except FileExistsError: # check whether directory already exists
if cfg.OVERWRITE:
print("""
Found already existing output
folder named "{}",
all its contents are now lost.
Reason: OVERWRITE set to True.""".format(self.output_folder))
rmtree(main_output_folder)
os.makedirs(main_output_folder)
self.output_folder = new_output_folder
self.main_output_folder = main_output_folder
self.DONE = False
print("")
pass
else:
print("""
Found already existing output
folder named "{}", aborting folder swap.
Reason: OVERWRITE set to False.""".format(self.output_folder))
raise ezSCUP.exceptions.PreviouslyUsedOutputFolder()
# save simulation setup file
print("Saving simulation setup file... ")
setup = {
"name": self.name,
"model": self.model,
"supercell": self.supercell,
"temp": self.temp,
"strain": self.strain,
"stress": self.stress,
"field": self.field,
"mc_steps": self.mc_steps,
"mc_step_interval": self.mc_step_interval,
"mc_equilibration_steps": self.mc_equilibration_steps,
"mc_annealing_rate": self.mc_annealing_rate,
"mc_max_jump": self.mc_max_jump,
"lat_output_interval": self.lat_output_interval,
"fixed_strain_components": self.fixed_strain_components,
}
simulation_setup_file = os.path.join(self.main_output_folder,
cfg.SIMULATION_SETUP_FILE)
with open(simulation_setup_file, "wb") as f:
pickle.dump(setup, f)
print('\nOutput folder swapped from "{}" to "{}".'.format(
previous, self.output_folder))
pass
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
def independent_launch(self, start_geo=None):
"""
Start a simulation run with all the possible combinations
of the given parameter grid.
Parameters:
----------
- start_geo (Geometry): starting geometry of every simulation.
"""
# check if setup() has been run
if self.SETUP != True:
raise ezSCUP.exceptions.MissingSetup(
"Run MCSimulation.setup() before launching any simulation.")
# check if somulation has already been carried out
if self.DONE == True:
return 0
print("\n ~ Independent simulation run engaged. ~")
# checks restart file matches loaded geometry
if start_geo != None and isinstance(start_geo, Geometry):
print("\nApplying starting geometry...")
if not np.all(self.generator.supercell == start_geo.supercell):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.nats != None and (start_geo.nats !=
self.model["nats"]):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.species != None and (set(
self.model["species"]) != set(self.model["species"])):
raise ezSCUP.exceptions.GeometryNotMatching()
self.generator.displacements = start_geo.displacements
# get a copy of the model file
copy(self.model["file"], "param_file.xml")
# parser to get partials
parser = MCSimulationParser(output_folder=self.output_folder)
# simulation counters
total_counter = 0
# total number of simulations
nsims = self.temp.size * len(self.strain) * len(self.field) * len(
self.stress)
# starting time of the simulation process
main_start_time = time.time()
print("\nStarting calculations...\n")
for t in self.temp:
temp_counter = np.where(self.temp == t)[0][0]
for p in self.stress:
stress_counter = [np.array_equal(p, x)
for x in self.stress].index(True)
for s in self.strain:
strain_counter = [
np.array_equal(s, x) for x in self.strain
].index(True)
for f in self.field:
field_counter = [
np.array_equal(f, x) for x in self.field
].index(True)
# update simulation counter
total_counter += 1
# starting time of the current configuration
conf_start_time = time.time()
print("##############################")
print("Configuration " + str(total_counter) +
" out of " + str(nsims))
print("Temperature:", str(t), "K")
print("Stress:", str(p), "GPa")
print("Strain:", str(s), r"% change")
print("Electric Field:", str(f), "V/m")
print("##############################")
# file base name
sim_name = self.name + "T{:d}".format(int(t))
