Table of contents

• 1 Introduction
• 2 Preparation
  • 2-1 Downloading source code
  • 2-2 Installing
• 3 Training
  • 3-1 Input script
    • 3-1-1 nvnmd
    • 3-1-2 learning_rate
    • 3-1-3 loss
    • 3-1-4 training
  • 3-2 Training
  • 3-3 Testing
• 4 Running MD
  • 4-1 Account application
  • 4-2 Adding task
  • 4-3 Cancelling calculation
  • 4-4 Downloading results
  • 4-5 Deleting record
  • 4-6 Clearing records

1 Introduction

This is the training code we used to generate the results in our paper entitled "Accurate and Efficient Molecular Dynamics based on Machine Learning and Non Von Neumann Architecture", which has been accepted by npj Computational Materials (DOI: 10.1038/s41524-022-00773-z).

NVNMD stands for non-von Neumann molecular dynamics.

Any user can follow two consecutive steps to run molecular dynamics (MD) on the proposed NVNMD computer, which has been released online: (i) to train a machine learning (ML) model that can decently reproduce the potential energy surface (PES); and (ii) to deploy the trained ML model on the proposed NVNMD computer, then run MD there to obtain the atomistic trajectories.

2 Preparation

2-1 Downloading source code

First, please visit https://github.com/LiuGroupHNU/nvnmd to download training and testing code for NVNMD.

Or get the source code with git

cd /some/workspace
git clone https://github.com/LiuGroupHNU/nvnmd.git $nvnmd_root
cd $nvnmd_root

where $nvnmd_root is the name of the directory you wish to create on your machine.

Now we assume that $nvnmd_source_dir is the path to the current directory.

2-2 Installing

Check the compiler version on your machine by gcc --version The C++ interface was tested with compiler gcc >= 6.0.0. However, gcc == 9.0.0 is better for fixing compatibility bugs.

Check you have installed conda on your machine by which conda && conda --version Then create a virtual environment and activate the environment to actually use it

conda create -n nvnmd
conda activate nvnmd

NVNMD can be installed by

bash install.sh

The install process consists of three steps:

1. check and install dependances, such as conda, gcc and python
2. install cmake-3.10.0
3. install tensorflow-2.7.0, libtensorflow_cc.so
4. install the python dependances of NVNMD, and NVNMD

NVNMD can also be available with conda by

conda install nvnmd libnvnmd -c nvnmd -c conda-forge

If everything works fine, you can use not only NVNMD but also DeePMD-kit. If the intermediate process reports an error due to network timeout, please re-execute the above installation command.

3 Training

Our training procedure consists of not only the continuous neural network (CNN) training, but also the quantized neural network (QNN) training which uses the results of CNN as inputs. It is performed on CPU or GPU by using the training codes we open-sourced online.

To train a ML model that can decently reproduce the PES, training and testing data set should be prepared first. This can be done by using either the state-of-the-art active learning tools, or the outdated (i.e., less efficient) brute-force density functional theory (DFT)-based ab-initio molecular dynamics (AIMD) sampling.

Then, copy the data set to working directory

mkdir -p $workspace
cd $workspace
mkdir -p data
cp -r $dataset data

where $dataset is the path to the data set and $workspace is the path to working directory. $nvnmd_root/examples/data is the path to the data set used in this example.

3-1 Input script

Create and go to the training directory.

mkdir train
cd train 

Then copy the input script train.json to the directory train

cp -r $nvnmd_root/examples/train/train.json train.json

The structure of the input script is as follows

{
    "nvnmd" : {},
    "learning_rate" : {},
    "loss" : {},
    "training": {}
}

3-1-1 nvnmd

The "nvnmd" section is defined as

{
    "net_size":32,
    "sel":[60, 60],
    "rcut":7.0,
    "rcut_smth":0.5
}

where items are defined as:

Item	Mean	Optional Value
net_size	the size of nueral network	32 or 128
sel	the number of neighbors	integer list of lengths 1 to 4 are acceptable
rcut	the cutoff radial	(0, 8.0]
rcut_smth	the smooth cutoff parameter	(0, 8.0]

3-1-2 learning_rate

The "learning_rate" section is defined as

{
    "type":"exp",
    "start_lr": 5e-3,
    "stop_lr": 5e-6,
    "decay_steps": 5000
}

where items are defined as:

Item	Mean	Optional Value
type	learning rate variant type	exp
start_lr	the learning rate at the beginning of the training	a positive real number
stop_lr	the desired learning rate at the end of the training	a positive real number
decay_stops	the learning rate is decaying every {decay_stops} training steps	a positive integer

3-1-3 loss

The "loss" section is defined as

{
    "start_pref_e": 0.02,
    "limit_pref_e": 2,
    "start_pref_f": 1000,
    "limit_pref_f": 1,
    "start_pref_v": 0,
    "limit_pref_v": 0
}

where items are defined as:

