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This manual is only for versions up to GPUMD-v3.5. Starting from GPUMD-v3.6, please use the new manual:

What is GPUMD?

  • GPUMD stands for Graphics Processing Units Molecular Dynamics. It is a general-purpose molecular dynamics (MD) package fully implemented on graphics processing units (GPU). It is written in CUDA C++ and requires a CUDA-enabled Nvidia GPU of compute capability no less than 3.5.
  • It is highly efficient for doing MD simulations with many-body potentials such as the Tersoff potential.
  • It has native support for the NEP machine learning potential. That is, it can be used to train a NEP potential and then run MD simulations with the trained potential.
  • Installation of GPUMD is easy. If you have a working CUDA development environment, it just requires a single make to install GPUMD in either Linux or Windows.


See the publications that developed or used GPUMD.

Versions of GPUMD

  • This website documents up to GPUMD-v3.5.
  • We have been recently focusing on developing the NEP machine-learned potential and the best version for empirical potentials should be GPUMD-v3.3.1.
  • For a full description of the various versions of GPUMD, see the Github page

Install and run GPUMD

Download GPUMD

  • Go to GitHub and download the version(s) you need.

Prerequisites for using GPUMD

  • Hardware: You need to have an Nvidia GPU card with compute capability no less than 3.5.
  • Software:
    • A CUDA toolkit 9.0 or newer.
    • In Linux system, you also need a g++ compiler supporting at least c++11.
    • In Windows system, you also need the cl.exe compiler from Microsoft Visual Studio and a 64-bit version of make.exe.

Compile GPUMD

  • Go to the src directory and type make. When the compilation finishes, two executables, nep and gpumd, will be generated in the src directory.
  • Please check the comments in the beginning of the makefile for some compiling options.


Up to GPUMD-3.3.1

  • To run each executable, one has to prepare some input files and a driver input file, which is used to do one or more simulations using a single launch of an executable. The driver input file should have the following format:

Here number_of_simulations is the number of individual simulations you want to run within a single launch (by the operating system) of the executable (src/nep or src/gpumd) and path_n is the path of the directory containing the actual input files for the n-th simulation. Output files will be created in the directories containing the corresponding input files.

Starting from GPUMD-v3.4

There will be no driver input file any more. To run one example, one just need to go to the directory of that example and type one of the following commands:


Prepared examples

Inputs and outputs for GPUMD

Inputs for the src/gpumd executable

  • To run one simulation using the src/gpumd executable, one has to prepare at least two input files:
Mandatory input files for the src/gpumd executable
Input filename Brief description Define the simulation model (before GPUMD-v3.4) Define the simulation model (starting from GPUMD-v3.4) Define the simulation protocol
  • The file is used to define the simulation protocol for gpumd. The code will execute the commands in this file one by one. If the code encounters an invalid command in this file, it will report an error message and exit. In this input file, blank lines and lines starting with # are ignored. One can thus write comments after #. All the other lines should be of the following form:
keyword parameter_1 parameter_2 ...
  • The overall structure of a file is as follows:
    • First, set up the potential model using the potential keyword.
    • Then, if needed, use the minimize keyword to minimize the energy of the whole system.
    • Then one can use the following keywords to do some static calculations (that is, non-MD simulations):
    • Then, if you want to do MD simulations, set up the initial velocities using the velocity keyword and do a number of MD runs in the following way:
      • Specify an integrator using the ensemble keyword and optionally add keywords to further control the evolution and measurement processes.
      • Use the keyword run to run a number of steps according to the above settings.
      • One can repeat the above two steps.
  • Here is the complete list of the keywords:
Keywords for the input file
Keyword Brief description Take action immediately? Propagating from one run to the next?
velocity Set up the initial velocities with a given temperature Yes N/A
potential (before GPUMD-v3.4) Set up a single potential Yes N/A
potential (starting from GPUMD-v3.4) Set up a single potential Yes N/A
minimize Perform an energy minimization Yes N/A
compute_cohesive Compute the cohesive energy curve Yes N/A
compute_elastic Compute the elastic constants Yes N/A
compute_phonon Compute the phonon dispersion Yes N/A
change_box Change the box Yes N/A
ensemble Specify an integrator for a run No No
time_step Specify the time step for integration No Yes
neighbor Control the neighbor list updating No No
fix Fix (freeze) some atoms No No
deform Deform the simulation box No No
dump_thermo Dump some thermodynamic quantities No No
dump_position Dump the atom positions No No
dump_netcdf Dump the atom positions in the netCDF format No No
dump_restart Dump a restart file No No
dump_velocity Dump the atom velocities No No
dump_force Dump the atom forces No No
dump_exyz Dump an extended XYZ file with some data No No
compute Compute some time- and space-averaged quantities No No
compute_shc Calculate spectral heat current No No
compute_dos Calculate the phonon density of states (PDOS) No No
compute_sdc Calculate the self diffusion coefficient (SDC) No No
compute_hac Calculate thermal conductivity using the EMD method No No
compute_hnemd Calculate thermal conductivity using the HNEMD method No No
compute_gkma Calculate modal heat current using the GKMA method No No
compute_hnema Calculate modal thermal conductivity using the HNEMA method No No
run Run a number of steps Yes No

