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.
- interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient.
- interfaced with high-performance classical MD and quantum (path-integral) MD packages, i.e., LAMMPS and i-PI, respectively.
- implements the Deep Potential series models, which have been successfully applied to finite and extended systems including organic molecules, metals, semiconductors, and insulators, etc.
- implements MPI and GPU supports, makes it highly efficient for high performance parallel and distributed computing.
- highly modularized, easy to adapt to different descriptors for deep learning based potential energy models.
The code is organized as follows:
-
data/raw: tools manipulating the raw data files. -
examples: example json parameter files. -
source/3rdparty: third-party packages used by DeePMD-kit. -
source/cmake: cmake scripts for building. -
source/ipi: source code of i-PI client. -
source/lib: source code of DeePMD-kit library. -
source/lmp: source code of Lammps module. -
source/md: source code of native MD. -
source/op: tensorflow op implementation. working with library. -
source/scripts: Python script for model freezing. -
source/train: Python modules and scripts for training and testing.
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.
The goal of Deep Potential is to employ deep learning techniques and realize an inter-atomic potential energy model that is general, accurate, computationally efficient and scalable. The key component is to respect the extensive and symmetry-invariant properties of a potential energy model by assigning a local reference frame and a local environment to each atom. Each environment contains a finite number of atoms, whose local coordinates are arranged in a symmetry preserving way. These local coordinates are then transformed, through a sub-network, to a so-called atomic energy. Summing up all the atomic energies gives the potential energy of the system.
The initial proof of concept is in the Deep Potential paper, which employed an approach that was devised to train the neural network model with the potential energy only. With typical ab initio molecular dynamics (AIMD) datasets this is insufficient to reproduce the trajectories. The Deep Potential Molecular Dynamics (DeePMD) model overcomes this limitation. In addition, the learning process in DeePMD improves significantly over the Deep Potential method thanks to the introduction of a flexible family of loss functions. The NN potential constructed in this way reproduces accurately the AIMD trajectories, both classical and quantum (path integral), in extended and finite systems, at a cost that scales linearly with system size and is always several orders of magnitude lower than that of equivalent AIMD simulations.
Although being highly efficient, the original Deep Potential model satisfies the extensive and symmetry-invariant properties of a potential energy model at the price of introducing discontinuities in the model. This has negligible influence on a trajectory from canonical sampling but might not be sufficient for calculations of dynamical and mechanical properties. These points motivated us to develop the Deep Potential-Smooth Edition (DeepPot-SE) model, which replaces the non-smooth local frame with a smooth and adaptive embedding network. DeepPot-SE shows great ability in modelling many kinds of systems that are of interests in the fields of physics, chemistry, biology, and materials science.
In addition to building up potential energy models, DeePMD-kit can also be used to build up coarse-grained models. In these models, the quantity that we want to parametrize is the free energy, or the coarse-grained potential, of the coarse-grained particles. See the DeePCG paper for more details.
Please follow our github webpage to see the latest released version and development version.
A docker for installing the DeePMD-kit on CentOS 7 is available here. We are currently working on installation methods using the conda package management system and pip tools. Hope these will come out soon.
Installing DeePMD-kit from scratch is lengthy, but do not be panic. Just follow step by step. Wish you good luck..
We tested two tensorflow installation options. You may follow either tf-1.8 or tf-1.12. Click one of the links and follow the instructions therein. Of course, other installation options are not forbidden.
The DeePMD-kit was tested with compiler gcc >= 4.9.
