DeePMD-kit’s documentation¶

DeePMD-kit is a package written in Python/C++, designed to minimize the effort required to build deep learning based model of interatomic potential energy and force field and to perform molecular dynamics (MD). This brings new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems.

Important

The project DeePMD-kit is licensed under GNU LGPLv3.0. If you use this code in any future publications, please cite this using Han Wang, Linfeng Zhang, Jiequn Han, and Weinan E. “DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics.” Computer Physics Communications 228 (2018): 178-184.

Easy installation methods¶

There various easy methods to install DeePMD-kit. Choose one that you prefer. If you want to build by yourself, jump to the next two sections.

After your easy installation, DeePMD-kit (dp) and LAMMPS (lmp) will be available to execute. You can try dp -h and lmp -h to see the help. mpirun is also available considering you may want to run LAMMPS in parallel.

Install off-line packages
Install with conda
Install with docker

Install off-line packages¶

Both CPU and GPU version offline packages are avaiable in the Releases page.

Install with conda¶

DeePMD-kit is avaiable with conda. Install Anaconda or Miniconda first.

To install the CPU version:

conda install deepmd-kit=*=*cpu lammps-dp=*=*cpu -c deepmodeling

To install the GPU version containing CUDA 10.1:

conda install deepmd-kit=*=*gpu lammps-dp=*=*gpu -c deepmodeling

Install with docker¶

A docker for installing the DeePMD-kit is available here.

To pull the CPU version:

docker pull ghcr.io/deepmodeling/deepmd-kit:2.0.0_cpu

To pull the GPU version:

docker pull ghcr.io/deepmodeling/deepmd-kit:2.0.0_cuda10.1_gpu

Install from source code¶

Please follow our github webpage to download the latest released version and development version.

Or get the DeePMD-kit source code by git clone

cd /some/workspace
git clone --recursive https://github.com/deepmodeling/deepmd-kit.git deepmd-kit

The --recursive option clones all submodules needed by DeePMD-kit.

For convenience, you may want to record the location of source to a variable, saying deepmd_source_dir by

cd deepmd-kit
deepmd_source_dir=`pwd`

Install the python interaction
- Install the Tensorflow’s python interface
- Install the DeePMD-kit’s python interface
Install the C++ interface
- Install the Tensorflow’s C++ interface
- Install the DeePMD-kit’s C++ interface
Install LAMMPS’s DeePMD-kit module

Install the python interface¶

Install the Tensorflow’s python interface¶

First, check the python version on your machine

python --version

We follow the virtual environment approach to install the tensorflow’s Python interface. The full instruction can be found on the tensorflow’s official website. Now we assume that the Python interface will be installed to virtual environment directory $tensorflow_venv

virtualenv -p python3 $tensorflow_venv
source $tensorflow_venv/bin/activate
pip install --upgrade pip
pip install --upgrade tensorflow==2.3.0

It is notice that everytime a new shell is started and one wants to use DeePMD-kit, the virtual environment should be activated by

source $tensorflow_venv/bin/activate

if one wants to skip out of the virtual environment, he/she can do

deactivate

If one has multiple python interpreters named like python3.x, it can be specified by, for example

virtualenv -p python3.7 $tensorflow_venv

If one does not need the GPU support of deepmd-kit and is concerned about package size, the CPU-only version of tensorflow should be installed by

pip install --upgrade tensorflow-cpu==2.3.0

To verify the installation, run

python -c "import tensorflow as tf;print(tf.reduce_sum(tf.random.normal([1000, 1000])))"

One should remember to activate the virtual environment every time he/she uses deepmd-kit.

Install the DeePMD-kit’s python interface¶

Execute

cd $deepmd_source_dir
pip install .

To test the installation, one should firstly jump out of the source directory

cd /some/other/workspace

then execute

dp -h

It will print the help information like

usage: dp [-h] {train,freeze,test} ...

DeePMD-kit: A deep learning package for many-body potential energy
representation and molecular dynamics

optional arguments:
  -h, --help           show this help message and exit

Valid subcommands:
  {train,freeze,test}
    train              train a model
    freeze             freeze the model
    test               test the model

Install the C++ interface¶

If one does not need to use DeePMD-kit with Lammps or I-Pi, then the python interface installed in the previous section does everything and he/she can safely skip this section.

Install the Tensorflow’s C++ interface¶

Check the compiler version on your machine

gcc --version

The C++ interface of DeePMD-kit was tested with compiler gcc >= 4.8. It is noticed that the I-Pi support is only compiled with gcc >= 4.9.

First the C++ interface of Tensorflow should be installed. It is noted that the version of Tensorflow should be in consistent with the python interface. You may follow the instruction to install the corresponding C++ interface.

Install the DeePMD-kit’s C++ interface¶

Now goto the source code directory of DeePMD-kit and make a build place.

cd $deepmd_source_dir/source
mkdir build 
cd build

I assume you want to install DeePMD-kit into path $deepmd_root, then execute cmake

cmake -DTENSORFLOW_ROOT=$tensorflow_root -DCMAKE_INSTALL_PREFIX=$deepmd_root ..

where the variable tensorflow_root stores the location where the tensorflow’s C++ interface is installed. The DeePMD-kit will automatically detect if a CUDA tool-kit is available on your machine and build the GPU support accordingly. If you want to force the cmake to find CUDA tool-kit, you can speicify the key USE_CUDA_TOOLKIT,

cmake -DUSE_CUDA_TOOLKIT=true -DTENSORFLOW_ROOT=$tensorflow_root -DCMAKE_INSTALL_PREFIX=$deepmd_root ..

and you may further asked to provide CUDA_TOOLKIT_ROOT_DIR. If the cmake has executed successfully, then

make
make install

If everything works fine, you will have the following executable and libraries installed in $deepmd_root/bin and $deepmd_root/lib

$ ls $deepmd_root/bin
dp_ipi
$ ls $deepmd_root/lib
libdeepmd_ipi.so  libdeepmd_op.so  libdeepmd.so

Install LAMMPS’s DeePMD-kit module¶

DeePMD-kit provide module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.

cd $deepmd_source_dir/source/build
make lammps

DeePMD-kit will generate a module called USER-DEEPMD in the build directory. Now download the LAMMPS code (29Oct2020 or later), and uncompress it:

cd /some/workspace
wget https://github.com/lammps/lammps/archive/stable_29Oct2020.tar.gz
tar xf stable_29Oct2020.tar.gz

The source code of LAMMPS is stored in directory lammps-stable_29Oct2020. Now go into the LAMMPS code and copy the DeePMD-kit module like this

cd lammps-stable_29Oct2020/src/
cp -r $deepmd_source_dir/source/build/USER-DEEPMD .

Now build LAMMPS

make yes-kspace
make yes-user-deepmd
make mpi -j4

The option -j4 means using 4 processes in parallel. You may want to use a different number according to your hardware.

If everything works fine, you will end up with an executable lmp_mpi.

