"""DeePMD-Kit entry point module."""
import argparse
import logging
import textwrap
from pathlib import (
Path,
)
from typing import (
List,
Optional,
)
from deepmd import (
__version__,
)
from deepmd.common import (
clear_session,
)
from deepmd.entrypoints import (
compress,
config,
convert,
doc_train_input,
freeze,
make_model_devi,
neighbor_stat,
test,
train_dp,
transfer,
)
from deepmd.loggers import (
set_log_handles,
)
from deepmd.nvnmd.entrypoints.train import (
train_nvnmd,
)
__all__ = ["main", "parse_args", "get_ll", "main_parser"]
[docs]def get_ll(log_level: str) -> int:
"""Convert string to python logging level.
Parameters
----------
log_level : str
allowed input values are: DEBUG, INFO, WARNING, ERROR, 3, 2, 1, 0
Returns
-------
int
one of python logging module log levels - 10, 20, 30 or 40
"""
if log_level.isdigit():
int_level = (4 - int(log_level)) * 10
else:
int_level = getattr(logging, log_level)
return int_level
class RawTextArgumentDefaultsHelpFormatter(
argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter
):
"""This formatter is used to print multile-line help message with default value."""
[docs]def main_parser() -> argparse.ArgumentParser:
"""DeePMD-Kit commandline options argument parser.
Returns
-------
argparse.ArgumentParser
main parser of DeePMD-kit
"""
parser = argparse.ArgumentParser(
description="DeePMD-kit: A deep learning package for many-body potential energy"
" representation and molecular dynamics",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
subparsers = parser.add_subparsers(title="Valid subcommands", dest="command")
# * logging options parser *********************************************************
# with use of the parent argument this options will be added to every parser
parser_log = argparse.ArgumentParser(
add_help=False, formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_log.add_argument(
"-v",
"--log-level",
choices=["DEBUG", "3", "INFO", "2", "WARNING", "1", "ERROR", "0"],
default="INFO",
help="set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO "
"and 3=DEBUG",
)
parser_log.add_argument(
"-l",
"--log-path",
type=str,
default=None,
help="set log file to log messages to disk, if not specified, the logs will "
"only be output to console",
)
# * mpi logging parser *************************************************************
parser_mpi_log = argparse.ArgumentParser(
add_help=False, formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser_mpi_log.add_argument(
"-m",
"--mpi-log",
type=str,
default="master",
choices=("master", "collect", "workers"),
help="Set the manner of logging when running with MPI. 'master' logs only on "
"main process, 'collect' broadcasts logs from workers to master and 'workers' "
"means each process will output its own log",
)
# * config script ******************************************************************
parser_cfig = subparsers.add_parser(
"config",
parents=[parser_log],
help="fast configuration of parameter file for smooth model",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser_cfig.add_argument(
"-o", "--output", type=str, default="input.json", help="the output json file"
)
# * transfer script ****************************************************************
parser_transfer = subparsers.add_parser(
"transfer", parents=[parser_log], help="pass parameters to another model"
)
parser_transfer.add_argument(
"-r",
"--raw-model",
default="raw_frozen_model.pb",
type=str,
help="the model receiving parameters",
)
parser_transfer.add_argument(
"-O",
"--old-model",
default="old_frozen_model.pb",
type=str,
help="the model providing parameters",
)
parser_transfer.add_argument(
"-o",
"--output",
default="frozen_model.pb",
type=str,
help="the model after passing parameters",
)
# * config parser ******************************************************************
parser_train = subparsers.add_parser(
"train",
parents=[parser_log, parser_mpi_log],
help="train a model",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp train input.json
dp train input.json --restart model.ckpt
dp train input.json --init-model model.ckpt
"""
),
)
parser_train.add_argument(
"INPUT", help="the input parameter file in json or yaml format"
)
parser_train_subgroup = parser_train.add_mutually_exclusive_group()
parser_train_subgroup.add_argument(
"-i",
"--init-model",
type=str,
default=None,
help="Initialize the model by the provided checkpoint.",
)
parser_train_subgroup.add_argument(
"-r",
"--restart",
type=str,
default=None,
help="Restart the training from the provided checkpoint.",
)
parser_train_subgroup.add_argument(
"-f",
"--init-frz-model",
type=str,
default=None,
help="Initialize the training from the frozen model.",
)
parser_train_subgroup.add_argument(
"-t",
"--finetune",
type=str,
default=None,
help="Finetune the frozen pretrained model.",
)
parser_train.add_argument(
"-o",
"--output",
type=str,
default="out.json",
help="The output file of the parameters used in training.",
)
parser_train.add_argument(
"--skip-neighbor-stat",
action="store_true",
help="Skip calculating neighbor statistics. Sel checking, automatic sel, and model compression will be disabled.",
)
# * freeze script ******************************************************************
parser_frz = subparsers.add_parser(
"freeze",
parents=[parser_log],