Firstly clone the DeePMD-kit source code
cd /some/workspace
git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kitIf one downloads the .zip file from the github, then the default folder of source code would be deepmd-kit-master rather than 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`Then goto the source code directory and make a build directory.
cd $deepmd_source_dir/source
mkdir build
cd buildI assume you want to install DeePMD-kit into path $deepmd_root, then execute cmake
cmake -DTF_GOOGLE_BIN=true -DTENSORFLOW_ROOT=$tensorflow_root \
-DCMAKE_INSTALL_PREFIX=$deepmd_root ..If you built the tensorflow's Python interface by gcc>=5.0, then remove the option -DTF_GOOGLE_BIN=true. If the cmake has executed successfully, then
make
make installIf everything works fine, you will have the following executables installed in $deepmd_root/bin
$ ls $deepmd_root/bin
dp_frz dp_ipi dp_test dp_trainDeePMD-kit provide module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.
cd $deepmd_source_dir/source/build
make lammpsDeePMD-kit will generate a module called USER-DEEPMD in the build directory. Now download your favorite LAMMPS code, and uncompress it (I assume that you have downloaded the tar lammps-stable.tar.gz)
cd /some/workspace
tar xf lammps-stable.tar.gzThe source code of LAMMPS is stored in directory, for example lammps-31Mar17. Now go into the LAMMPS code and copy the DeePMD-kit module like this
cd lammps-31Mar17/src/
cp -r $deepmd_source_dir/source/build/USER-DEEPMD .Now build LAMMPS
make yes-user-deepmd
make mpi -j4The 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.
The DeePMD-kit module can be removed from LAMMPS source code by
make no-user-deepmdIf your system has a NVIDIA GPU, you can build TensorFlow with GPU support, which will be inherited by DeePMD-kit and LAMMPS. To achieve this, please carefully check the webpage Install TensorFlow from Source and look for the GPU version. In particular, you have to make sure that the required NVIDIA softwares, namely CUDA Toolkit, GPU drivers, and cuDNN SDK, must be installed on your system.
To install TensorFlow with GPU support, all the installation steps will be the same as the non-GPU version, except that one may allow the GPU option when doing configure, e.g.,
Do you wish to build TensorFlow with CUDA support? [y/N] Y
CUDA support will be enabled for TensorFlow
Do you want to use clang as CUDA compiler? [y/N]
nvcc will be used as CUDA compiler
Please specify the CUDA SDK version you want to use. [Leave empty to default to CUDA 9.0]: 9.0
Please specify the location where CUDA 9.0 toolkit is installed. Refer to README.md for more details. [Default is /usr/local/cuda]:
Please specify which gcc should be used by nvcc as the host compiler. [Default is /usr/bin/gcc]:
Please specify the cuDNN version you want to use. [Leave empty to default to cuDNN 7.0]: 7
Please specify the location where cuDNN 7 library is installed. Refer to README.md for more details. [Default is /usr/local/cuda]:
Please specify a list of comma-separated CUDA compute capabilities you want to build with.
You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.
Please note that each additional compute capability significantly increases your build time and binary size.After sucessfully installing TensorFlow with GPU support, you should install DeePMD, LAMMPS, etc., in the same way of the non-GPU version. Sometimes you may need to explicitly tell the compiler the place of the CUDA Toolkit and cuDNN libraries, i.e.,
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/cuda_toolkit/lib64
$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/path/to/cudnn/lib64In 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 the model
- MD runs with the model (Native MD code or LAMMPS)
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 |
| 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 0.343This 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. 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 tyep.raw of a system that has 2 atoms with 0 and 1:
$ cat type.raw
0 1The 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.rawIt generates three sets set.000, set.001 and set.002, with each set contains 2000 frames. The last set (set.002) is used as testing set, while the rest sets (set.000 and set.001) are used as training sets. 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.
