10.1. Introduction

NVNMD stands for non-von Neumann molecular dynamics.

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).

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.

10.2. 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 This can be done by using either the state-of-the-art active learning tools, or the outdated (i.e., less efficient) brute-force density functional theory (DFT)-based ab-initio molecular dynamics (AIMD) sampling.

If you just want to simply test the training function, you can use the example in the $deepmd_source_dir/examples/nvnmd directory. If you want to fully experience training and running MD functions, you can download the complete example from the website.

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.

10.2.1. Input script

Create and go to the training directory.

mkdir train
cd train 

Then copy the input script train_cnn.json and train_qnn.json to the directory train

cp -r $deepmd_source_dir/examples/nvnmd/train/train_cnn.json train_cnn.json
cp -r $deepmd_source_dir/examples/nvnmd/train/train_qnn.json train_qnn.json

The structure of the input script is as follows

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

10.2.1.1. nvnmd

The “nvnmd” section is defined as

{
    "net_size":128,
    "sel":[60, 60],
    "rcut":6.0,
    "rcut_smth":0.5
}

where items are defined as:

Item	Mean	Optional Value
net_size	the size of nueral network	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]

10.2.1.2. learning_rate

The “learning_rate” section is defined as

{
    "type":"exp",
    "start_lr": 1e-3,
    "stop_lr": 3e-8,
    "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

10.2.1.3. 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

10.2.1.4. training

The “training” section is defined as

{
  "seed": 1,
    "stop_batch": 1000000,
    "numb_test": 1,
    "disp_file": "lcurve.out",
    "disp_freq": 1000,
    "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

10.2.2. Training

Training can be invoked by

# step1: train CNN
dp train-nvnmd train_cnn.json -s s1
# step2: train QNN
dp train-nvnmd train_qnn.json -s s2

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]

10.3. 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 -l test/output.log

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.

10.4. Running MD

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

10.4.1. 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).

ALT

Figure.1 The login interface

To obtain an account, please send your application to the email (jie_liu@hnu.edu.cn, liujie@uw.edu). The username and password will be sent to you by email.

10.4.2. 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).

ALT

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).

ALT

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 model.pb
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).

ALT

Figure.4 The homepage with a new record

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

10.4.3. 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).

ALT

Figure.5 The homepage with a cancelled task

10.4.4. 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).

ALT

Figure.6 The interface for downloading a zipped package

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

ALT

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.

10.4.5. 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.

10.4.6. Clearing records

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

Records cannot be retrieved after clearing.