def prepare_stacking_fault_map_2D(database_name, run_directory_name,
pot_kwargs=None, **kwargs):
"""
Calls prepare stacking_fault_map_2D for each unique family
"""
# Load database
database = iprPy.load_database(database_name)
# Build kwargs for each family
families = np.unique(database.get_records_df(style='stacking_fault').family)
for family in families:
print(family, flush=True)
kwargs['parent_family'] = kwargs['defect_family'] = family
# Prepare
prepare.stacking_fault_map_2D.main(database_name, run_directory_name,
pot_kwargs=pot_kwargs, **kwargs)
def prepare_surface_energy_static(database_name, run_directory_name,
pot_kwargs=None, **kwargs):
"""
Calls prepare surface_energy_static for each unique family
"""
# Load database
database = iprPy.load_database(database_name)
# Build kwargs for each family
families = np.unique(database.get_records_df(style='free_surface').family)
for family in families:
print(family, flush=True)
kwargs['parent_family'] = kwargs['defect_family'] = family
# Prepare
prepare.surface_energy_static.main(database_name, run_directory_name,
pot_kwargs=pot_kwargs, **kwargs)
def main():
"""
Primary prepare workflow for setting up calculations consistent with how
they are performed for the NIST Interatomic Potentials Repository.
GLOBAL SETTINGS:
- database - The iprPy.Database to use
- prepare_terms - A dict of prepare settings to use.
- all_lmppot_ids - The list of LAMMPS potential ids to use.
INDIVIDUAL POOL SETTINGS:
- styles - The list of calculation + workflow branch styles to prepare.
- run_directory - The run directory where the prepared calculations are put.
- np_per_runner - The expected number of processors per calculation.
- num_lmppot_ids - The max number of LAMMPS potentials to prepare at a time.
"""
################### Set database and global prepare_terms #################
# Load database
database = iprPy.load_database('master')
print(database)
# Define executables and commands
prepare_terms = {}
prepare_terms['lammps_command'] = 'E:/LAMMPS/2020-03-03/bin/lmp_mpi'
prepare_terms['mpi_command'] = 'mpiexec -localonly {np_per_runner}'
prepare_terms['lammps_command_snap_1'] = 'E:/LAMMPS/2017-01-27/bin/lmp_mpi'
prepare_terms['lammps_command_snap_2'] = 'E:/LAMMPS/2019-06-05/bin/lmp_mpi'
prepare_terms['lammps_command_old'] = 'E:/LAMMPS/2019-06-05/bin/lmp_mpi'
#prepare_terms['lammps_command_aenet'] = '/users/lmh1/LAMMPS/bin/lmp_mpi_2020_03_03_aenet'
######################## Specify potentials to use ########################
# Option #1: Select potentials from database to use
#lmppots_df = database.potdb.get_lammps_potentials(return_df = True,
# status = 'active',
#potid = ['1999--Mishin-Y-Farkas-D-Mehl-M-J-Papaconstantopoulos-D-A--Ni'],
#pair_style = ['eam', 'eam/alloy', 'eam/fs'],
# symbols = ['Cu'],
#)[1]
#all_lmppot_ids = np.unique(lmppots_df.id).tolist()
# Option #2: Specify potential ids directly
all_lmppot_ids = [
'2019--Plummer-G--Ti-Al-C--LAMMPS--ipr1',
'2019--Plummer-G--Ti-Si-C--LAMMPS--ipr1',
'2021--Plummer-G--Ti-Al-C--LAMMPS--ipr1',
# '2022--Hiremath-P--W--LAMMPS--ipr1',
# '2022--Mendelev-M-I--Ni-Nb--LAMMPS--ipr1'
]
print(len(all_lmppot_ids), 'potential ids found')
print()
########################### Pool settings #################################
# Pool #1: Basic potential evaluations and scans
styles = [
'isolated_atom',
'diatom_scan',
'E_vs_r_scan:bop',
'E_vs_r_scan',
]
run_directory = 'master_1'
np_per_runner = '1'
num_lmppot_ids = 100
prepare_pool(database, styles, run_directory, np_per_runner,
all_lmppot_ids, num_lmppot_ids, prepare_terms)
# Pool #2: Round 1 of crystal structure relaxations
styles = [
'relax_box',
'relax_static',