The method of training is explained in our DeePMD paper. With the source code we provide a small training dataset taken from 400 frames generated by NVT ab-initio water MD trajectory with 300 frames for training and 100 for testing. An example training parameter file is provided. One can try with the training by
$ cd $deepmd_source_dir/examples/train/
$ $deepmd_root/bin/dp_train water.json$deepmd_root/bin/dp_train is the training program, and water.json is the json format parameter file that controls the training. The components of the water.json are
{
"_comment": " model parameters",
"use_smooth": false,
"sel_a": [16, 32],
"sel_r": [30, 60],
"rcut": 6.00,
"axis_rule": [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0],
"_comment": " default rule: []",
"_comment": " user defined rule: for each type provides two axes, ",
"_comment": " for each axis: (a_or_r, type, idx)",
"_comment": " if type < 0, exclude type -(type+1)",
"_comment": " for water (O:0, H:1) it can be",
"_comment": " [0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0]",
"fitting_neuron": [240, 120, 60, 30, 10],
"_comment": " training controls",
"systems": ["../data/water/"],
"set_prefix": "set",
"stop_batch": 1000000,
"batch_size": 4,
"start_lr": 0.001,
"decay_steps": 5000,
"decay_rate": 0.95,
"start_pref_e": 0.02,
"limit_pref_e": 8,
"start_pref_f": 1000,
"limit_pref_f": 1,
"start_pref_v": 0,
"limit_pref_v": 0,
"seed": 1,
"_comment": " display and restart",
"_comment": " frequencies counted in batch",
"disp_file": "lcurve.out",
"disp_freq": 100,
"numb_test": 100,
"save_freq": 100,
"save_ckpt": "model.ckpt",
"load_ckpt": "model.ckpt",
"disp_training": true,
"time_training": true,
"_comment": "that's all"
}The option rcut is the cut-off radius for neighbor searching. The sel_a and sel_r are the maximum selected numbers of fully-local-coordinate and radial-only-coordinate atoms from the neighbor list, respectively. sel_a + sel_r should be larger than the maximum possible number of neighbors in the cut-off radius. sel_a and sel_r are vectors, the length of the vectors are same as the number of atom types in the system. sel_a[i] and sel_r[i] denote the selected number of neighbors of type i.
The option axis_rule specifies how to make the axis for the local coordinate of each atom. For each atom type, 6 integers should be provided. The first three for the first axis, while the last three for the second axis. Within the three integers, the first one specifies if the axis atom is fully-local-coordinated (0) or radial-only-coordinated (1). The second integer specifies the type of the axis atom. If this number is less than 0, saying t < 0, then this axis exclude atom of type -(t+1). If the third integer is, saying s, then the axis atom is the sth nearest neighbor satisfying the previous two conditions.
The option fitting_neuron (deprecated name n_neuron) is an integer vector that determines the shape the neural network. The size of the vector is identical to the number of hidden layers of the network. From left to right the members denote the sizes of each hidden layers from input end to the output end, respectively. If two neighboring layers are of the same size, then a ResNet architecture is build between them. If the option fitting_resnet_dt is set true, then a timestep is used in the ResNet.
The option systems provide location of the systems (path to set.* and type.raw). It is a vector, thus DeePMD-kit allows you to provide multiple systems. DeePMD-kit will train the model with the systems in the vector one by one in a cyclic manner.
The option batch_size specifies the number of frames in each batch.
The option stop_batch specifies the total number of batches will be used in the training.
The option start_lr, decay_rate and decay_steps specify how the learning rate changes. For example, the tth batch will be trained with learning rate:
The options start_pref_e, limit_pref_e, start_pref_f, limit_pref_f, start_pref_v and limit_pref_v determine how the prefactors of energy error, force error and virial error changes in the loss function (see the appendix of the DeePMD paper for details). Taking the prefactor of force error for example, the prefactor at batch t is
Since we do not have virial data, the virial prefactors start_pref_v and limit_pref_v are set to 0.
The option seed specifies the random seed for neural network initialization. If not provided, the seed will be initialized with None.
During the training, the error of the model is tested every disp_freq batches with numb_test frames from the last set in the systems directory on the fly, and the results are output to disp_file.
Checkpoints will be written to files with prefix save_ckpt every save_freq batches. If restart is set to true, then the training will start from the checkpoint named load_ckpt, rather than from scratch.