help="freeze the model",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp freeze
dp freeze -o graph.pb
"""
),
)
parser_frz.add_argument(
"-c",
"--checkpoint-folder",
type=str,
default=".",
help="path to checkpoint folder",
)
parser_frz.add_argument(
"-o",
"--output",
type=str,
default="frozen_model.pb",
help="name of graph, will output to the checkpoint folder",
)
parser_frz.add_argument(
"-n",
"--node-names",
type=str,
default=None,
help="the frozen nodes, if not set, determined from the model type",
)
parser_frz.add_argument(
"-w",
"--nvnmd-weight",
type=str,
default=None,
help="the name of weight file (.npy), if set, save the model's weight into the file",
)
parser_frz.add_argument(
"--united-model",
action="store_true",
default=False,
help="When in multi-task mode, freeze all nodes into one united model",
)
# * test script ********************************************************************
parser_tst = subparsers.add_parser(
"test",
parents=[parser_log],
help="test the model",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp test -m graph.pb -s /path/to/system -n 30
"""
),
)
parser_tst.add_argument(
"-m",
"--model",
default="frozen_model.pb",
type=str,
help="Frozen model file to import",
)
parser_tst_subgroup = parser_tst.add_mutually_exclusive_group()
parser_tst_subgroup.add_argument(
"-s",
"--system",
default=".",
type=str,
help="The system dir. Recursively detect systems in this directory",
)
parser_tst_subgroup.add_argument(
"-f",
"--datafile",
default=None,
type=str,
help="The path to file of test list.",
)
parser_tst.add_argument(
"-S", "--set-prefix", default="set", type=str, help="The set prefix"
)
parser_tst.add_argument(
"-n", "--numb-test", default=100, type=int, help="The number of data for test"
)
parser_tst.add_argument(
"-r", "--rand-seed", type=int, default=None, help="The random seed"
)
parser_tst.add_argument(
"--shuffle-test", action="store_true", default=False, help="Shuffle test data"
)
parser_tst.add_argument(
"-d",
"--detail-file",
type=str,
default=None,
help="The prefix to files where details of energy, force and virial accuracy/accuracy per atom will be written",
)
parser_tst.add_argument(
"-a",
"--atomic",
action="store_true",
default=False,
help="Test the accuracy of atomic label, i.e. energy / tensor (dipole, polar)",
)
# * compress model *****************************************************************
# Compress a model, which including tabulating the embedding-net.
# The table is composed of fifth-order polynomial coefficients and is assembled
# from two sub-tables. The first table takes the step(parameter) as it's uniform
# step, while the second table takes 10 * step as it\s uniform step
# The range of the first table is automatically detected by deepmd-kit, while the
# second table ranges from the first table's upper boundary(upper) to the
# extrapolate(parameter) * upper.
parser_compress = subparsers.add_parser(
"compress",
parents=[parser_log, parser_mpi_log],
help="compress a model",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp compress
dp compress -i graph.pb -o compressed.pb
"""
),
)
parser_compress.add_argument(
"-i",
"--input",
default="frozen_model.pb",
type=str,
help="The original frozen model, which will be compressed by the code",
)
parser_compress.add_argument(
"-o",
"--output",
default="frozen_model_compressed.pb",
type=str,
help="The compressed model",
)
parser_compress.add_argument(
"-s",
"--step",
default=0.01,
type=float,
help="Model compression uses fifth-order polynomials to interpolate the embedding-net. "
"It introduces two tables with different step size to store the parameters of the polynomials. "
"The first table covers the range of the training data, while the second table is an extrapolation of the training data. "
"The domain of each table is uniformly divided by a given step size. "
"And the step(parameter) denotes the step size of the first table and the second table will "
"use 10 * step as it's step size to save the memory. "
"Usually the value ranges from 0.1 to 0.001. "
"Smaller step means higher accuracy and bigger model size",
)
parser_compress.add_argument(
"-e",
"--extrapolate",
default=5,
type=int,
help="The domain range of the first table is automatically detected by the code: [d_low, d_up]. "
"While the second table ranges from the first table's upper boundary(d_up) to the extrapolate(parameter) * d_up: [d_up, extrapolate * d_up]",
)
parser_compress.add_argument(
"-f",
"--frequency",
default=-1,
type=int,
help="The frequency of tabulation overflow check(Whether the input environment "
"matrix overflow the first or second table range). "
"By default do not check the overflow",
)
parser_compress.add_argument(
"-c",
"--checkpoint-folder",
type=str,
default="model-compression",
help="path to checkpoint folder",
)
parser_compress.add_argument(
"-t",
"--training-script",
type=str,
default=None,
help="The training script of the input frozen model",
)
# * print docs script **************************************************************
parsers_doc = subparsers.add_parser(
"doc-train-input",
parents=[parser_log],
help="print the documentation (in rst format) of input training parameters.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parsers_doc.add_argument(
"--out-type", default="rst", type=str, help="The output type"
)