./lmp_mpi -h

The DeePMD-kit module can be removed from LAMMPS source code by

make no-user-deepmd

Install i-PI¶

The i-PI works in a client-server model. The i-PI provides the server for integrating the replica positions of atoms, while the DeePMD-kit provides a client named dp_ipi that computes the interactions (including energy, force and virial). The server and client communicates via the Unix domain socket or the Internet socket. A full instruction of i-PI can be found here. The source code and a complete installation instructions of i-PI can be found here. To use i-PI with already existing drivers, install and update using Pip:

pip install -U i-PI

Test with Pytest:

pip install pytest
pytest --pyargs ipi.tests

Getting Started¶

In this text, we will call the deep neural network that is used to represent the interatomic interactions (Deep Potential) the model. The typical procedure of using DeePMD-kit is

Prepare data
Train a model
Freeze a model
Test a model
Compress a model
Model inference
- Python interface
- C++ interface
Run MD
Known limitations

Prepare data¶

One needs to provide the following information to train a model: the atom type, the simulation box, the atom coordinate, the atom force, system energy and virial. A snapshot of a system that contains these information is called a frame. We use the following convention of units:

Property	Unit
Time	ps
Length	Å
Energy	eV
Force	eV/Å
Virial	eV
Pressure	Bar

The frames of the system are stored in two formats. A raw file is a plain text file with each information item written in one file and one frame written on one line. The default files that provide box, coordinate, force, energy and virial are box.raw, coord.raw, force.raw, energy.raw and virial.raw, respectively. We recommend you use these file names. Here is an example of force.raw:

$ cat force.raw
-0.724  2.039 -0.951  0.841 -0.464  0.363
 6.737  1.554 -5.587 -2.803  0.062  2.222
-1.968 -0.163  1.020 -0.225 -0.789  0.343

This force.raw contains 3 frames with each frame having the forces of 2 atoms, thus it has 3 lines and 6 columns. Each line provides all the 3 force components of 2 atoms in 1 frame. The first three numbers are the 3 force components of the first atom, while the second three numbers are the 3 force components of the second atom. The coordinate file coord.raw is organized similarly. In box.raw, the 9 components of the box vectors should be provided on each line. In virial.raw, the 9 components of the virial tensor should be provided on each line in the order XX XY XZ YX YY YZ ZX ZY ZZ. The number of lines of all raw files should be identical.

We assume that the atom types do not change in all frames. It is provided by type.raw, which has one line with the types of atoms written one by one. The atom types should be integers. For example the type.raw of a system that has 2 atoms with 0 and 1:

$ cat type.raw
0 1

Sometimes one needs to map the integer types to atom name. The mapping can be given by the file type_map.raw. For example

$ cat type_map.raw
O H

The type 0 is named by "O" and the type 1 is named by "H".

The second format is the data sets of numpy binary data that are directly used by the training program. User can use the script $deepmd_source_dir/data/raw/raw_to_set.sh to convert the prepared raw files to data sets. For example, if we have a raw file that contains 6000 frames,

$ ls 
box.raw  coord.raw  energy.raw  force.raw  type.raw  virial.raw
$ $deepmd_source_dir/data/raw/raw_to_set.sh 2000
nframe is 6000
nline per set is 2000
will make 3 sets
making set 0 ...
making set 1 ...
making set 2 ...
$ ls 
box.raw  coord.raw  energy.raw  force.raw  set.000  set.001  set.002  type.raw  virial.raw

It generates three sets set.000, set.001 and set.002, with each set contains 2000 frames. One do not need to take care of the binary data files in each of the set.* directories. The path containing set.* and type.raw is called a system.

Data preparation with dpdata¶

One can use the a convenient tool dpdata to convert data directly from the output of first priciple packages to the DeePMD-kit format. One may follow the example of using dpdata to find out how to use it.

Train a model¶

Write the input script¶

A model has two parts, a descriptor that maps atomic configuration to a set of symmetry invariant features, and a fitting net that takes descriptor as input and predicts the atomic contribution to the target physical property.

DeePMD-kit implements the following descriptors:

se_e2_a: DeepPot-SE constructed from all information (both angular and radial) of atomic configurations. The embedding takes the distance between atoms as input.
se_e2_r: DeepPot-SE constructed from radial information of atomic configurations. The embedding takes the distance between atoms as input.
se_e3: DeepPot-SE constructed from all information (both angular and radial) of atomic configurations. The embedding takes angles between two neighboring atoms as input.
loc_frame: Defines a local frame at each atom, and the compute the descriptor as local coordinates under this frame.
hybrid: Concate a list of descriptors to form a new descriptor.

The fitting of the following physical properties are supported

ener: Fitting the energy of the system. The force (derivative with atom positions) and the virial (derivative with the box tensor) can also be trained. See the example.
dipole: The dipole moment.
polar: The polarizability.

Training¶

The training can be invoked by

$ dp train input.json

where input.json is the name of the input script. See the example for more details.

During the training, checkpoints will be written to files with prefix save_ckpt every save_freq training steps.

Several command line options can be passed to dp train, which can be checked with

$ dp train --help

An explanation will be provided

positional arguments:
  INPUT                 the input json database

optional arguments:
  -h, --help            show this help message and exit
  --init-model INIT_MODEL
                        Initialize a model by the provided checkpoint
  --restart RESTART     Restart the training from the provided checkpoint

--init-model model.ckpt, initializes the model training with an existing model that is stored in the checkpoint model.ckpt, the network architectures should match.

--restart model.ckpt, continues the training from the checkpoint model.ckpt.

On some resources limited machines, one may want to control the number of threads used by DeePMD-kit. This is achieved by three environmental variables: OMP_NUM_THREADS, TF_INTRA_OP_PARALLELISM_THREADS and TF_INTER_OP_PARALLELISM_THREADS. OMP_NUM_THREADS controls the multithreading of DeePMD-kit implemented operations. TF_INTRA_OP_PARALLELISM_THREADS and TF_INTER_OP_PARALLELISM_THREADS controls intra_op_parallelism_threads and inter_op_parallelism_threads, which are Tensorflow configurations for multithreading. An explanation is found here.

For example if you wish to use 3 cores of 2 CPUs on one node, you may set the environmental variables and run DeePMD-kit as follows:

export OMP_NUM_THREADS=6
export TF_INTRA_OP_PARALLELISM_THREADS=3
export TF_INTER_OP_PARALLELISM_THREADS=2
dp train input.json

Training analysis with Tensorboard¶

If enbled in json/yaml input file DeePMD-kit will create log files which can be used to analyze training procedure with Tensorboard. For a short tutorial please read this document.

Freeze a model¶

The trained neural network is extracted from a checkpoint and dumped into a database. This process is called “freezing” a model. The idea and part of our code are from Morgan. To freeze a model, typically one does

$ dp freeze -o graph.pb

in the folder where the model is trained. The output database is called graph.pb.

