Merge pull request #17 from Exabyte-io/feat/SOF-7540

SOF-7540: NanoLabo LAMMPS+M3GNet example

Author: timurbazhirov

README.md

@@ -1,7 +1,7 @@
 # Mat3ra CLI Examples
 
 This repository contains example data for command-line jobs using commonly-deployed materials modeling packages on
-Mat3ra.com [[1,2](#links)]. The package is pre-installed for all users of the platform as explained in the
+Mat3ra.com [^1],[^2]. The package is pre-installed for all users of the platform as explained in the
 corresponding [documentation](https://docs.mat3ra.com/data-on-disk/directories/#job-script-templates), however, the data
 can also be used outside the platform as a standalone tool. The main goal of the repository is to provide a quick start
 for the users.
@@ -15,6 +15,7 @@ Quantum ESPRESSO  | [espresso/gpu](espresso/gpu/job.gpu.pbs)         | CUDA/GPU
 VASP              | [vasp/](vasp/job.pbs)                            | Self-consistent total energy calculation for FCC Silicon with VASP (same as QE above).
 DeePMD            | [deepmd/train_mlff_qe-cp-traj](deepmd/README.md) | Constructing Machine-learned Force Field using ab-initio data, neural networks, and further deployment using molecular dynamics package (LAMMPS).
 LAMMPS            | [lammps/](lammps/README.md)                      | Basic Molecular Dynamics run with LAMMPS for Copper using Lennard-Jones potential or EAM potential.
+LAMMPS+M3GNet     | [lammps/m3gnet](lammps/m3gnet/job.pbs)           | LAMMPS using M3GNet pair potential.
 GROMACS           | [gromacs/cpu-double](gromacs/cpu-double)         | Basic Molecular Dynamics run with GROMACS for multiple computational setups: CPU single and double-precision, and GPU single precision.
 NWChem            | [nwchem/](nwchem/job.pbs)                        | Basic Total Energy DFT calculation with NWChem for a water molecule.
 CP2K              | [cp2k/](cp2k/job.pbs)                            | Basic Total Energy DFT calculation with NWChem for Si.
@@ -44,7 +45,7 @@ Sources are batch job scripts and can be cloned as below:
 
 > [!NOTE]
 > We use `git-lfs` to store some data (binary files, non-version-controllable sources). Please be sure to
-> install `git-lfs` [[3](#links)] in order to get access to these data files.
+> install `git-lfs` [^3] in order to get access to these data files.
 
 ```bash
 git clone git@github.com:exabyte-io/cli-job-examples.git
@@ -60,38 +61,41 @@ git clone https://github.com/exabyte-io/cli-job-examples.git
 
 ### 2.1. Folder Structure.
 
-The folder structure (circa 2024-01) is as follows:
+The folder structure (circa 2024-12) is as follows:
 
 ```bash
 .
 ├── cp2k
 ├── deepmd
 │    └── train_mlff_qe-cp-traj
-│        ├── step_01_generate_dft_data -> ../../espresso/cp.x/cp-wf_h2o
-│        ├── step_02_preprocess_dft_data
-│        │    ├── input
-│        │    ├── output
-│        │    └── output-reference/**
-│        ├── step_03_train_mlff
-│        │    ├── input
-│        │    ├── output
-│        │    └── output-reference
-│        └── step_04_run_mlff_md
-│            ├── input
-│            ├── output
-│            └── output-reference
+│         ├── step_01_generate_dft_data -> ../../espresso/cp.x/cp-wf_h2o
+│         ├── step_02_preprocess_dft_data
+│         │    ├── input
+│         │    ├── output
+│         │    └── output-reference/**
+│         ├── step_03_train_mlff
+│         │    ├── input
+│         │    ├── output
+│         │    └── output-reference
+│         └── step_04_run_mlff_md
+│              ├── input
+│              ├── output
+│              └── output-reference
 ├── espresso
 │    ├── cp.x
 │    │    └── cp-wf_h2o
-│    │        ├── input
-│    │        ├── output
-│    │        └── output-reference
+│    │         ├── input
+│    │         ├── output
+│    │         └── output-reference
+│    ├── gpu
+│    ├── simple.x
 │    └── pw.x
 ├── gromacs
 │    ├── cpu-double
 │    ├── cpu-single
 │    └── gpu-single
 ├── lammps
+│    └── m3gnet
 ├── nwchem
 ├── sisso
 │    ├── classification
@@ -114,11 +118,11 @@ be submitted from the root folder of the use case.
 
 This repository is an [open-source](LICENSE.md) work-in-progress and we welcome contributions. We suggest forking this
 repository and introducing the adjustments there, the changes in the fork can further be considered for merging into
-this repository as it is commonly done on Github [[4](#links)].
+this repository as it is commonly done on Github [^4].
 
