def main():
info()
parser = argparse.ArgumentParser(description="""
dpgen is a convenient script that uses DeepGenerator to prepare initial
data, drive DeepMDkit and analyze results. This script works based on
several sub-commands with their own options. To see the options for the
sub-commands, type "dpgen sub-command -h".""",
epilog="""
Author: DeepGenTeam
Version: {}
Last updated: {}""".format(__version__, __date__))
subparsers = parser.add_subparsers()
# init surf model
parser_init_surf = subparsers.add_parser(
"init_surf", help="Generating initial data for surface systems.")
parser_init_surf.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_init_surf.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_init_surf.set_defaults(func=gen_init_surf)
# init bulk model
parser_init_bulk = subparsers.add_parser(
"init_bulk", help="Generating initial data for bulk systems.")
parser_init_bulk.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_init_bulk.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_init_bulk.set_defaults(func=gen_init_bulk)
# parser_init.add_argument("-p",'--parameter', type=str, dest='param',
# help="parameter file, json/yaml format")
# parser_init.add_argument("-s","--stage", type=int, dest='stage',
# help="the stage of init, can be 1, 2, 3 or 4. "
# "1: Setup vasp jobs for relaxation. "
# "2: Collect vasp relaxed confs (if relax is not skiped). Perturb system. "
# "3: Setup vasp jobs for MD of perturbed system. "
# "4: Collect vasp md confs, make deepmd data. ")
# parser_init.add_argument("directories", metavar="dir", default=".",
# type=str, nargs="*",
# help="directory to process (default to .)")
# parser_init.set_defaults(func=gen_data)
# run
parser_run = subparsers.add_parser("run",
help="Main process of Deep Generator.")
parser_run.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_run.add_argument('MACHINE',
type=str,
help="machine file, json/yaml format")
parser_run.add_argument('-d',
'--debug',
action='store_true',
help="log debug info")
parser_run.set_defaults(func=gen_run)
# test
parser_test = subparsers.add_parser("test",
help="Auto-test for Deep Potential.")
parser_test.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_test.add_argument('MACHINE',
type=str,
help="machine file, json/yaml format")
parser_test.set_defaults(func=gen_test)
# db
parser_db = subparsers.add_parser(
"db", help="Collecting data from Deep Generator.")
parser_db.add_argument('PATH',
type=str,
help="root path for dpgen modeling")
parser_db.add_argument(
'CALCULATOR',
type=str,
help="calculator used for labeling: vasp/pwscf/gaussian")
parser_db.add_argument('OUTPUT',
type=str,
help="output filename : file.json/file.yaml")
parser_db.add_argument("ID_PREFIX",
type=str,
default=None,
nargs="?",
help="prefix of an entry id")
parser_db.set_defaults(func=db_run)
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
# argcomplete not present.
pass
args = parser.parse_args()
try:
getattr(args, "func")
except AttributeError:
parser.print_help()
sys.exit(0)
args.func(args)
def main():
info()
print("Description\n------------")
parser = argparse.ArgumentParser(description="""
dpgen is a convenient script that uses DeepGenerator to prepare initial
data, drive DeepMDkit and analyze results. This script works based on
several sub-commands with their own options. To see the options for the
sub-commands, type "dpgen sub-command -h".""")
subparsers = parser.add_subparsers()
# init surf model
parser_init_surf = subparsers.add_parser(
"init_surf", help="Generating initial data for surface systems.")
parser_init_surf.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_init_surf.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_init_surf.set_defaults(func=gen_init_surf)
# init bulk model
parser_init_bulk = subparsers.add_parser(
"init_bulk", help="Generating initial data for bulk systems.")
parser_init_bulk.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_init_bulk.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_init_bulk.set_defaults(func=gen_init_bulk)
parser_auto_gen_param = subparsers.add_parser("auto_gen_param",
help="auto gen param.json")
# parser_auto_gen_param.add_argument('meltpoint', type=float, help="melt point")
parser_auto_gen_param.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_auto_gen_param.set_defaults(func=auto_gen_param)
# parser_init_reaction
parser_init_reaction = subparsers.add_parser(
"init_reaction", help="Generating initial data for reactive systems.")