Test a model¶

The frozen model can be used in many ways. The most straightforward test can be performed using dp test. A typical usage of dp test is

dp test -m graph.pb -s /path/to/system -n 30

where -m gives the tested model, -s the path to the tested system and -n the number of tested frames. Several other command line options can be passed to dp test, which can be checked with

$ dp test --help

An explanation will be provided

usage: dp test [-h] [-m MODEL] [-s SYSTEM] [-S SET_PREFIX] [-n NUMB_TEST]
               [-r RAND_SEED] [--shuffle-test] [-d DETAIL_FILE]

optional arguments:
  -h, --help            show this help message and exit
  -m MODEL, --model MODEL
                        Frozen model file to import
  -s SYSTEM, --system SYSTEM
                        The system dir
  -S SET_PREFIX, --set-prefix SET_PREFIX
                        The set prefix
  -n NUMB_TEST, --numb-test NUMB_TEST
                        The number of data for test
  -r RAND_SEED, --rand-seed RAND_SEED
                        The random seed
  --shuffle-test        Shuffle test data
  -d DETAIL_FILE, --detail-file DETAIL_FILE
                        The file containing details of energy force and virial
                        accuracy

Compress a model¶

Once the frozen model is obtained from deepmd-kit, we can get the neural network structure and its parameters (weights, biases, etc.) from the trained model, and compress it in the following way:

dp compress input.json -i graph.pb -o graph-compress.pb

where input.json denotes the original training input script, -i gives the original frozen model, -o gives the compressed model. Several other command line options can be passed to dp compress, which can be checked with

$ dp compress --help

An explanation will be provided

usage: dp compress [-h] [-i INPUT] [-o OUTPUT] [-e EXTRAPOLATE] [-s STRIDE]
                   [-f FREQUENCY] [-d FOLDER]
                   INPUT

positional arguments:
  INPUT                 The input parameter file in json or yaml format, which
                        should be consistent with the original model parameter
                        file

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        The original frozen model, which will be compressed by
                        the deepmd-kit
  -o OUTPUT, --output OUTPUT
                        The compressed model
  -e EXTRAPOLATE, --extrapolate EXTRAPOLATE
                        The scale of model extrapolation
  -s STRIDE, --stride STRIDE
                        The uniform stride of tabulation's first table, the
                        second table will use 10 * stride as it's uniform
                        stride
  -f FREQUENCY, --frequency FREQUENCY
                        The frequency of tabulation overflow check(If the
                        input environment matrix overflow the first or second
                        table range). By default do not check the overflow
  -d FOLDER, --folder FOLDER
                        path to checkpoint folder

Parameter explanation

Model compression, which including tabulating the embedding-net. The table is composed of fifth-order polynomial coefficients and is assembled from two sub-tables. The first sub-table takes the stride(parameter) as it’s uniform stride, while the second sub-table takes 10 * stride as it’s uniform stride. 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. Finally, we added a check frequency parameter. It indicates how often the program checks for overflow(if the input environment matrix overflow the first or second table range) during the MD inference.

Justification of model compression

Model compression, with little loss of accuracy, can greatly speed up MD inference time. According to different simulation systems and training parameters, the speedup can reach more than 10 times at both CPU and GPU devices. At the same time, model compression can greatly change the memory usage, reducing as much as 20 times under the same hardware conditions.

Acceptable original model version

The model compression method requires that the version of DeePMD-kit used in original model generation should be 1.3 or above. If one has a frozen 1.2 model, one can first use the convenient conversion interface of DeePMD-kit-v1.2.4 to get a 1.3 executable model.(eg: dp convert-to-1.3 -i frozen_1.2.pb -o frozen_1.3.pb)

Model inference¶

Python interface¶

One may use the python interface of DeePMD-kit for model inference, an example is given as follows

from deepmd.infer import DeepPot
import numpy as np
dp = DeepPot('graph.pb')
coord = np.array([[1,0,0], [0,0,1.5], [1,0,3]]).reshape([1, -1])
cell = np.diag(10 * np.ones(3)).reshape([1, -1])
atype = [1,0,1]
e, f, v = dp.eval(coord, cell, atype)

where e, f and v are predicted energy, force and virial of the system, respectively.

C++ interface¶

The C++ interface of DeePMD-kit is also avaiable for model interface, which is considered faster than Python interface. An example infer_water.cpp is given below:

#include "deepmd/DeepPot.h"

int main(){
  deepmd::DeepPot dp ("graph.pb");
  std::vector<double > coord = {1., 0., 0., 0., 0., 1.5, 1. ,0. ,3.};
  std::vector<double > cell = {10., 0., 0., 0., 10., 0., 0., 0., 10.};
  std::vector<int > atype = {1, 0, 1};
  double e;
  std::vector<double > f, v;
  dp.compute (e, f, v, coord, atype, cell);
}

where e, f and v are predicted energy, force and virial of the system, respectively.

You can compile infer_water.cpp using gcc:

gcc infer_water.cpp -D HIGH_PREC -L $deepmd_root/lib -L $tensorflow_root/lib -I $deepmd_root/include -I $tensorflow_root/lib -Wl,--no-as-needed -ldeepmd_op -ldeepmd -ldeepmd_cc -ltensorflow_cc -ltensorflow_framework -lstdc++ -Wl,-rpath=$deepmd_root/lib -Wl,-rpath=$tensorflow_root/lib -o infer_water

and then run the program:

./infer_water

Run MD¶

Run MD with LAMMPS¶

Include deepmd in the pair_style

Syntax¶

pair_style deepmd models ... keyword value ...

deepmd = style of this pair_style
models = frozen model(s) to compute the interaction. If multiple models are provided, then the model deviation will be computed
keyword = out_file or out_freq or fparam or atomic or relative

    out_file value = filename
        filename = The file name for the model deviation output. Default is model_devi.out
    out_freq value = freq
        freq = Frequency for the model deviation output. Default is 100.
    fparam value = parameters
        parameters = one or more frame parameters required for model evaluation.
    atomic = no value is required. 
        If this keyword is set, the model deviation of each atom will be output.
    relative value = level
        level = The level parameter for computing the relative model deviation

Examples¶

pair_style deepmd graph.pb
pair_style deepmd graph.pb fparam 1.2
pair_style deepmd graph_0.pb graph_1.pb graph_2.pb out_file md.out out_freq 10 atomic relative 1.0

Description¶

Evaluate the interaction of the system by using Deep Potential or Deep Potential Smooth Edition. It is noticed that deep potential is not a “pairwise” interaction, but a multi-body interaction.

This pair style takes the deep potential defined in a model file that usually has the .pb extension. The model can be trained and frozen by package DeePMD-kit.

The model deviation evalulate the consistency of the force predictions from multiple models. By default, only the maximal, minimal and averge model deviations are output. If the key atomic is set, then the model deviation of force prediction of each atom will be output.

By default, the model deviation is output in absolute value. If the keyword relative is set, then the relative model deviation will be output. The relative model deviation of the force on atom i is defined by

           |Df_i|
Ef_i = -------------
       |f_i| + level

where Df_i is the absolute model deviation of the force on atom i, |f_i| is the norm of the the force and level is provided as the parameter of the keyword relative.

Restrictions¶

The deepmd pair style is provided in the USER-DEEPMD package, which is compiled from the DeePMD-kit, visit the DeePMD-kit website for more information.

