8. Command line interface
DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics
usage: dp [-h] [--version]
{config,transfer,train,freeze,test,compress,doc-train-input,model-devi,convert-from,neighbor-stat}
...
8.1. Named Arguments
- --version
show program’s version number and exit
8.2. Valid subcommands
- command
Possible choices: config, transfer, train, freeze, test, compress, doc-train-input, model-devi, convert-from, neighbor-stat
8.3. Sub-commands:
8.3.1. config
fast configuration of parameter file for smooth model
dp config [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-o OUTPUT]
8.3.1.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -o, --output
the output json file
Default: “input.json”
8.3.2. transfer
pass parameters to another model
dp transfer [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-r RAW_MODEL] [-O OLD_MODEL] [-o OUTPUT]
8.3.2.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -r, --raw-model
the model receiving parameters
Default: “raw_frozen_model.pb”
- -O, --old-model
the model providing parameters
Default: “old_frozen_model.pb”
- -o, --output
the model after passing parameters
Default: “frozen_model.pb”
8.3.3. train
train a model
dp train [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-m {master,collect,workers}] [-i INIT_MODEL] [-r RESTART]
[-o OUTPUT] [-f INIT_FRZ_MODEL] [--skip-neighbor-stat]
INPUT
8.3.3.1. Positional Arguments
- INPUT
the input parameter file in json or yaml format
8.3.3.2. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -m, --mpi-log
Possible choices: master, collect, workers
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
Default: “master”
- -i, --init-model
Initialize the model by the provided checkpoint.
- -r, --restart
Restart the training from the provided checkpoint.
- -o, --output
The output file of the parameters used in training.
Default: “out.json”
- -f, --init-frz-model
Initialize the training from the frozen model.
- --skip-neighbor-stat
Skip calculating neighbor statistics. Sel checking, automatic sel, and model compression will be disabled.
Default: False
8.3.4. freeze
freeze the model
dp freeze [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-c CHECKPOINT_FOLDER] [-o OUTPUT] [-n NODE_NAMES]
8.3.4.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -c, --checkpoint-folder
path to checkpoint folder
Default: “.”
- -o, --output
name of graph, will output to the checkpoint folder
Default: “frozen_model.pb”
- -n, --node-names
the frozen nodes, if not set, determined from the model type
8.3.5. test
test the model
dp test [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH] [-m MODEL]
[-s SYSTEM] [-S SET_PREFIX] [-n NUMB_TEST] [-r RAND_SEED]
[--shuffle-test] [-d DETAIL_FILE] [-a]
8.3.5.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -m, --model
Frozen model file to import
Default: “frozen_model.pb”
- -s, --system
The system dir. Recursively detect systems in this directory
Default: “.”
- -S, --set-prefix
The set prefix
Default: “set”
- -n, --numb-test
The number of data for test
Default: 100
- -r, --rand-seed
The random seed
- --shuffle-test
Shuffle test data
Default: False
- -d, --detail-file
File where details of energy force and virial accuracy will be written
- -a, --atomic
Test the accuracy of atomic label, i.e. energy / tensor (dipole, polar)
Default: False
8.3.6. compress
compress a model
dp compress [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-m {master,collect,workers}] [-i INPUT] [-o OUTPUT] [-s STEP]
[-e EXTRAPOLATE] [-f FREQUENCY] [-c CHECKPOINT_FOLDER]
[-t TRAINING_SCRIPT]
8.3.6.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -m, --mpi-log
Possible choices: master, collect, workers
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
Default: “master”
- -i, --input
The original frozen model, which will be compressed by the code
Default: “frozen_model.pb”
- -o, --output
The compressed model
Default: “frozen_model_compressed.pb”
- -s, --step
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
Default: 0.01
- -e, --extrapolate
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]
Default: 5
- -f, --frequency
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
Default: -1
- -c, --checkpoint-folder
path to checkpoint folder
Default: “model-compression”
- -t, --training-script
The training script of the input frozen model
8.3.7. doc-train-input
print the documentation (in rst format) of input training parameters.
dp doc-train-input [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[--out-type OUT_TYPE]
8.3.7.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- --out-type
The output type
Default: “rst”
8.3.8. model-devi
calculate model deviation
dp model-devi [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-m MODELS [MODELS ...]] [-s SYSTEM] [-S SET_PREFIX] [-o OUTPUT]
[-f FREQUENCY]
8.3.8.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -m, --models
Frozen models file to import
Default: [‘graph.000.pb’, ‘graph.001.pb’, ‘graph.002.pb’, ‘graph.003.pb’]
- -s, --system
The system directory. Recursively detect systems in this directory.
Default: “.”
- -S, --set-prefix
The set prefix
Default: “set”
- -o, --output
The output file for results of model deviation
Default: “model_devi.out”
- -f, --frequency
The trajectory frequency of the system
Default: 1
8.3.9. convert-from
convert lower model version to supported version
dp convert-from [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-i INPUT_MODEL] [-o OUTPUT_MODEL]
{0.12,1.0,1.1,1.2,1.3,2.0}
8.3.9.1. Positional Arguments
- FROM
Possible choices: 0.12, 1.0, 1.1, 1.2, 1.3, 2.0
The original model compatibility
8.3.9.2. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -i, --input-model
the input model
Default: “frozen_model.pb”
- -o, --output-model
the output model
Default: “convert_out.pb”
8.3.10. neighbor-stat
Calculate neighbor statistics
dp neighbor-stat [-h] [-v {DEBUG,3,INFO,2,WARNING,1,ERROR,0}] [-l LOG_PATH]
[-s SYSTEM] -r RCUT -t TYPE_MAP [TYPE_MAP ...]
8.3.10.1. Named Arguments
- -v, --log-level
Possible choices: DEBUG, 3, INFO, 2, WARNING, 1, ERROR, 0
set verbosity level by string or number, 0=ERROR, 1=WARNING, 2=INFO and 3=DEBUG
Default: “INFO”
- -l, --log-path
set log file to log messages to disk, if not specified, the logs will only be output to console
- -s, --system
The system dir. Recursively detect systems in this directory
Default: “.”
- -r, --rcut
cutoff radius
- -t, --type-map
type map