parser_init_reaction.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_init_reaction.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_init_reaction.set_defaults(func=gen_init_reaction)
# run
parser_run = subparsers.add_parser(
"run", help="Main process of Deep Potential Generator.")
parser_run.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_run.add_argument('MACHINE',
type=str,
help="machine file, json/yaml format")
parser_run.add_argument('-d',
'--debug',
action='store_true',
help="log debug info")
parser_run.set_defaults(func=gen_run)
# run/report
parser_rr = subparsers.add_parser(
"run/report",
help=
"Report the systems and the thermodynamic conditions of the labeled frames."
)
parser_rr.add_argument("JOB_DIR",
type=str,
help="the directory of the DP-GEN job,")
parser_rr.add_argument('-s',
"--stat-sys",
action='store_true',
help="count the labeled frames for each system")
parser_rr.add_argument(
'-i',
"--stat-iter",
action='store_true',
help=
"print the iteration candidate,failed,accurate count and fp calculation,success and fail count"
)
parser_rr.add_argument(
'-t',
"--stat-time",
action='store_true',
help=
"print the iteration time, warning!! assume model_devi parallel cores == 1"
)
parser_rr.add_argument(
'-p',
"--param",
type=str,
default='param.json',
help=
"the json file provides DP-GEN paramters, should be located in JOB_DIR"
)
parser_rr.add_argument('-v',
"--verbose",
action='store_true',
help="being loud")
parser_rr.set_defaults(func=run_report)
# collect
parser_coll = subparsers.add_parser("collect", help="Collect data.")
parser_coll.add_argument("JOB_DIR",
type=str,
help="the directory of the DP-GEN job")
parser_coll.add_argument("OUTPUT",
type=str,
help="the output directory of data")
parser_coll.add_argument(
'-p',
"--parameter",
type=str,
default='param.json',
help=
"the json file provides DP-GEN paramters, should be located in JOB_DIR"
)
parser_coll.add_argument('-v',
"--verbose",
action='store_true',
help="print number of data in each system")
parser_coll.add_argument(
'-m',
"--merge",
action='store_true',
help="merge the systems with the same chemical formula")
parser_coll.add_argument('-s',
"--shuffle",
action='store_true',
help="shuffle the data systems")
parser_coll.set_defaults(func=gen_collect)
# simplify
parser_run = subparsers.add_parser("simplify", help="Simplify data.")
parser_run.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_run.add_argument('MACHINE',
type=str,
help="machine file, json/yaml format")
parser_run.add_argument('-d',
'--debug',
action='store_true',
help="log debug info")
parser_run.set_defaults(func=gen_simplify)
# test
parser_test = subparsers.add_parser("autotest",
help="Auto-test for Deep Potential.")
parser_test.add_argument('TASK',
type=str,
help="task can be make, run or post")
parser_test.add_argument('PARAM',
type=str,
help="parameter file, json/yaml format")
parser_test.add_argument('MACHINE',
type=str,
default=None,
nargs="?",
help="machine file, json/yaml format")
parser_test.add_argument('-d',
'--debug',
action='store_true',
help="log debug info")
parser_test.set_defaults(func=gen_test)
# db
parser_db = subparsers.add_parser("db",
help="Collecting data from DP-GEN.")
parser_db.add_argument('PARAM',
type=str,
help="parameter file, json format")
parser_db.set_defaults(func=db_run)
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
# argcomplete not present.
pass
args = parser.parse_args()
try:
getattr(args, "func")
except AttributeError:
parser.print_help()
sys.exit(0)
args.func(args)
def main():
info()
print("Description\n------------")
parser = argparse.ArgumentParser(description="""
dpgen is a convenient script that uses DeepGenerator to prepare initial
data, drive DeepMDkit and analyze results. This script works based on
several sub-commands with their own options. To see the options for the
sub-commands, type "dpgen sub-command -h".""")