Long-range interaction¶

The reciprocal space part of the long-range interaction can be calculated by LAMMPS command kspace_style. To use it with DeePMD-kit, one writes

pair_style	deepmd graph.pb
pair_coeff
kspace_style	pppm 1.0e-5
kspace_modify	gewald 0.45

Please notice that the DeePMD does nothing to the direct space part of the electrostatic interaction, because this part is assumed to be fitted in the DeePMD model (the direct space cut-off is thus the cut-off of the DeePMD model). The splitting parameter gewald is modified by the kspace_modify command.

Run path-integral MD with i-PI¶

The i-PI works in a client-server model. The i-PI provides the server for integrating the replica positions of atoms, while the DeePMD-kit provides a client named dp_ipi that computes the interactions (including energy, force and virial). The server and client communicates via the Unix domain socket or the Internet socket. Installation instructions of i-PI can be found here. The client can be started by

i-pi input.xml &
dp_ipi water.json

It is noted that multiple instances of the client is allow for computing, in parallel, the interactions of multiple replica of the path-integral MD.

water.json is the parameter file for the client dp_ipi, and an example is provided:

{
    "verbose":		false,
    "use_unix":		true,
    "port":		31415,
    "host":		"localhost",
    "graph_file":	"graph.pb",
    "coord_file":	"conf.xyz",
    "atom_type" : {
	"OW":		0, 
	"HW1":		1,
	"HW2":		1
    }
}

The option use_unix is set to true to activate the Unix domain socket, otherwise, the Internet socket is used.

The option port should be the same as that in input.xml:

<port>31415</port>

The option graph_file provides the file name of the frozen model.

The dp_ipi gets the atom names from an XYZ file provided by coord_file (meanwhile ignores all coordinates in it), and translates the names to atom types by rules provided by atom_type.

Use deep potential with ASE¶

Deep potential can be set up as a calculator with ASE to obtain potential energies and forces.

from ase import Atoms
from deepmd.calculator import DP

water = Atoms('H2O',
              positions=[(0.7601, 1.9270, 1),
                         (1.9575, 1, 1),
                         (1., 1., 1.)],
              cell=[100, 100, 100],
              calculator=DP(model="frozen_model.pb"))
print(water.get_potential_energy())
print(water.get_forces())

Optimization is also available:

from ase.optimize import BFGS
dyn = BFGS(water)
dyn.run(fmax=1e-6)
print(water.get_positions())

Known limitations¶

If you use deepmd-kit in a GPU environment, the acceptable value range of some variables are additionally restricted compared to the CPU environment due to the software’s GPU implementations:

The number of atom type of a given system must be less than 128.
The maximum distance between an atom and it’s neighbors must be less than 128. It can be controlled by setting the rcut value of training parameters.
Theoretically, the maximum number of atoms that a single GPU can accept is about 10,000,000. However, this value is actually limited by the GPU memory size currently, usually within 1000,000 atoms even at the model compression mode.
The total sel value of training parameters(in model/descriptor section) must be less than 4096.

TensorBoard Usage¶

TensorBoard provides the visualization and tooling needed for machine learning experimentation. A full instruction of tensorboard can be found here.

Highlighted features¶

DeePMD-kit can now use most of the interesting features enabled by tensorboard!

Tracking and visualizing metrics, such as l2_loss, l2_energy_loss and l2_force_loss
Visualizing the model graph (ops and layers)
Viewing histograms of weights, biases, or other tensors as they change over time.
Viewing summaries of trainable viriables

How to use Tensorboard with DeePMD-kit¶

Before running TensorBoard, make sure you have generated summary data in a log directory by modifying the the input script, set “tensorboard” true in training subsection will enable the tensorboard data analysis. eg. water_se_a.json.

    "training" : {
	"systems":	["../data/"],
	"set_prefix":	"set",    
	"stop_batch":	1000000,
	"batch_size":	1,

	"seed":		1,

	"_comment": " display and restart",
	"_comment": " frequencies counted in batch",
	"disp_file":	"lcurve.out",
	"disp_freq":	100,
	"numb_test":	10,
	"save_freq":	1000,
	"save_ckpt":	"model.ckpt",
	"load_ckpt":	"model.ckpt",
	"disp_training":true,
	"time_training":true,
	"tensorboard":	true,
	"tensorboard_log_dir":"log",
	"profiling":	false,
	"profiling_file":"timeline.json",
	"_comment":	"that's all"
    }

Once you have event files, run TensorBoard and provide the log directory. This should print that TensorBoard has started. Next, connect to http://tensorboard_server_ip:6006.

TensorBoard requires a logdir to read logs from. For info on configuring TensorBoard, run tensorboard –help. One can easily change the log name with “tensorboard_log_dir”.

tensorboard --logdir path/to/logs

Examples¶

Tracking and visualizing loss metrics(red:train, blue:test)¶

ALT

Visualizing deepmd-kit model graph¶

ALT

Viewing histograms of weights, biases, or other tensors as they change over time¶

ALT

Viewing summaries of trainable variables¶

ALT

Attention¶

Allowing the tensorboard analysis will takes extra execution time.(eg, 15% increasing @Nvidia GTX 1080Ti double precision with default water sample)

TensorBoard can be used in Google Chrome or Firefox. Other browsers might work, but there may be bugs or performance issues.

FAQs¶

In consequence of various differences of computers or systems, problems may occur. Some common circumstances are listed as follows. In addition, some frequently asked questions about parameters setting are listed as follows. If other unexpected problems occur, you’re welcome to contact us for help.

Trouble shooting¶

Parameters setting¶

Data¶

In this example we will convert the DFT labeled data stored in VASP OUTCAR format into the data format used by DeePMD-kit. The example OUTCAR can be found in the directory.

$deepmd_source_dir/examples/data_conv

Definition¶

The DeePMD-kit organize data in systems. Each system is composed by a number of frames. One may roughly view a frame as a snap short on an MD trajectory, but it does not necessary come from an MD simulation. A frame records the coordinates and types of atoms, cell vectors if the periodic boundary condition is assumed, energy, atomic forces and virial. It is noted that the frames in one system share the same number of atoms with the same type.

Data conversion¶

It is conveninent to use dpdata to convert data generated by DFT packages to the data format used by DeePMD-kit.

To install one can execute

pip install dpdata

An example of converting data VASP data in OUTCAR format to DeePMD-kit data can be found at

$deepmd_source_dir/examples/data_conv

Switch to that directory, then one can convert data by using the following python script

import dpdata
dsys = dpdata.LabeledSystem('OUTCAR')
dsys.to('deepmd/npy', 'deepmd_data', set_size = dsys.get_nframes())

get_nframes() method gets the number of frames in the OUTCAR, and the argument set_size enforces that the set size is equal to the number of frames in the system, viz. only one set is created in the system.

The data in DeePMD-kit format is stored in the folder deepmd_data.

A list of all supported data format and more nice features of dpdata can be found at the official website.