Several command line options can be passed to dp_train, which can be checked with
$ $deepmd_root/bin/dp_train --helpAn explanation will be provided
positional arguments:
INPUT the input json database
optional arguments:
-h, --help show this help message and exit
-t INTER_THREADS, --inter-threads INTER_THREADS
With default value 0. Setting the "inter_op_parallelism_threads" key for the tensorflow, the "intra_op_parallelism_threads" will be set by the env variable OMP_NUM_THREADS
--init-model INIT_MODEL
Initialize a model by the provided checkpoint
--restart RESTART Restart the training from the provided checkpoint
The keys intra_op_parallelism_threads and inter_op_parallelism_threads are Tensorflow configurations for multithreading, which are explained here. Skipping -t and OMP_NUM_THREADS leads to the default setting of these keys in the Tensorflow.
--init-model model.ckpt, for example, 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.
The smooth version of DeePMD, or the DeepPot-SE model, can also be trained by DeePMD-kit. An example training parameter file is provided. One can try with the training by
$ cd $deepmd_source_dir/examples/train/
$ $deepmd_root/bin/dp_train water_smth.jsonThe difference between the standard and smooth DeePMD models lies in the model parameters:
{
"use_smooth": true,
"sel_a": [46, 92],
"rcut_smth": 5.80,
"rcut": 6.00,
"filter_neuron": [25, 50, 100],
"filter_resnet_dt": false,
"axis_neuron": 16,
"fitting_neuron": [240, 240, 240],
"fitting_resnet_dt": true,
"_comment": "that's all"
}The sel_r option is skipped by the smooth version and the model use fully-local-coordinate for all neighboring atoms. The sel_a should larger than the maximum possible number of neighbors in the cut-off radius rcut.
The descriptors will decay smoothly from rcut_smth to the cutoff radius rcut.
The filter_neuron provides the size of the filter network (also called local-embedding network). If the size of the next layer is the same or twice as the previous layer, then a skip connection is build (ResNet). The filter_resnet_dt tells if a timestep is used in the skip connection. By default it is false. axis_neuron (deprecated name n_axis_neuron) specifies the number of axis filter, which should be much smaller than the size of the last layer of the filter network.
fitting_neuron (deprecated name n_neuron) specifies the fitting network. If the size of the next layer is the same as the previous layer, then a skip connection is build (ResNet). fitting_resnet_dt (deprecated name resnet_dt) tells if a timestep is used in the skip connection. By default it is true.
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
$ $deepmd_root/bin/dp_frz -o graph.pbin the folder where the model is trained. The output database is called graph.pb.
The frozen model can be used in many ways. The most straightforward test can be performed using dp_test. Several command line options can be passed to dp_test, which can be checked with
$ $deepmd_root/bin/dp_test --helpAn explanation will be provided
usage: dp_test [-h] [-m MODEL] [-s SYSTEM] [-S SET_PREFIX] [-n NUMB_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
-d DETAIL_FILE, --detail-file DETAIL_FILE
The file containing details of energy force and virial
accuracy
The files dp_frz and dp_test may also serve as a python template for further analyses and more user-specific applications.
Running an MD simulation with LAMMPS is simpler. In the LAMMPS input file, one needs to specify the pair style as follows
pair_style deepmd graph.pb
pair_coeff where graph.pb is the file name of the frozen model. The pair_coeff should be left blank. It should be noted that LAMMPS counts atom types starting from 1, therefore, all LAMMPS atom type will be firstly subtracted by 1, and then passed into the DeePMD-kit engine to compute the interactions.
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 0.45Please 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.
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. The client can be started by
$ dp_ipi water.jsonIt 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 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.
DeePMD-kit provides a simple MD implementation that runs under either NVE or NVT ensemble. One needs to provide the following input files
$ ls
conf.gro graph.pb water.jsonconf.gro is the file that provides the initial coordinates and/or velocities of all atoms in the system. It is of Gromacs gro format. Details of this format can be find in this website. It should be notice that the length unit of the gro format is nm rather than A.
graph.pb is the frozen model.
water.json is the parameter file that specifies how the MD runs. An example parameter file for water NVT simulation is provided.
