DeePMD-kit is a software to implement Deep Potential. There is a lot of information on the Internet, but there are not so many tutorials for the new hand, and the official guide is too long. Today, I'll take you 5 minutes to get started with DeePMD-kit.
Let's take a look at the training process of DeePMD-kit:
graph LR A[Prepare data] --> B[Training] B --> C[Freeze the model]
What? Only three steps? Yes, it's that simple.
- Preparing data is converting the computational results of DFT to data that can be recognized by the DeePMD-kit.
- Training is train a Deep Potential model using the DeePMD-kit with data prepared in the previous step.
- Finally, what we need to do is to freeze the restart file in the training process into a model, in other words is to extract the neural network parameters into a file for subsequent use. I believe you can't wait to get started. Let's go!
The data format of the DeePMD-kit is introduced in the official document but seems complex. Don't worry, I'd like to introduce a data processing tool: dpdata! You can use only one line Python scripts to process data. So easy!
In this example, we converted the computational results of the VASP in the
OUTCAR to the data format of the DeePMD-kit and saved in to a directory named
npy is the compressed format of the numpy, which is required by the DeePMD-kit training. We assume
OUTCAR stores 1000 frames of molecular dynamics trajectory, then where will be 1000 points after converting.
set_size=200 means these 1000 points will be divided into 5 subsets, which is named as
data/set.004, respectively. The size of each set is 200. In these 5 sets,
data/set.003 will be considered as the training set by the DeePMD-kit, and
data/set.004 will be considered as the test set. The last set will be considered as the test set by the DeePMD-kit by default. If there is only one set, the set will be both the training set and the test set. (Of course, such test set is meaningless.)
It's required to prepare an input script to start the DeePMD-kit training. Are you still out of the fear of being dominated by INCAR script? Don't worry, it's much easier to configure the DeePMD-kit than configuring the VASP. First, let's download an example and save to
wget https://raw.githubusercontent.com/deepmodeling/deepmd-kit/v1.3.3/examples/water/train/water_se_a.json -O input.json
The strength of the DeePMD-kit is that the same training parameters are suitable for different systems, so we only need to slightly modify
input.json to start training. Here is the first parameter to modify:
"type_map": ["O", "H"],
In the DeePMD-kit data, each atom type is numbered as an integer starting from 0. The parameter gives an element name to each atom in the numbering system. Here, we can copy from the content of
data/type_map.raw. For example,
"type_map": ["A", "B","C"],
Next, we are going to modify the neighbour searching parameter:
"sel": [46, 92],
Each number in this list gives the maximum number of atoms of each type among neighbor atoms of an atom. For example,
46 means there are at most 46
0) neighbours. Here, our elements were modified to
C, so this parameters is also required to modify. What to do if you don't know the maximum number of neighbors? You can be roughly estimate one by the density of the system, or try a number blindly. If it is not big enough, the DeePMD-kit will shoot WARNINGS. Below we changed it to
"sel": [64, 64, 64]
In addtion, we need to modify
It is because that the directory to write to is
./data/ in the current directory. Here I'd like to introduce the definition of the data system. The DeePMD-kit considers that data with corresponding element types and atomic numbers form a system. Our data is generated from a molecular dynamics simulation and meets this condition, so we can put them into one system. Dpdata works the same way. If data cannot be put into a system, multiple systems is required to be set as a list here:
Finnally, we are likely to modify another two parameters:
stop_batch is the numebr of training step using the SGD method of deep learning, and
batch_size is the mini-batch size of data in each step.
If we want to reduce
stop_batch and use
batch_size that the DeePMD-kit recommends, we can use
Now we have succesfully set a input file! To start training, we execuate
dp train input.json
and wait for results. During the training process, we can see
lcurve.out to observe the error reduction.Among them, Column 4 and 5 are the test and training errors of energy (normalized by the number of atoms), and Column 6 and 7 are the test and training errors of the force.
After training, we can use the following script to freeze the model:
The default filename of the output model is
frozen_model.pb. As so, we have got a good or bad DP model. As for the reliability of this model and how to use it, I will give you a detailed tutorial in the next post.