Training Parameters¶

model:

type: dict

argument path: model

type_map:: type: list, optional

argument path: model/type_map

A list of strings. Give the name to each type of atoms.

data_stat_nbatch:: type: int, optional, default: 10

argument path: model/data_stat_nbatch

The model determines the normalization from the statistics of the data. This key specifies the number of frames in each system used for statistics.

data_stat_protect:: type: float, optional, default: 0.01

argument path: model/data_stat_protect

Protect parameter for atomic energy regression.

use_srtab:: type: str, optional

argument path: model/use_srtab

The table for the short-range pairwise interaction added on top of DP. The table is a text data file with (N_t + 1) * N_t / 2 + 1 columes. The first colume is the distance between atoms. The second to the last columes are energies for pairs of certain types. For example we have two atom types, 0 and 1. The columes from 2nd to 4th are for 0-0, 0-1 and 1-1 correspondingly.

smin_alpha:: type: float, optional

argument path: model/smin_alpha

The short-range tabulated interaction will be swithed according to the distance of the nearest neighbor. This distance is calculated by softmin. This parameter is the decaying parameter in the softmin. It is only required when use_srtab is provided.

sw_rmin:: type: float, optional

argument path: model/sw_rmin

The lower boundary of the interpolation between short-range tabulated interaction and DP. It is only required when use_srtab is provided.

sw_rmax:: type: float, optional

argument path: model/sw_rmax

The upper boundary of the interpolation between short-range tabulated interaction and DP. It is only required when use_srtab is provided.

type_embedding:

type: dict

argument path: model/type_embedding

The type embedding.

neuron:: type: list, optional, default: [2, 4, 8]

argument path: model/type_embedding/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/type_embedding/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: False

argument path: model/type_embedding/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:: type: str, optional, default: float64

argument path: model/type_embedding/precision

The precision of the embedding net parameters, supported options are “default”, “float16”, “float32”, “float64”.

trainable:: type: bool, optional, default: True

argument path: model/type_embedding/trainable

If the parameters in the embedding net are trainable

seed:: type: int | NoneType, optional

argument path: model/type_embedding/seed

Random seed for parameter initialization

descriptor:

type: dict

argument path: model/descriptor

The descriptor of atomic environment.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)
argument path: model/descriptor/type
possible choices: loc_frame, se_e2_a, se_e2_r, se_e3, se_a_tpe, hybrid

The type of the descritpor. See explanation below.

loc_frame: Defines a local frame at each atom, and the compute the descriptor as local coordinates under this frame.
se_e2_a: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor.
se_e2_r: Used by the smooth edition of Deep Potential. Only the distance between atoms is used to construct the descriptor.
se_e3: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Three-body embedding will be used by this descriptor.
se_a_tpe: Used by the smooth edition of Deep Potential. The full relative coordinates are used to construct the descriptor. Type embedding will be used by this descriptor.
hybrid: Concatenate of a list of descriptors as a new descriptor.

When type is set to loc_frame:

sel_a:: type: list

argument path: model/descriptor[loc_frame]/sel_a

A list of integers. The length of the list should be the same as the number of atom types in the system. sel_a[i] gives the selected number of type-i neighbors. The full relative coordinates of the neighbors are used by the descriptor.

sel_r:: type: list

argument path: model/descriptor[loc_frame]/sel_r

A list of integers. The length of the list should be the same as the number of atom types in the system. sel_r[i] gives the selected number of type-i neighbors. Only relative distance of the neighbors are used by the descriptor. sel_a[i] + sel_r[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:: type: float, optional, default: 6.0

argument path: model/descriptor[loc_frame]/rcut

The cut-off radius. The default value is 6.0

axis_rule:

type: list

argument path: model/descriptor[loc_frame]/axis_rule

A list of integers. The length should be 6 times of the number of types.

axis_rule[i*6+0]: class of the atom defining the first axis of type-i atom. 0 for neighbors with full coordinates and 1 for neighbors only with relative distance.
axis_rule[i*6+1]: type of the atom defining the first axis of type-i atom.
axis_rule[i*6+2]: index of the axis atom defining the first axis. Note that the neighbors with the same class and type are sorted according to their relative distance.
axis_rule[i*6+3]: class of the atom defining the first axis of type-i atom. 0 for neighbors with full coordinates and 1 for neighbors only with relative distance.
axis_rule[i*6+4]: type of the atom defining the second axis of type-i atom.
axis_rule[i*6+5]: class of the atom defining the second axis of type-i atom. 0 for neighbors with full coordinates and 1 for neighbors only with relative distance.

When type is set to se_e2_a (or its alias se_a):

sel:: type: list

argument path: model/descriptor[se_e2_a]/sel

A list of integers. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:: type: float, optional, default: 6.0

argument path: model/descriptor[se_e2_a]/rcut

The cut-off radius.

rcut_smth:: type: float, optional, default: 0.5

argument path: model/descriptor[se_e2_a]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:: type: list, optional, default: [10, 20, 40]

argument path: model/descriptor[se_e2_a]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:: type: int, optional, default: 4

argument path: model/descriptor[se_e2_a]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:: type: str, optional, default: tanh

argument path: model/descriptor[se_e2_a]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_a]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_a]/type_one_side

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:: type: str, optional, default: float64

argument path: model/descriptor[se_e2_a]/precision

The precision of the embedding net parameters, supported options are “default”, “float16”, “float32”, “float64”.

trainable:: type: bool, optional, default: True

argument path: model/descriptor[se_e2_a]/trainable

If the parameters in the embedding net is trainable

seed:: type: int | NoneType, optional

argument path: model/descriptor[se_e2_a]/seed

Random seed for parameter initialization

exclude_types:: type: list, optional, default: []

argument path: model/descriptor[se_e2_a]/exclude_types

The Excluded types

set_davg_zero:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_a]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

When type is set to se_e2_r (or its alias se_r):

sel:: type: list

argument path: model/descriptor[se_e2_r]/sel

A list of integers. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:: type: float, optional, default: 6.0

argument path: model/descriptor[se_e2_r]/rcut

The cut-off radius.

rcut_smth:: type: float, optional, default: 0.5

argument path: model/descriptor[se_e2_r]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:: type: list, optional, default: [10, 20, 40]

argument path: model/descriptor[se_e2_r]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/descriptor[se_e2_r]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_r]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_r]/type_one_side

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:: type: str, optional, default: float64

argument path: model/descriptor[se_e2_r]/precision

The precision of the embedding net parameters, supported options are “default”, “float16”, “float32”, “float64”.

trainable:: type: bool, optional, default: True

argument path: model/descriptor[se_e2_r]/trainable

If the parameters in the embedding net are trainable

seed:: type: int | NoneType, optional

argument path: model/descriptor[se_e2_r]/seed

Random seed for parameter initialization

exclude_types:: type: list, optional, default: []

argument path: model/descriptor[se_e2_r]/exclude_types

The Excluded types

set_davg_zero:: type: bool, optional, default: False

argument path: model/descriptor[se_e2_r]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

When type is set to se_e3 (or its aliases se_at, se_a_3be, se_t):

sel:: type: list

argument path: model/descriptor[se_e3]/sel

A list of integers. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:: type: float, optional, default: 6.0

argument path: model/descriptor[se_e3]/rcut

The cut-off radius.

rcut_smth:: type: float, optional, default: 0.5

argument path: model/descriptor[se_e3]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:: type: list, optional, default: [10, 20, 40]

argument path: model/descriptor[se_e3]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/descriptor[se_e3]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: False

argument path: model/descriptor[se_e3]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:: type: str, optional, default: float64

argument path: model/descriptor[se_e3]/precision

The precision of the embedding net parameters, supported options are “default”, “float16”, “float32”, “float64”.