{
"conf_file": "conf.gro",
"conf_format": "gro",
"graph_file": "graph.pb",
"nsteps": 500000,
"dt": 5e-4,
"ener_freq": 20,
"ener_file": "energy.out",
"xtc_freq": 20,
"xtc_file": "traj.xtc",
"trr_freq": 20,
"trr_file": "traj.trr",
"print_force": false,
"T": 300,
"tau_T": 0.1,
"rand_seed": 2017,
"atom_type" : {
"OW": 0,
"HW1": 1,
"HW2": 1
},
"atom_mass" : {
"OW": 16,
"HW1": 1,
"HW2": 1
}
}The options conf_file, conf_format and graph_file are self-explanatory. It should be noticed, again, the length unit is nm in the gro format file.
The option nsteps specifies the number of time steps of the MD simulation. The option dt specifies the timestep of the simulation.
The options ener_file and ener_freq specify the energy output file and frequency.
The options xtc_file, xtc_freq, trr_file and trr_freq are similar options that specify the output files and frequencies of the xtc and trr trajectory, respectively. When the frequencies are set to 0, the corresponding file will not be output. The instructions of the xtc and trr formats can be found in xtc manual and trr manual. It is noticed that the length unit in the xtc and trr files is nm.
If the option print_force is set to true, then the atomic force will be output.
The option T specifies the temperature of the simulation, and the option tau_T specifies the timescale of the thermostat. We implement the Langevin thermostat for the NVT simulation. rand_seed set the random seed of the random generator in the thermostat.
The atom_type set the type for the atoms in the system. The names of the atoms are those provided in the conf_file file. The atom_mass set the mass for the atoms. Again, the name of the atoms are those provided in the conf_file.
In consequence of various differences of computers or systems, problems may occur. Some common circumstances are listed as follows. If other unexpected problems occur, you're welcome to contact us for help.
Sometimes you may use a gcc/g++ of version <4.9. If you have a gcc/g++ of version > 4.9, say, 7.2.0, you may choose to use it by doing
export CC=/path/to/gcc-7.2.0/bin/gcc
export CXX=/path/to/gcc-7.2.0/bin/g++If, for any reason, for example, you only have a gcc/g++ of version 4.8.5, you can still compile all the parts of TensorFlow and most of the parts of DeePMD-kit. In this case, follow the following steps.
First, goto the source code directory, open the file CMakeLists.txt
cd $deepmd_source_dir/source
vi CMakeLists.txtNext, comment the following 4 lines out:
# set (LIB_DEEPMD_NATIVE "deepmd_native_md")
# set (LIB_DEEPMD_IPI "deepmd_ipi")
# add_subdirectory (md/)
# add_subdirectory (ipi/)
Then you may continue with the installation procedure.
When you try to build a second time when installing DeePMD-kit, files produced before may contribute to failure. Thus, you may clear them by
cd build
rm -r *and redo the cmake process.
If you confront such kind of error:
$deepmd_root/lib/deepmd/libop_abi.so: undefined symbol:
_ZN10tensorflow8internal21CheckOpMessageBuilder9NewStringB5cxx11Ev
you may set -DTF_GOOGLE_BIN=true in the process of cmake.
Another possible reason might be the large gap between the python version of TensorFlow and the TensorFlow c++ interface.
This typically happens when you install a new version of DeePMD-kit and copy directly the generated USER-DEEPMD to a LAMMPS source code folder and re-install LAMMPS.
To solve this problem, it suffices to first remove USER-DEEPMD from LAMMPS source code by
make no-user-deepmdand then install the new USER-DEEPMD.
If this does not solve your problem, try to decompress the LAMMPS source tarball and install LAMMPS from scratch again, which typically should be very fast.
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