self.sim.settings["system_name"].value = sim_name
# configuration name
conf_name = "c{:02d}{:02d}{:02d}{:02d}".format(
temp_counter, stress_counter, strain_counter,
field_counter)
# subfolder name
subfolder_name = self.name + "." + conf_name
# modify target temperature
self.sim.settings["mc_temperature"].value = t
if self.stress != None: # modify target stress, if needed
self.sim.settings["external_stress"] = [p]
else:
p = np.zeros(6)
if self.strain != None: # set target strain, if needed
self.generator.strains = s
else:
s = np.zeros(6)
if self.field != None: # modify target field, if needed
self.sim.settings["static_electric_field"] = [f]
else:
f = np.zeros(3)
# define human output filename
output = sim_name + ".out"
# create restart file
self.sim.settings["geometry_restart"] = FDFSetting(
sim_name + ".restart")
self.generator.write_restart(sim_name + ".restart")
# simulate the current configuration
self.sim.launch(output_file=output)
# move all the output to its corresponding folder
configuration_folder = os.path.join(
self.main_output_folder, subfolder_name)
os.makedirs(configuration_folder)
files = os.listdir(self.current_path)
for fi in files:
if sim_name in fi:
move(fi, configuration_folder)
# finish time of the current conf
conf_finish_time = time.time()
conf_time = conf_finish_time - conf_start_time
print(
"\nConfiguration finished! (time elapsed: {:.3f}s)"
.format(conf_time))
# calculate equilibrium geometry
print("Calculating equilibrium geometry...")
partials = parser.find_partials(
t,
p=p,
s=s,
f=f,
min_step=self.mc_equilibration_steps)
aux_geo = Geometry(self.supercell,
self.model["species"],
self.model["nats"])
aux_geo.load_equilibrium_displacements(partials)
aux_geo.write_restart(
os.path.join(configuration_folder,
sim_name + "_EQUILIBRIUM.restart"))
print("All files stored in output/" + subfolder_name +
" succesfully.\n")
self.generator.reset_geom()
# remove the copy of the model
os.remove("param_file.xml")
main_finished_time = time.time()
main_time = main_finished_time - main_start_time
print("Simulation process complete!")
print("Total simulation time: {:.3f}s".format(main_time))
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
def sequential_launch_by_temperature(self,
start_geo=None,
inverse_order=False):
"""
Simulation run where the equilibrium geometry of the simulation for
the previous temperature is used as starting geometry of the next one.
Parameters:
----------
- start_geo (RestartGenerator): starting geometry of the first temperature.
"""
# check if setup() has been run
if self.SETUP != True:
raise ezSCUP.exceptions.MissingSetup(
"Run MCSimulation.setup() before launching any simulation.")
# check if somulation has already been carried out
if self.DONE == True:
return 0
print("\n ~ Sequential simulation run by temperature engaged. ~ ")
# checks restart file matches loaded geometry
if start_geo != None and isinstance(start_geo, Geometry):
print("\nApplying starting geometry...")
if not np.all(self.generator.supercell == start_geo.supercell):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.nats != None and (start_geo.nats !=
self.model["nats"]):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.species != None and (set(
self.model["species"]) != set(self.model["species"])):
raise ezSCUP.exceptions.GeometryNotMatching()
# get a copy of the model file
copy(self.model["file"], "param_file.xml")
# parser to get equilibrium geometry
parser = MCSimulationParser(output_folder=self.output_folder)
# adjust temperature ordering
if inverse_order:
temp_sequence = list(reversed(list(self.temp)))
else:
temp_sequence = list(self.temp)
# simulation counters
total_counter = 0
# total number of simulations
nsims = self.temp.size * len(self.strain) * len(self.field) * len(
self.stress)
# starting time of the simulation process
main_start_time = time.time()