trainable:: type: bool, optional, default: True

argument path: model/descriptor[se_e3]/trainable

If the parameters in the embedding net are trainable

seed:: type: int | NoneType, optional

argument path: model/descriptor[se_e3]/seed

Random seed for parameter initialization

set_davg_zero:: type: bool, optional, default: False

argument path: model/descriptor[se_e3]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

When type is set to se_a_tpe (or its alias se_a_ebd):

sel:: type: list

argument path: model/descriptor[se_a_tpe]/sel

A list of integers. The length of the list should be the same as the number of atom types in the system. sel[i] gives the selected number of type-i neighbors. sel[i] is recommended to be larger than the maximally possible number of type-i neighbors in the cut-off radius.

rcut:: type: float, optional, default: 6.0

argument path: model/descriptor[se_a_tpe]/rcut

The cut-off radius.

rcut_smth:: type: float, optional, default: 0.5

argument path: model/descriptor[se_a_tpe]/rcut_smth

Where to start smoothing. For example the 1/r term is smoothed from rcut to rcut_smth

neuron:: type: list, optional, default: [10, 20, 40]

argument path: model/descriptor[se_a_tpe]/neuron

Number of neurons in each hidden layers of the embedding net. When two layers are of the same size or one layer is twice as large as the previous layer, a skip connection is built.

axis_neuron:: type: int, optional, default: 4

argument path: model/descriptor[se_a_tpe]/axis_neuron

Size of the submatrix of G (embedding matrix).

activation_function:: type: str, optional, default: tanh

argument path: model/descriptor[se_a_tpe]/activation_function

The activation function in the embedding net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: False

argument path: model/descriptor[se_a_tpe]/resnet_dt

Whether to use a “Timestep” in the skip connection

type_one_side:: type: bool, optional, default: False

argument path: model/descriptor[se_a_tpe]/type_one_side

Try to build N_types embedding nets. Otherwise, building N_types^2 embedding nets

precision:: type: str, optional, default: float64

argument path: model/descriptor[se_a_tpe]/precision

The precision of the embedding net parameters, supported options are “default”, “float16”, “float32”, “float64”.

trainable:: type: bool, optional, default: True

argument path: model/descriptor[se_a_tpe]/trainable

If the parameters in the embedding net is trainable

seed:: type: int | NoneType, optional

argument path: model/descriptor[se_a_tpe]/seed

Random seed for parameter initialization

exclude_types:: type: list, optional, default: []

argument path: model/descriptor[se_a_tpe]/exclude_types

The Excluded types

set_davg_zero:: type: bool, optional, default: False

argument path: model/descriptor[se_a_tpe]/set_davg_zero

Set the normalization average to zero. This option should be set when atom_ener in the energy fitting is used

type_nchanl:: type: int, optional, default: 4

argument path: model/descriptor[se_a_tpe]/type_nchanl

number of channels for type embedding

type_nlayer:: type: int, optional, default: 2

argument path: model/descriptor[se_a_tpe]/type_nlayer

number of hidden layers of type embedding net

numb_aparam:: type: int, optional, default: 0

argument path: model/descriptor[se_a_tpe]/numb_aparam

dimension of atomic parameter. if set to a value > 0, the atomic parameters are embedded.

When type is set to hybrid:

list:: type: list

argument path: model/descriptor[hybrid]/list

A list of descriptor definitions

fitting_net:

type: dict

argument path: model/fitting_net

The fitting of physical properties.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key), default: ener
argument path: model/fitting_net/type
possible choices: ener, dipole, polar, global_polar

The type of the fitting. See explanation below.

ener: Fit an energy model (potential energy surface).
dipole: Fit an atomic dipole model. Atomic dipole labels for all the selected atoms (see sel_type) should be provided by dipole.npy in each data system. The file has number of frames lines and 3 times of number of selected atoms columns.
polar: Fit an atomic polarizability model. Atomic polarizability labels for all the selected atoms (see sel_type) should be provided by polarizability.npy in each data system. The file has number of frames lines and 9 times of number of selected atoms columns.
global_polar: Fit a polarizability model. Polarizability labels should be provided by polarizability.npy in each data system. The file has number of frames lines and 9 columns.

When type is set to ener:

numb_fparam:: type: int, optional, default: 0

argument path: model/fitting_net[ener]/numb_fparam

The dimension of the frame parameter. If set to >0, file fparam.npy should be included to provided the input fparams.

numb_aparam:: type: int, optional, default: 0

argument path: model/fitting_net[ener]/numb_aparam

The dimension of the atomic parameter. If set to >0, file aparam.npy should be included to provided the input aparams.

neuron:: type: list, optional, default: [120, 120, 120]

argument path: model/fitting_net[ener]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/fitting_net[ener]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

precision:: type: str, optional, default: float64

argument path: model/fitting_net[ener]/precision

The precision of the fitting net parameters, supported options are “default”, “float16”, “float32”, “float64”.

resnet_dt:: type: bool, optional, default: True

argument path: model/fitting_net[ener]/resnet_dt

Whether to use a “Timestep” in the skip connection

trainable:

type: bool | list, optional, default: True

argument path: model/fitting_net[ener]/trainable

Whether the parameters in the fitting net are trainable. This option can be

bool: True if all parameters of the fitting net are trainable, False otherwise.
list of bool: Specifies if each layer is trainable. Since the fitting net is composed by hidden layers followed by a output layer, the length of tihs list should be equal to len(neuron)+1.

rcond:: type: float, optional, default: 0.001

argument path: model/fitting_net[ener]/rcond

The condition number used to determine the inital energy shift for each type of atoms.

seed:: type: int | NoneType, optional

argument path: model/fitting_net[ener]/seed

Random seed for parameter initialization of the fitting net

atom_ener:: type: list, optional, default: []

argument path: model/fitting_net[ener]/atom_ener

Specify the atomic energy in vacuum for each type

When type is set to dipole:

neuron:: type: list, optional, default: [120, 120, 120]

argument path: model/fitting_net[dipole]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/fitting_net[dipole]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: True

argument path: model/fitting_net[dipole]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:: type: str, optional, default: float64

argument path: model/fitting_net[dipole]/precision

The precision of the fitting net parameters, supported options are “default”, “float16”, “float32”, “float64”.

sel_type:: type: int | NoneType | list, optional

argument path: model/fitting_net[dipole]/sel_type

The atom types for which the atomic dipole will be provided. If not set, all types will be selected.

seed:: type: int | NoneType, optional

argument path: model/fitting_net[dipole]/seed

Random seed for parameter initialization of the fitting net

When type is set to polar:

neuron:: type: list, optional, default: [120, 120, 120]

argument path: model/fitting_net[polar]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/fitting_net[polar]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: True

argument path: model/fitting_net[polar]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:: type: str, optional, default: float64

argument path: model/fitting_net[polar]/precision

The precision of the fitting net parameters, supported options are “default”, “float16”, “float32”, “float64”.