'relax_dynamic',
]
run_directory = 'master_2'
np_per_runner = '1'
num_lmppot_ids = 100
prepare_pool(database, styles, run_directory, np_per_runner,
all_lmppot_ids, num_lmppot_ids, prepare_terms)
# Pool #3: Round 2 of crystal structure relaxations
styles = ['relax_static:from_dynamic']
run_directory = 'master_3'
np_per_runner = '1'
num_lmppot_ids = 100
prepare_pool(database, styles, run_directory, np_per_runner,
all_lmppot_ids, num_lmppot_ids, prepare_terms)
# Pool #4: Crystal space group analysis
styles = ['crystal_space_group:relax']
run_directory = 'master_4'
np_per_runner = '1'
num_lmppot_ids = 100
prepare_pool(database, styles, run_directory, np_per_runner,
all_lmppot_ids, num_lmppot_ids, prepare_terms)
# import libraries
import numpy as np
import potentials
import atomman as am
import iprPy
# Load database
database = iprPy.load_database('iprhub')
print(database)
# Define executables and commands
prepare_terms = {}
prepare_terms['lammps_command'] = '/users/lmh1/LAMMPS/2020_03_03/src/lmp_mpi'
prepare_terms['mpi_command'] = '/cluster/deb9/bin/mpirun -n {np_per_runner}'
prepare_terms[
'lammps_command_snap_1'] = '/users/lmh1/LAMMPS/2017_03_31/src/lmp_mpi'
prepare_terms[
'lammps_command_snap_2'] = '/users/lmh1/LAMMPS/2019_06_05/src/lmp_mpi'
prepare_terms[
'lammps_command_old'] = '/users/lmh1/LAMMPS/2019_06_05/src/lmp_mpi'
prepare_terms[
'lammps_command_aenet'] = '/users/lmh1/LAMMPS/bin/lmp_mpi_2020_03_03_aenet'
# Potential settings
prepare_terms['potential_status'] = 'all'
lmppots, lmppots_df = database.potdb.get_lammps_potentials(return_df=True,
status=None)
all_lmppot_ids = np.unique(lmppots_df.id).tolist()
print(len(all_lmppot_ids), 'potential ids found')
print()
from multiprocessing import Pool
import iprPy
from iprPy.workflow import multi_runners
import iprPy.workflow.prepare as prepare
if __name__ == '__main__':
# Database, run directory and number of processors to use
database_name = 'testDB'
run_directory_name = 'testDB_1'
database = iprPy.load_database(name=database_name)
run_directory = iprPy.load_run_directory(name=run_directory_name)
np = 1
# Lammps and mpi commands
lammps_command = 'lmp_mpi -p 8x1'
mpi_command = 'mpiexec -localonly 8'
number_replicas = 8
# Potential-based modifiers
pot_kwargs = {}
#pot_kwargs['id'] = '2008--Zhou-X-W--Pd-H--LAMMPS--ipr1'
pot_kwargs['currentIPR'] = 'False'
pot_kwargs['pair_style'] = ['eam', 'eam/alloy', 'eam/fs', 'eam/cd']
# Prototype-based modifiers
families = [
'A1--Cu--fcc',
# 'A2--W--bcc',
# import libraries
import numpy as np
import potentials
import atomman as am
import iprPy
# Load database
database = iprPy.load_database('master')
print(database)
# Define executables and commands
prepare_terms = {}
prepare_terms['lammps_command'] = 'E:/LAMMPS/2020-03-03/bin/lmp_mpi'
prepare_terms['mpi_command'] = 'mpiexec -localonly {np_per_runner}'
prepare_terms['lammps_command_snap_1'] = 'E:/LAMMPS/2017-01-27/bin/lmp_mpi'
prepare_terms['lammps_command_snap_2'] = 'E:/LAMMPS/2019-06-05/bin/lmp_mpi'
prepare_terms['lammps_command_old'] = 'E:/LAMMPS/2019-06-05/bin/lmp_mpi'
#prepare_terms['lammps_command_aenet'] = '/users/lmh1/LAMMPS/bin/lmp_mpi_2020_03_03_aenet'
# Potential settings
all_lmppot_ids = [
'2019--Plummer-G--Ti-Al-C--LAMMPS--ipr1',
'2019--Plummer-G--Ti-Si-C--LAMMPS--ipr1',
'2021--Plummer-G--Ti-Al-C--LAMMPS--ipr1',
# '2022--Hiremath-P--W--LAMMPS--ipr1',
# '2022--Mendelev-M-I--Ni-Nb--LAMMPS--ipr1'
]
prepare_terms['potential_status'] = 'all'
#lmppots, lmppots_df = database.potdb.get_lammps_potentials(return_df=True, status=None)
#all_lmppot_ids = np.unique(lmppots_df.id).tolist()
print(len(all_lmppot_ids), 'potential ids found')