print("\nStarting calculations...\n")
for p in self.stress:
stress_counter = [np.array_equal(p, x)
for x in self.stress].index(True)
for s in self.strain:
strain_counter = [np.array_equal(s, x)
for x in self.strain].index(True)
for f in self.field:
field_counter = [np.array_equal(f, x)
for x in self.field].index(True)
# set starting geometry
if start_geo != None and isinstance(start_geo, Geometry):
self.generator.displacements = start_geo.displacements
tcount = 0
for t in temp_sequence:
temp_counter = np.where(self.temp == t)[0][0]
# update simulation counter
total_counter += 1
tcount += 1
# starting time of the current configuration
conf_start_time = time.time()
print("##############################")
print("Configuration " + str(total_counter) +
" out of " + str(nsims))
print("Temperature:", str(t), "K")
print("Stress:", str(p), "GPa")
print("Strain:", str(s), r"% change")
print("Electric Field:", str(f), "V/m")
print("##############################")
# file base name
sim_name = self.name + "T{:d}".format(int(t))
self.sim.settings["system_name"].value = sim_name
# configuration name
conf_name = "c{:02d}{:02d}{:02d}{:02d}".format(
temp_counter, stress_counter, strain_counter,
field_counter)
# subfolder name
subfolder_name = self.name + "." + conf_name
# modify target temperature
self.sim.settings["mc_temperature"].value = t
if self.stress != None: # modify target stress, if needed
self.sim.settings["external_stress"] = [p]
if self.strain != None: # set target strain, if needed
self.generator.strains = s
if self.field != None: # modify target field, if needed
self.sim.settings["static_electric_field"] = [f]
# define human output filename
output = sim_name + ".out"
# create restart file
self.sim.settings["geometry_restart"] = FDFSetting(
sim_name + ".restart")
self.generator.write_restart(sim_name + ".restart")
# simulate the current configuration
self.sim.launch(output_file=output)
# move all the output to its corresponding folder
configuration_folder = os.path.join(
self.main_output_folder, subfolder_name)
os.makedirs(configuration_folder)
files = os.listdir(self.current_path)
for fi in files:
if sim_name in fi:
move(fi, configuration_folder)
# finish time of the current conf
conf_finish_time = time.time()
conf_time = conf_finish_time - conf_start_time
print(
"\nConfiguration finished! (time elapsed: {:.3f}s)"
.format(conf_time))
# calculate equilibrium geometry
print("Calculating equilibrium geometry...")
partials = parser.find_partials(
t,
p=p,
s=s,
f=f,
min_step=self.mc_equilibration_steps)
aux_geo = Geometry(self.supercell,
self.model["species"],
self.model["nats"])
aux_geo.load_equilibrium_displacements(partials)
aux_geo.write_restart(
os.path.join(configuration_folder,
sim_name + "_EQUILIBRIUM.restart"))
# grab final geometry for next run if needed
if tcount < len(temp_sequence):
geo = parser.access_geometry(t, p=p, s=s, f=f)
self.generator.displacements = geo.displacements
print("All files stored in output/" + subfolder_name +
" succesfully.\n")
# remove the copy of the model
os.remove("param_file.xml")
self.generator.reset_geom()
main_finished_time = time.time()
main_time = main_finished_time - main_start_time
print("Simulation process complete!")
print("Total simulation time: {:.3f}s".format(main_time))
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
def sequential_launch_by_strain(self, start_geo=None, inverse_order=False):
"""
Simulation run where the equilibrium geometry of the simulation for
the previous temperature is used as starting geometry of the next one.
Parameters:
----------
- start_geo (RestartGenerator): starting geometry of the first temperature.
"""
# check if setup() has been run
if self.SETUP != True:
raise ezSCUP.exceptions.MissingSetup(
"Run MCSimulation.setup() before launching any simulation.")