subparsers = parser.add_subparsers()
# init surf model
parser_init_surf = subparsers.add_parser(
"init_surf", help="Generating initial data for surface systems.")
parser_init_surf.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_init_surf.add_argument('MACHINE', type=str,default=None,nargs="?",
help="machine file, json/yaml format")
parser_init_surf.set_defaults(func=gen_init_surf)
# init bulk model
parser_init_bulk = subparsers.add_parser(
"init_bulk", help="Generating initial data for bulk systems.")
parser_init_bulk.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_init_bulk.add_argument('MACHINE', type=str,default=None,nargs="?",
help="machine file, json/yaml format")
parser_init_bulk.set_defaults(func=gen_init_bulk)
parser_auto_gen_param = subparsers.add_parser(
"auto_gen_param", help="auto gen param.json")
# parser_auto_gen_param.add_argument('meltpoint', type=float, help="melt point")
parser_auto_gen_param.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_auto_gen_param.set_defaults(func=auto_gen_param)
# parser_init.add_argument("-p",'--parameter', type=str, dest='param',
# help="parameter file, json/yaml format")
# parser_init.add_argument("-s","--stage", type=int, dest='stage',
# help="the stage of init, can be 1, 2, 3 or 4. "
# "1: Setup vasp jobs for relaxation. "
# "2: Collect vasp relaxed confs (if relax is not skiped). Perturb system. "
# "3: Setup vasp jobs for MD of perturbed system. "
# "4: Collect vasp md confs, make deepmd data. ")
# parser_init.add_argument("directories", metavar="dir", default=".",
# type=str, nargs="*",
# help="directory to process (default to .)")
# parser_init.set_defaults(func=gen_data)
parser_init_reaction = subparsers.add_parser(
"init_reaction", help="Generating initial data for reactive systems.")
parser_init_reaction.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_init_reaction.add_argument('MACHINE', type=str,default=None,nargs="?",
help="machine file, json/yaml format")
parser_init_reaction.set_defaults(func=gen_init_reaction)
# run
parser_run = subparsers.add_parser(
"run",
help="Main process of Deep Potential Generator.")
parser_run.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_run.add_argument('MACHINE', type=str,
help="machine file, json/yaml format")
parser_run.add_argument('-d','--debug', action='store_true',
help="log debug info")
parser_run.set_defaults(func=gen_run)
# run/report
parser_rr = subparsers.add_parser(
"run/report",
help="Report the systems and the thermodynamic conditions of the labeled frames.")
parser_rr.add_argument("JOB_DIR", type=str,
help="the directory of the DP-GEN job,")
parser_rr.add_argument('-s',"--stat-sys", action = 'store_true',
help="count the labeled frames for each system")
parser_rr.add_argument('-i', "--stat-iter", action= 'store_true',
help="print the iteration candidate,failed,accurate count and fp calculation,success and fail count")
parser_rr.add_argument('-t', "--stat-time", action= 'store_true',
help="print the iteration time, warning!! assume model_devi parallel cores == 1")
parser_rr.add_argument('-p',"--param", type=str, default = 'param.json',
help="the json file provides DP-GEN paramters, should be located in JOB_DIR")
parser_rr.add_argument('-v',"--verbose", action = 'store_true',
help="being loud")
parser_rr.set_defaults(func=run_report)
# test
parser_test = subparsers.add_parser("test", help="Auto-test for Deep Potential.")
parser_test.add_argument('PARAM', type=str,
help="parameter file, json/yaml format")
parser_test.add_argument('MACHINE', type=str,
help="machine file, json/yaml format")
parser_test.set_defaults(func=gen_test)
# db
parser_db = subparsers.add_parser(
"db",
help="Collecting data from DP-GEN.")