Output files for the src/gpumd executable

Output files for the src/gpumd executable
Output filename Generated by which keyword? Brief description Output mode
thermo.out dump_thermo Some global thermodynamic quantities Append dump_position Trajectory (atom positions) Append
restart.out (Before GPUMD-v3.4) or (Starting from GPUMD-v3.4) dump_restart The restart file Overwrite
velocity.out dump_velocity The velocity file Append
force.out dump_force The force file Append
compute.out compute Time and space (group) averaged quantities Append
hac.out compute_hac Thermal conductivity data from the EMD method Append
kappa.out compute_hnemd Thermal conductivity data from the HNEMD method Append
shc.out compute_shc Spectral heat current data Append
heatmode.out compute_gkma Modal heat current data from GKMA method Append
kappamode.out compute_hnema Modal thermal conductivity data from HNEMA method Append


compute_dos Phonon density of states data Append
sdc.out compute_sdc Self diffusion coefficient data Append
D.out compute_phonon Dynamical matrices [math]D(\vec{k})[/math] for the input k points Overwrite
omega2.out compute_phonon Phonon frequency square [math]\omega^2(\vec{k})[/math] for the input k points Overwrite

Inputs for the src/nep executable

  • To run one simulation using the src/nep executable, one has to prepare at least three input files:
Input files for the src/nep executable
Input filename Brief description Define the NEP potential and Provide the training and testing data (before GPUMD-v3.4) and Provide the training and testing data (starting from GPUMD-v3.4)

Outputs for the src/nep executable

  • The output files for the src/nep executable are described here.

Tutorials for using GPUMD

Tutorials for using the src/gpumd executable

Tutorials for using the src/gpumd executable
Tutorial name Brief description
Tutorial: Thermal expansion Study thermal expansion of silicon crystal from 100 K to 1000 K
Tutorial: Density of states Calculate the vibrational density of states of graphene at 300 K
Tutorial: Thermal conductivity from EMD Calculate the lattice thermal conductivity of graphene at 300 K using the EMD method
Tutorial: Thermal transport from NEMD Calculate the spectral ballistic conductance of graphene using the NEMD and spectral decomposition
Tutorial: Thermal transport from HNEMD Calculate the spectral conductivity of graphene using the HNEMD method and spectral decomposition
Tutorial: Phonon dispersion Calculate the phonon dispersion of silicon crystal
Tutorial: Phonon vibration visualization Visualize phonon vibrations
Tutorial: Phonon participation ratio Calculating the phonon participation ratio in the frequency domain for prsitine and defect graphene
Tutorial: Elastic constant Elastic constant calculations from strain fluctuations

Tutorials for using the src/nep executable

Tutorials for using the src/nep executable
Tutorial name Brief description
Tutorial: NEP tutorial Train a NEP machine-learning potential for PbTe crystal

Python interfaces of GPUMD

Name Brief description
gpyumd Pre- and post-process GPUMD simulations with Python
pyNEP Python interface for the NEP machine learning potential
calorine Python library to manage GPUMD simulations

Theoretical formulations of GPUMD

Mailing list and discussion group of GPUMD

  • Discussion group
    • There is a Chinese discussion group based on the following QQ 群:
      • 887975816

Want to develop GPUMD?

Developers of GPUMD

  • GPUMD was first developed by Zheyong Fan (Previously Aalto University; brucenju(at), with help from his colleagues Ville Vierimaa, Mikko Ervasti, and Ari Harju during 2012-2017.
  • In 2018, Alexander J. Gabourie (PhD candidate at Stanford University; gabourie(at) joined in and he is now an active developer.

Important coding conventions of GPUMD

  • We want to keep GPUMD as a standalone code. So we only use standard C++ (currently only up to c++11) and CUDA (currently only up to CUDA 9.0) libraries.
  • We will make sure that the code is correct for any Nvidia GPU with compute capability no less than 3.5 and in both Linux and Windows systems.
  • We use the .clang-format file in the package to format any CUDA C++ source code.

Units system adopted within GPUMD

  • We use the following basic units
    • Energy: eV (electron volt)
    • Length: A (angstrom)
    • Mass: amu (atomic mass unit)
    • Temperature: K (kelvin)
    • Charge: e (elementary charge)
  • The units for all the quantities are thus fixed.
  • One only needs to make units conversions when dealing with inputs and outputs; all the quantities should be defined in the above units system elsewhere.