# * make model deviation ***********************************************************
parser_model_devi = subparsers.add_parser(
"model-devi",
parents=[parser_log],
help="calculate model deviation",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp model-devi -m graph.000.pb graph.001.pb graph.002.pb graph.003.pb -s ./data -o model_devi.out
"""
),
)
parser_model_devi.add_argument(
"-m",
"--models",
default=["graph.000.pb", "graph.001.pb", "graph.002.pb", "graph.003.pb"],
nargs="+",
type=str,
help="Frozen models file to import",
)
parser_model_devi.add_argument(
"-s",
"--system",
default=".",
type=str,
help="The system directory. Recursively detect systems in this directory.",
)
parser_model_devi.add_argument(
"-S", "--set-prefix", default="set", type=str, help="The set prefix"
)
parser_model_devi.add_argument(
"-o",
"--output",
default="model_devi.out",
type=str,
help="The output file for results of model deviation",
)
parser_model_devi.add_argument(
"-f",
"--frequency",
default=1,
type=int,
help="The trajectory frequency of the system",
)
# * convert models
parser_transform = subparsers.add_parser(
"convert-from",
parents=[parser_log],
help="convert lower model version to supported version",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp convert-from -i graph.pb -o graph_new.pb
dp convert-from auto -i graph.pb -o graph_new.pb
dp convert-from 1.0 -i graph.pb -o graph_new.pb
"""
),
)
parser_transform.add_argument(
"FROM",
nargs="?",
default="auto",
type=str,
choices=["auto", "0.12", "1.0", "1.1", "1.2", "1.3", "2.0", "pbtxt"],
help="The original model compatibility",
)
parser_transform.add_argument(
"-i",
"--input-model",
default="frozen_model.pb",
type=str,
help="the input model",
)
parser_transform.add_argument(
"-o",
"--output-model",
default="convert_out.pb",
type=str,
help="the output model",
)
# neighbor_stat
parser_neighbor_stat = subparsers.add_parser(
"neighbor-stat",
parents=[parser_log],
help="Calculate neighbor statistics",
formatter_class=RawTextArgumentDefaultsHelpFormatter,
epilog=textwrap.dedent(
"""\
examples:
dp neighbor-stat -s data -r 6.0 -t O H
"""
),
)
parser_neighbor_stat.add_argument(
"-s",
"--system",
default=".",
type=str,
help="The system dir. Recursively detect systems in this directory",
)
parser_neighbor_stat.add_argument(
"-r",
"--rcut",
type=float,
required=True,
help="cutoff radius",
)
parser_neighbor_stat.add_argument(
"-t",
"--type-map",
type=str,
nargs="+",
required=True,
help="type map",
)
parser_neighbor_stat.add_argument(
"--one-type",
action="store_true",
default=False,
help="treat all types as a single type. Used with se_atten descriptor.",
)
# --version
parser.add_argument(
"--version", action="version", version="DeePMD-kit v%s" % __version__
)
# * train nvnmd script ******************************************************************
parser_train_nvnmd = subparsers.add_parser(
"train-nvnmd",
parents=[parser_log],
help="train nvnmd model",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser_train_nvnmd.add_argument(
"INPUT", help="the input parameter file in json format"
)
parser_train_nvnmd.add_argument(
"-r",
"--restart",
type=str,
default=None,
help="Restart the training from the provided checkpoint.",
)
parser_train_nvnmd.add_argument(
"-s",
"--step",
default="s1",
type=str,
choices=["s1", "s2"],
help="steps to train model of NVNMD: s1 (train CNN), s2 (train QNN)",
)
return parser
[docs]def parse_args(args: Optional[List[str]] = None) -> argparse.Namespace:
"""Parse arguments and convert argument strings to objects.
Parameters
----------
args : List[str]
list of command line arguments, main purpose is testing default option None
takes arguments from sys.argv
Returns
-------
argparse.Namespace
the populated namespace
"""
parser = main_parser()
parsed_args = parser.parse_args(args=args)
if parsed_args.command is None:
parser.print_help()
else:
parsed_args.log_level = get_ll(parsed_args.log_level)
return parsed_args
[docs]def main(args: Optional[List[str]] = None):
"""DeePMD-Kit entry point.
Parameters
----------
args : List[str], optional
list of command line arguments, used to avoid calling from the subprocess,
as it is quite slow to import tensorflow
Raises
------
RuntimeError
if no command was input
"""
if args is not None:
clear_session()
args = parse_args(args=args)
# do not set log handles for None, it is useless
# log handles for train will be set separatelly
# when the use of MPI will be determined in `RunOptions`
if args.command not in (None, "train"):
set_log_handles(args.log_level, Path(args.log_path) if args.log_path else None)
dict_args = vars(args)
if args.command == "train":
train_dp(**dict_args)
elif args.command == "freeze":
freeze(**dict_args)
elif args.command == "config":
config(**dict_args)
elif args.command == "test":
test(**dict_args)
elif args.command == "transfer":
transfer(**dict_args)
elif args.command == "compress":
compress(**dict_args)
elif args.command == "doc-train-input":
doc_train_input(**dict_args)
elif args.command == "model-devi":
make_model_devi(**dict_args)
elif args.command == "convert-from":
convert(**dict_args)
elif args.command == "neighbor-stat":
neighbor_stat(**dict_args)
elif args.command == "train-nvnmd": # nvnmd
train_nvnmd(**dict_args)
elif args.command is None:
pass
else:
raise RuntimeError(f"unknown command {args.command}")
if args is not None:
clear_session()