# check if simulation has already been carried out
if self.DONE == True:
return 0
print("\n ~ Sequential simulation run by strain engaged. ~ ")
# checks restart file matches loaded geometry
if start_geo != None and isinstance(start_geo, Geometry):
print("\nApplying starting geometry...")
if not np.all(self.generator.supercell == start_geo.supercell):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.nats != None and (start_geo.nats !=
self.model["nats"]):
raise ezSCUP.exceptions.GeometryNotMatching()
if self.generator.species != None and (set(
self.model["species"]) != set(self.model["species"])):
raise ezSCUP.exceptions.GeometryNotMatching()
# get a copy of the model file
copy(self.model["file"], "param_file.xml")
# parser to get equilibrium geometry
parser = MCSimulationParser(output_folder=self.output_folder)
# adjust strain ordering
if inverse_order:
strain_sequence = list(reversed(list(self.strain)))
else:
strain_sequence = list(self.strain)
# simulation counters
total_counter = 0
# total number of simulations
nsims = self.temp.size * len(self.strain) * len(self.field) * len(
self.stress)
# starting time of the simulation process
main_start_time = time.time()
print("\nStarting calculations...\n")
for t in self.temp:
temp_counter = np.where(self.temp == t)[0][0]
for p in self.stress:
stress_counter = [np.array_equal(p, x)
for x in self.stress].index(True)
for f in self.field:
field_counter = [np.array_equal(f, x)
for x in self.field].index(True)
# set starting geometry
if start_geo != None and isinstance(start_geo, Geometry):
self.generator.displacements = start_geo.displacements
scount = 0
for s in strain_sequence:
strain_counter = [
np.array_equal(s, x) for x in self.strain
].index(True)
# update simulation counter
total_counter += 1
scount += 1
# starting time of the current configuration
conf_start_time = time.time()
print("##############################")
print("Configuration " + str(total_counter) +
" out of " + str(nsims))
print("Temperature:", str(t), "K")
print("Stress:", str(p), "GPa")
print("Strain:", str(s), r"% change")
print("Electric Field:", str(f), "V/m")
print("##############################")
# file base name
sim_name = self.name + "T{:d}".format(int(t))
self.sim.settings["system_name"].value = sim_name
# configuration name
conf_name = "c{:02d}{:02d}{:02d}{:02d}".format(
temp_counter, stress_counter, strain_counter,
field_counter)
# subfolder name
subfolder_name = self.name + "." + conf_name
# modify target temperature
self.sim.settings["mc_temperature"].value = t
if self.stress != None: # modify target stress, if needed
self.sim.settings["external_stress"] = [p]
if self.strain != None: # set target strain, if needed
self.generator.strains = s
if self.field != None: # modify target field, if needed
self.sim.settings["static_electric_field"] = [f]
# define human output filename
output = sim_name + ".out"
# create restart file
self.sim.settings["geometry_restart"] = FDFSetting(
sim_name + ".restart")
self.generator.write_restart(sim_name + ".restart")
# simulate the current configuration
self.sim.launch(output_file=output)
# move all the output to its corresponding folder
configuration_folder = os.path.join(
self.main_output_folder, subfolder_name)
os.makedirs(configuration_folder)
files = os.listdir(self.current_path)
for fi in files:
if sim_name in fi:
move(fi, configuration_folder)
# finish time of the current conf
conf_finish_time = time.time()
conf_time = conf_finish_time - conf_start_time
print(
"\nConfiguration finished! (time elapsed: {:.3f}s)"
.format(conf_time))
# calculate equilibrium geometry
print("Calculating equilibrium geometry...")
partials = parser.find_partials(
t,
p=p,
s=s,
f=f,
min_step=self.mc_equilibration_steps)
aux_geo = Geometry(self.supercell,
self.model["species"],
self.model["nats"])
aux_geo.load_equilibrium_displacements(partials)
aux_geo.write_restart(
os.path.join(configuration_folder,
sim_name + "_EQUILIBRIUM.restart"))
# grab final geometry for next run if needed
if scount < len(strain_sequence):
geo = parser.access_geometry(t, p=p, s=s, f=f)
self.generator.displacements = geo.displacements
print("All files stored in output/" + subfolder_name +
" succesfully.\n")
# remove the copy of the model
os.remove("param_file.xml")
self.generator.reset_geom()
main_finished_time = time.time()
main_time = main_finished_time - main_start_time
print("Simulation process complete!")
print("Total simulation time: {:.3f}s".format(main_time))