fit_diag:: type: bool, optional, default: True

argument path: model/fitting_net[polar]/fit_diag

Fit the diagonal part of the rotational invariant polarizability matrix, which will be converted to normal polarizability matrix by contracting with the rotation matrix.

scale:: type: float | list, optional, default: 1.0

argument path: model/fitting_net[polar]/scale

The output of the fitting net (polarizability matrix) will be scaled by scale

diag_shift:: type: float | list, optional, default: 0.0

argument path: model/fitting_net[polar]/diag_shift

The diagonal part of the polarizability matrix will be shifted by diag_shift. The shift operation is carried out after scale.

sel_type:: type: int | NoneType | list, optional

argument path: model/fitting_net[polar]/sel_type

The atom types for which the atomic polarizability will be provided. If not set, all types will be selected.

seed:: type: int | NoneType, optional

argument path: model/fitting_net[polar]/seed

Random seed for parameter initialization of the fitting net

When type is set to global_polar:

neuron:: type: list, optional, default: [120, 120, 120]

argument path: model/fitting_net[global_polar]/neuron

The number of neurons in each hidden layers of the fitting net. When two hidden layers are of the same size, a skip connection is built.

activation_function:: type: str, optional, default: tanh

argument path: model/fitting_net[global_polar]/activation_function

The activation function in the fitting net. Supported activation functions are “relu”, “relu6”, “softplus”, “sigmoid”, “tanh”, “gelu”.

resnet_dt:: type: bool, optional, default: True

argument path: model/fitting_net[global_polar]/resnet_dt

Whether to use a “Timestep” in the skip connection

precision:: type: str, optional, default: float64

argument path: model/fitting_net[global_polar]/precision

The precision of the fitting net parameters, supported options are “default”, “float16”, “float32”, “float64”.

fit_diag:: type: bool, optional, default: True

argument path: model/fitting_net[global_polar]/fit_diag

Fit the diagonal part of the rotational invariant polarizability matrix, which will be converted to normal polarizability matrix by contracting with the rotation matrix.

scale:: type: float | list, optional, default: 1.0

argument path: model/fitting_net[global_polar]/scale

The output of the fitting net (polarizability matrix) will be scaled by scale

diag_shift:: type: float | list, optional, default: 0.0

argument path: model/fitting_net[global_polar]/diag_shift

The diagonal part of the polarizability matrix will be shifted by diag_shift. The shift operation is carried out after scale.

sel_type:: type: int | NoneType | list, optional

argument path: model/fitting_net[global_polar]/sel_type

The atom types for which the atomic polarizability will be provided. If not set, all types will be selected.

seed:: type: int | NoneType, optional

argument path: model/fitting_net[global_polar]/seed

Random seed for parameter initialization of the fitting net

modifier:

type: dict, optional

argument path: model/modifier

The modifier of model output.

Depending on the value of type, different sub args are accepted.

type:

type: str (flag key)
argument path: model/modifier/type
possible choices: dipole_charge

The type of modifier. See explanation below.

-dipole_charge: Use WFCC to model the electronic structure of the system. Correct the long-range interaction

When type is set to dipole_charge:

model_name:: type: str

argument path: model/modifier[dipole_charge]/model_name

The name of the frozen dipole model file.

model_charge_map:: type: list

argument path: model/modifier[dipole_charge]/model_charge_map

The charge of the WFCC. The list length should be the same as the sel_type.

sys_charge_map:: type: list

argument path: model/modifier[dipole_charge]/sys_charge_map

The charge of real atoms. The list length should be the same as the type_map

ewald_beta:: type: float, optional, default: 0.4

argument path: model/modifier[dipole_charge]/ewald_beta

The splitting parameter of Ewald sum. Unit is A^-1

ewald_h:: type: float, optional, default: 1.0

argument path: model/modifier[dipole_charge]/ewald_h

The grid spacing of the FFT grid. Unit is A

loss:

type: dict, optional

argument path: loss

The definition of loss function. The loss type should be set to the fitting type or left unset. .

Depending on the value of type, different sub args are accepted.

type:: type: str (flag key), default: ener

argument path: loss/type

possible choices: ener, dipole, polar, global_polar

The type of the loss. The loss type should be set to the fitting type or left unset. .

When type is set to ener:

start_pref_e:: type: float | int, optional, default: 0.02

argument path: loss[ener]/start_pref_e

The prefactor of energy loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the energy label should be provided by file energy.npy in each data system. If both start_pref_energy and limit_pref_energy are set to 0, then the energy will be ignored.

limit_pref_e:: type: float | int, optional, default: 1.0

argument path: loss[ener]/limit_pref_e

The prefactor of energy loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_f:: type: float | int, optional, default: 1000

argument path: loss[ener]/start_pref_f

The prefactor of force loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the force label should be provided by file force.npy in each data system. If both start_pref_force and limit_pref_force are set to 0, then the force will be ignored.

limit_pref_f:: type: float | int, optional, default: 1.0

argument path: loss[ener]/limit_pref_f

The prefactor of force loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_v:: type: float | int, optional, default: 0.0

argument path: loss[ener]/start_pref_v

The prefactor of virial loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the virial label should be provided by file virial.npy in each data system. If both start_pref_virial and limit_pref_virial are set to 0, then the virial will be ignored.

limit_pref_v:: type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_v

The prefactor of virial loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

start_pref_ae:: type: float | int, optional, default: 0.0

argument path: loss[ener]/start_pref_ae

The prefactor of atom_ener loss at the start of the training. Should be larger than or equal to 0. If set to none-zero value, the atom_ener label should be provided by file atom_ener.npy in each data system. If both start_pref_atom_ener and limit_pref_atom_ener are set to 0, then the atom_ener will be ignored.

limit_pref_ae:: type: float | int, optional, default: 0.0

argument path: loss[ener]/limit_pref_ae

The prefactor of atom_ener loss at the limit of the training, Should be larger than or equal to 0. i.e. the training step goes to infinity.

relative_f:: type: float | NoneType, optional

argument path: loss[ener]/relative_f

If provided, relative force error will be used in the loss. The difference of force will be normalized by the magnitude of the force in the label with a shift given by relative_f, i.e. DF_i / ( || F || + relative_f ) with DF denoting the difference between prediction and label and || F || denoting the L2 norm of the label.

When type is set to dipole:

pref_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[dipole]/pref_weight

The prefactor of the weight of global loss. It should be larger than or equal to 0. If not provided, training will be atomic mode, i.e. atomic label should be provided.

pref_atomic_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[dipole]/pref_atomic_weight

The prefactor of the weight of atomic loss. It should be larger than or equal to 0. If it’s not provided and global weight is provided, training will be global mode, i.e. global label should be provided. If both global and atomic weight are not provided, training will be atomic mode, i.e. atomic label should be provided.

When type is set to polar:

pref_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[polar]/pref_weight

The prefactor of the weight of global loss. It should be larger than or equal to 0. If not provided, training will be atomic mode, i.e. atomic label should be provided.

pref_atomic_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[polar]/pref_atomic_weight

The prefactor of the weight of atomic loss. It should be larger than or equal to 0. If it’s not provided and global weight is provided, training will be global mode, i.e. global label should be provided. If both global and atomic weight are not provided, training will be atomic mode, i.e. atomic label should be provided.

