E2EMolMats/main.py at master · InfluenceFunctional/E2EMolMats · GitHub

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"""
generate an .xyz file and automatically prep LAMMPS inputs
"""

import itertools
import os
import sys
import warnings
import argparse
from distutils.dir_util import copy_tree

warnings.filterwarnings('ignore', message='.*OVITO.*PyPI')
from lammps_prepper import create_xyz_and_run_lammps

'''import run config'''
from configs.dev import batch_config  # todo convert to command line arg

parser = argparse.ArgumentParser()
args = parser.parse_known_args()[1]

if '--run_num' in args:
    run_num = int(args[1])
    print(f"Running job {run_num}")
else:
    run_num = None

dynamic_configs = {key: value for key, value in batch_config.items() if isinstance(value, list)}
run_args = list(itertools.product(*list(dynamic_configs.values())))
dynamic_arg_keys = {key: i for i, key in enumerate(dynamic_configs.keys())}

n_runs = len(run_args)
print(f"Running {int(n_runs)} LAMMPS MD Jobs")

'''setup working directory'''
machine = batch_config['machine']  # 'cluster' or 'local'
if machine == 'local':
    head_dir = r'C:\Users\mikem\crystals\clusters/cluster_structures/' + batch_config['run_name']
    crystals_path = r'C:\Users\mikem\crystals\clusters\crystals_reference/'
elif machine == 'cluster':
    head_dir = r'/vast/mk8347/molecule_clusters/' + batch_config['run_name']
    crystals_path = r'/vast/mk8347/molecule_clusters/CrystalStructures/'
else:
    print("Machine must be 'local' or 'cluster'")
    sys.exit()

if not os.path.exists(head_dir):
    os.mkdir(head_dir)

source_path = os.getcwd()
os.chdir(head_dir)

if not os.path.exists('common'):
    os.mkdir('common')
    copy_tree(source_path + '/common', './common/')  # copy from source

if run_num is not None:  # for running in batches or just one at a time
    run_config = run_args[run_num]
    create_xyz_and_run_lammps({
        'run_num': run_num,
        'head_dir': head_dir,
        'crystals_path': crystals_path,

        'print_steps': batch_config['print_steps'],
        'run_time': batch_config['run_time'],
        'integrator': batch_config['integrator'],
        'box_type': batch_config['box_type'],
        'bulk_crystal': batch_config['bulk_crystal'],
        'min_inter_cluster_distance': batch_config['min_inter_cluster_distance'],
        'cluster_type': batch_config['cluster_type'],
        'min_lattice_length': batch_config['min_lattice_length'],
        'prep_crystal_in_melt': batch_config['prep_crystal_in_melt'],
        'equil_time': batch_config['equil_time'],
        'melt_temperature': batch_config['melt_temperature'],
        'ramp_temperature': batch_config['ramp_temperature'],
        'init_temperature': batch_config['init_temperature'],

        'max_sphere_radius': run_config[dynamic_arg_keys['max_sphere_radius']],
        'cluster_size': run_config[dynamic_arg_keys['cluster_size']],
        'seed': run_config[dynamic_arg_keys['seed']],
        'damping': run_config[dynamic_arg_keys['damping']],
        'structure_identifier': run_config[dynamic_arg_keys['structure_identifier']],
        'temperature': run_config[dynamic_arg_keys['temperature']],
        'defect_rate': run_config[dynamic_arg_keys['defect_rate']],
        'defect_type': run_config[dynamic_arg_keys['defect_type']],
        'gap_rate': run_config[dynamic_arg_keys['gap_rate']],
        'scramble_rate': run_config[dynamic_arg_keys['scramble_rate']],
    }
    )
else:
    for run_num, run_config in enumerate(run_args):
        create_xyz_and_run_lammps({
            'run_num': run_num,
            'head_dir': head_dir,
            'crystals_path': crystals_path,

            'print_steps': batch_config['print_steps'],
            'run_time': batch_config['run_time'],
            'integrator': batch_config['integrator'],
            'box_type': batch_config['box_type'],
            'bulk_crystal': batch_config['bulk_crystal'],
            'min_inter_cluster_distance': batch_config['min_inter_cluster_distance'],
            'cluster_type': batch_config['cluster_type'],
            'min_lattice_length': batch_config['min_lattice_length'],
            'prep_crystal_in_melt': batch_config['prep_crystal_in_melt'],
            'equil_time': batch_config['equil_time'],
            'melt_temperature': batch_config['melt_temperature'],
            'ramp_temperature': batch_config['ramp_temperature'],
            'init_temperature': batch_config['init_temperature'],

            'max_sphere_radius': run_config[dynamic_arg_keys['max_sphere_radius']],
            'cluster_size': run_config[dynamic_arg_keys['cluster_size']],
            'seed': run_config[dynamic_arg_keys['seed']],
            'damping': run_config[dynamic_arg_keys['damping']],
            'structure_identifier': run_config[dynamic_arg_keys['structure_identifier']],
            'temperature': run_config[dynamic_arg_keys['temperature']],
            'defect_rate': run_config[dynamic_arg_keys['defect_rate']],
            'defect_type': run_config[dynamic_arg_keys['defect_type']],
            'gap_rate': run_config[dynamic_arg_keys['gap_rate']],
            'scramble_rate': run_config[dynamic_arg_keys['scramble_rate']],
        }
        )