Item	Mean	Optional Value
start_pref_e	the loss factor of energy at the beginning of the training	zero or positive real number
limit_pref_e	the loss factor of energy at the end of the training	zero or positive real number
start_pref_f	the loss factor of force at the beginning of the training	zero or positive real number
limit_pref_f	the loss factor of force at the end of the training	zero or positive real number
start_pref_v	the loss factor of virial at the beginning of the training	zero or positive real number
limit_pref_v	the loss factor of virial at the end of the training	zero or positive real number

3-1-4 training

The "training" section is defined as

{
  "seed": 1,
    "stop_batch": 500000,
    "numb_test": 10,
    "disp_file": "lcurve.out",
    "disp_freq": 100,
    "save_ckpt": "model.ckpt",
    "save_freq": 10000,
    "training_data":{
      "systems":["system1_path", "system2_path", "..."],
      "set_prefix": "set",
      "batch_size": ["batch_size_of_system1", "batch_size_of_system2", "..."]
    }
}

where items are defined as:

Item	Mean	Optional Value
seed	the randome seed	a integer
stop_batch	the total training steps	a positive integer
numb_test	the accuracy is test by using {numb_test} sample	a positive integer
disp_file	the log file where the training message display	a string
disp_freq	display frequency	a positive integer
save_ckpt	check point file	a string
save_freq	save frequency	a positive integer
systems	a list of data directory which contains the dataset	string list
set_prefix	the prefix of dataset	a string
batch_size	a list of batch size of corresponding dataset	a integer list

3-2 Training

training can be invoked by

dp train_nvnmd train.json

After training process, you will get two folders: nvnmd_cnn and nvnmd_qnn. The nvnmd_cnn contains the model after continuous neural network (CNN) training. The nvnmd_qnn contains the model after quantized neural network (QNN) training. The binary file nvnmd_qnn/model.pb is the model file which is used to performs NVNMD in server [http://nvnmd.picp.vip]

3-3 Testing

The frozen model can be used in many ways. The most straightforward testing can be invoked by

mkdir test
dp test -m ./nvnmd_qnn/frozen_model.pb -s path/to/system -d ./test/detail -n 99999 | tee test/output

where the frozen model file to import is given via the -m command line flag, the path to the testing data set is given via the -s command line flag, the file containing details of energy, force and virial accuracy is given via the -d command line flag, the amount of data for testing is given via the -n command line flag.

4 Running MD

After CNN and QNN training, you can upload the ML model to our online NVNMD system and run MD there.

4-1 Account application

The server website of NVNMD is available at http://nvnmd.picp.vip. You can visit the URL and enter the login interface (Figure.1).

Figure.1 The login interface

To obtain an account, please send your application to the email ([email protected], [email protected]). The username and password will be sent to you by email.

4-2 Adding task

After successfully obtaining the account, enter the username and password in the login interface, and click "Login" to enter the homepage (Figure.2).

Figure.2 The homepage

The homepage displays the remaining calculation time and all calculation records not deleted. Click Add a new task to enter the interface for adding a new task (Figure.3).

Figure.3 The interface for adding a new task

• Task name: name of the task
• Upload mode: two modes of uploading results to online data storage, including Manual upload and Automatic upload. Results need to be uploaded manually to online data storage with Manual upload mode, and will be uploaded automatically with Automatic upload mode.
• Input script: input file of the MD simulation.

In the input script, one needs to specify the pair style as follows

pair_style nvnmd
pair_coeff

• Model file: the ML model named model.pb obtained by QNN training.
• Data files: data files containing information required for running an MD simulation (e.g., coord.lmp containing initial atom coordinates).

Next, you can click Submit to submit the task and then automatically return to the homepage (Figure.4).

Figure.4 The homepage with a new record

Then, click Refresh to view the latest status of all calculation tasks.

4-3 Cancelling calculation

For the task whose calculation status is Pending and Running, you can click the corresponding Cancel on the homepage to stop the calculation (Figure.5).

Figure.5 The homepage with a cancelled task

4-4 Downloading results

For the task whose calculation status is Completed, Failed and Cancelled, you can click the corresponding Package or Separate files in the Download results bar on the homepage to download results.

Click Package to download a zipped package of all files including input files and output results (Figure.6).

Figure.6 The interface for downloading a zipped package

Click Separate files to download the required separate files (Figure.7).

Figure.7 The interface for downloading separate files

If Manual upload mode is selected or the file has expired, click Upload on the download interface to upload manually.

4-5 Deleting record

For the task no longer needed, you can click the corresponding Delete on the homepage to delete the record.

Records cannot be retrieved after deletion.

4-6 Clearing records

Click Clear calculation records on the homepage to clear all records.

Records cannot be retrieved after clearing.