When type is set to global_polar:

pref_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[global_polar]/pref_weight

The prefactor of the weight of global loss. It should be larger than or equal to 0. If it’s not provided and atomic weight is provided, training will be atomic mode, i.e. atomic label should be provided. If both global and atomic weight are not provided, training will be global mode, i.e. global label should be provided.

pref_atomic_weight:: type: float | NoneType | int, optional, default: None

argument path: loss[global_polar]/pref_atomic_weight

The prefactor of the weight of atomic loss. It should be larger than or equal to 0. If not provided, training will be global mode, i.e. global label should be provided.

learning_rate:

type: dict

argument path: learning_rate

The definitio of learning rate

Depending on the value of type, different sub args are accepted.

type:: type: str (flag key), default: exp

argument path: learning_rate/type

possible choices: exp

The type of the learning rate.

When type is set to exp:

start_lr:: type: float, optional, default: 0.001

argument path: learning_rate[exp]/start_lr

The learning rate the start of the training.

stop_lr:: type: float, optional, default: 1e-08

argument path: learning_rate[exp]/stop_lr

The desired learning rate at the end of the training.

decay_steps:: type: int, optional, default: 5000

argument path: learning_rate[exp]/decay_steps

The learning rate is decaying every this number of training steps.

training:

type: dict

argument path: training

The training options.

training_data:

type: dict

argument path: training/training_data

Configurations of training data.

systems:: type: list | str

argument path: training/training_data/systems

The data systems for training. This key can be provided with a list that specifies the systems, or be provided with a string by which the prefix of all systems are given and the list of the systems is automatically generated.

set_prefix:: type: str, optional, default: set

argument path: training/training_data/set_prefix

The prefix of the sets in the systems.

batch_size:

type: int | list | str, optional, default: auto

argument path: training/training_data/batch_size

This key can be

list: the length of which is the same as the systems. The batch size of each system is given by the elements of the list.
int: all systems use the same batch size.
string “auto”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than 32.
string “auto:N”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.

auto_prob:

type: str, optional, default: prob_sys_size, alias: auto_prob_style

argument path: training/training_data/auto_prob

Determine the probability of systems automatically. The method is assigned by this key and can be

“prob_uniform” : the probability all the systems are equal, namely 1.0/self.get_nsystems()
“prob_sys_size” : the probability of a system is proportional to the number of batches in the system
“prob_sys_size;stt_idx:end_idx:weight;stt_idx:end_idx:weight;…” : the list of systems is devided into blocks. A block is specified by stt_idx:end_idx:weight, where stt_idx is the starting index of the system, end_idx is then ending (not including) index of the system, the probabilities of the systems in this block sums up to weight, and the relatively probabilities within this block is proportional to the number of batches in the system.

sys_probs:: type: NoneType | list, optional, default: None, alias: sys_weights

argument path: training/training_data/sys_probs

A list of float if specified. Should be of the same length as systems, specifying the probability of each system.

validation_data:

type: NoneType | dict, optional, default: None

argument path: training/validation_data

Configurations of validation data. Similar to that of training data, except that a numb_btch argument may be configured

systems:: type: list | str

argument path: training/validation_data/systems

The data systems for validation. This key can be provided with a list that specifies the systems, or be provided with a string by which the prefix of all systems are given and the list of the systems is automatically generated.

set_prefix:: type: str, optional, default: set

argument path: training/validation_data/set_prefix

The prefix of the sets in the systems.

batch_size:

type: int | list | str, optional, default: auto

argument path: training/validation_data/batch_size

This key can be

list: the length of which is the same as the systems. The batch size of each system is given by the elements of the list.
int: all systems use the same batch size.
string “auto”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than 32.
string “auto:N”: automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.

auto_prob:

type: str, optional, default: prob_sys_size, alias: auto_prob_style

argument path: training/validation_data/auto_prob

Determine the probability of systems automatically. The method is assigned by this key and can be

“prob_uniform” : the probability all the systems are equal, namely 1.0/self.get_nsystems()
“prob_sys_size” : the probability of a system is proportional to the number of batches in the system
“prob_sys_size;stt_idx:end_idx:weight;stt_idx:end_idx:weight;…” : the list of systems is devided into blocks. A block is specified by stt_idx:end_idx:weight, where stt_idx is the starting index of the system, end_idx is then ending (not including) index of the system, the probabilities of the systems in this block sums up to weight, and the relatively probabilities within this block is proportional to the number of batches in the system.

sys_probs:: type: NoneType | list, optional, default: None, alias: sys_weights

argument path: training/validation_data/sys_probs

A list of float if specified. Should be of the same length as systems, specifying the probability of each system.

numb_btch:: type: int, optional, default: 1, alias: numb_batch

argument path: training/validation_data/numb_btch

An integer that specifies the number of systems to be sampled for each validation period.

numb_steps:: type: int, alias: stop_batch

argument path: training/numb_steps

Number of training batch. Each training uses one batch of data.

seed:: type: int | NoneType, optional

argument path: training/seed

The random seed for getting frames from the training data set.

disp_file:: type: str, optional, default: lcueve.out

argument path: training/disp_file

The file for printing learning curve.

disp_freq:: type: int, optional, default: 1000

argument path: training/disp_freq

The frequency of printing learning curve.

numb_test:: type: int | list | str, optional, default: 1

argument path: training/numb_test

Number of frames used for the test during training.

save_freq:: type: int, optional, default: 1000

argument path: training/save_freq

The frequency of saving check point.

save_ckpt:: type: str, optional, default: model.ckpt

argument path: training/save_ckpt

The file name of saving check point.

disp_training:: type: bool, optional, default: True

argument path: training/disp_training

Displaying verbose information during training.

time_training:: type: bool, optional, default: True

argument path: training/time_training

Timing durining training.

profiling:: type: bool, optional, default: False

argument path: training/profiling

Profiling during training.

profiling_file:: type: str, optional, default: timeline.json

argument path: training/profiling_file

Output file for profiling.

tensorboard:: type: bool, optional, default: False

argument path: training/tensorboard

Enable tensorboard

tensorboard_log_dir:: type: str, optional, default: log

argument path: training/tensorboard_log_dir

The log directory of tensorboard outputs

Developer Guide¶

License¶

The project DeePMD-kit is licensed under GNU LGPLv3.0.

Authors and Credits¶

Package Contributors¶

amacadmus
AnguseZhang
denghuilu
bwang-ecnu
frankhan91
GeiduanLiu
gzq942560379
haidi-ustc
hlyang1992
hsulab
iProzd
JiabinYang
marian-code
njzjz
tuoping
wsyxbcl
y1xiaoc
YWolfeee
zhouwei25
ZiyaoLi

Other Credits¶

Zhang ZiXuan for designing the Deepmodeling logo.
Everyone on the Deepmodeling mailing list for contributing to many discussions and decisions!

(If you have contributed to the deepmd-kit core package and your name is missing, please send an email to the contributors, or open a pull request in the deepmd-kit repository)