parser_db.add_argument('PARAM', type=str,
help="parameter file, json format")
parser_db.set_defaults(func=db_run)
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
# argcomplete not present.
pass
args = parser.parse_args()
try:
getattr(args, "func")
except AttributeError:
parser.print_help()
sys.exit(0)
args.func(args)
def main():
info()
parser = argparse.ArgumentParser(description="""
dpgen is a convenient script that uses DeepGenerator to prepare initial
data, drive DeepMDkit and analyze results. This script works based on
several sub-commands with their own options. To see the options for the
sub-commands, type "dpgen sub-command -h".""",
epilog="""
Author: DeepGenTeam
Version: {}
Last updated: {}""".format(__version__, __date__))
subparsers = parser.add_subparsers()
# init surf model
parser_init_surf = subparsers.add_parser(
"init_surf", help="dpgen initial data preparation tools for surface systems.")
parser_init_surf.add_argument('PARAM', type=str,
help="parameter file, json format")
parser_init_surf.add_argument('STAGE', type=int,
help="the stage of init, can be 1 or 2 "
"1: Setup vasp jobs for relaxation. "
"2: Collect vasp relaxed confs (if relax is not skiped). Perturb system.")
parser_init_surf.set_defaults(func=gen_init_surf)
# init bulk model
parser_init_bulk = subparsers.add_parser(
"init_bulk", help="dpgen initial data preparation tools for bulk systems.")
parser_init_bulk.add_argument('PARAM', type=str,
help="parameter file, json format")
parser_init_bulk.add_argument('STAGE', type=int,
help="the stage of init, can be 1, 2, 3 or 4. "
"1: Setup vasp jobs for relaxation. "
"2: Collect vasp relaxed confs (if relax is not skiped). Perturb system. "
"3: Setup vasp jobs for MD of perturbed system. "
"4: Collect vasp md confs, make deepmd data. "
)
parser_init_bulk.set_defaults(func=gen_init_bulk)
# parser_init.add_argument("-p",'--parameter', type=str, dest='param',
# help="parameter file, json format")
# parser_init.add_argument("-s","--stage", type=int, dest='stage',
# help="the stage of init, can be 1, 2, 3 or 4. "
# "1: Setup vasp jobs for relaxation. "
# "2: Collect vasp relaxed confs (if relax is not skiped). Perturb system. "
# "3: Setup vasp jobs for MD of perturbed system. "
# "4: Collect vasp md confs, make deepmd data. ")
# parser_init.add_argument("directories", metavar="dir", default=".",
# type=str, nargs="*",
# help="directory to process (default to .)")
# parser_init.set_defaults(func=gen_data)
# run
parser_run = subparsers.add_parser(
"run",
help="Runing DeepMD with generator model.")
parser_run.add_argument('PARAM', type=str,
help="parameter file, json format")
parser_run.add_argument('MACHINE', type=str,
help="machine file, json format")
parser_run.set_defaults(func=gen_run)
# test
parser_test = subparsers.add_parser("test", help="auto test for deep potential.")
parser_test.add_argument('PARAM', type=str,
help="parameter file, json format")
parser_test.add_argument('MACHINE', type=str,
help="machine file, json format")
parser_test.set_defaults(func=gen_test)
# # convert model
# parser_structure = subparsers.add_parser(
# "struct",
# help="structure conversion and analysis tools.")
# parser_structure.add_argument(
# "-f", "--filenames", dest="filenames",
# metavar="filename", nargs="+",
# help="List of structure files.")
# groups = parser_structure.add_mutually_exclusive_group(required=True)
# groups.add_argument("-c", "--convert", dest="convert", action="store_true",
# help="Convert from structure file 1 to structure "
# "file 2. Format determined from filename. "
# "Supported formats include POSCAR/CONTCAR, "
# "CIF, lmp.")
# groups.add_argument("-s", "--symmetry", dest="symmetry",
# metavar="tolerance", type=float,
# help="Determine the spacegroup using the "
# "specified tolerance. 0.1 is usually a good "
# "value for DFT calculations.")
# parser_structure.set_defaults(func=gen_struct)
try:
import argcomplete
argcomplete.autocomplete(parser)
except ImportError:
# argcomplete not present.
pass
args = parser.parse_args()
try:
getattr(args, "func")
except AttributeError:
parser.print_help()
sys.exit(0)
args.func(args)