 ## Links
 
-1. [Mat3ra.com Documentation](https://docs.mat3ra.com)
-2. [Command-line Jobs in the Mat3ra.com](https://docs.mat3ra.com/jobs-cli/overview/)
-3. [Git Large File Storage](https://git-lfs.github.com/)
-4. [GitHub Standard Fork & Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962)
+[^1]: [Mat3ra.com Documentation](https://docs.mat3ra.com)
+[^2]: [Command-line Jobs in the Mat3ra.com](https://docs.mat3ra.com/jobs-cli/overview/)
+[^3]: [Git Large File Storage](https://git-lfs.github.com/)
+[^4]: [GitHub Standard Fork & Pull Request Workflow](https://gist.github.com/Chaser324/ce0505fbed06b947d962)

lammps/README.md

@@ -1,7 +1,17 @@
 # LAMMPS
 
-LAMMPS [1] is a classical molecular dynamics simulation code focusing on materials modeling. It was designed to run efficiently on parallel computers and to be easy to extend and modify. Originally developed at Sandia National Laboratories, a US Department of Energy facility, LAMMPS now includes contributions from many research groups and individuals from many institutions. Most of the funding for LAMMPS has come from the US Department of Energy (DOE). LAMMPS is open-source software distributed under the terms of the GNU Public License Version 2 (GPLv2).
+LAMMPS [^1] is a classical molecular dynamics simulation code focusing on
+materials modeling. It was designed to run efficiently on parallel computers and
+to be easy to extend and modify. Originally developed at Sandia National
+Laboratories, a US Department of Energy facility, LAMMPS now includes
+contributions from many research groups and individuals from many institutions.
+Most of the funding for LAMMPS has come from the US Department of Energy (DOE).
+LAMMPS is open-source software distributed under the terms of the GNU Public
+License Version 2 (GPLv2).
+
+# LAMMPS+M3GNet
+The example under the [m3gnet](./m3gnet) directory uses M3GNet pair potential.
 
 
 ## Links
-[1] - https://docs.lammps.org/Manual.html
+[^1]: https://docs.lammps.org/Manual.html

lammps/m3gnet/job.pbs

@@ -0,0 +1,48 @@
+#!/bin/bash
+# ---------------------------------------------------------------- #
+#                                                                  #
+#  Example job submission script for Mat3ra.com platform           #
+#                                                                  #
+#  Shows resource manager directives for:                          #
+#                                                                  #
+#    1. the name of the job                (-N)                    #
+#    2. the number of nodes to be used     (-l nodes=)             #
+#    3. the number of processors per node  (-l ppn=)               #
+#    4. the walltime in dd:hh:mm:ss format (-l walltime=)          #
+#    5. queue                              (-q) D, OR, OF, SR, SF  #
+#    6. merging standard output and error  (-j oe)                 #
+#    7. email about job abort, begin, end  (-m abe)                #
+#    8. email address to use               (-M)                    #
+#                                                                  #
+#  For more info visit https://docs.mat3ra.com/jobs-cli/overview/  #
+# ---------------------------------------------------------------- #
+
+#PBS -N m3gnet
+#PBS -j oe
+#PBS -l nodes=1
+#PBS -l ppn=8
+#PBS -l walltime=00:01:00:00
+#PBS -q GOF
+##PBS -m abe
+##PBS -M info@exabyte.io
+#
+## Uncomment the line below and put a desired project name, e.g.:
+## "seminar-default" or "john-project"
+## NOTE: this is required when using organizational accounts.
+## more at https://docs.mat3ra.com/jobs-cli/batch-scripts/directives/.
+## The job will be charged to the corresponding project.
+## When commented out, the default project for the user is assumed.
+##PBS -A <PROJECT_NAME_IN_ACCOUNTING_SYSTEM>
+
+# load module
+module load nanolabo/3.0
+export OMP_NUM_THREADS=8
+
+# go to the job working directory
+cd $PBS_O_WORKDIR
+
+# Uncomment to clean up the output directory
+# if [ -d output ]; then rm -rf output; fi
+mkdir -p output
+
+lammps_m3gnet < lammps.lmp | tee output.log

lammps/m3gnet/lammps.dat

@@ -0,0 +1,76 @@
+# This file is created by Advance/NanoLabo.
+# Force-Field: M3GNet
+
+      26  atoms
+
+       3  atom types
+
+ 0.00000000e+00  5.62400207e+00  xlo xhi
+ 0.00000000e+00  4.87052866e+00  ylo yhi
+ 0.00000000e+00  4.18714052e+01  zlo zhi
+-2.81200103e+00  0.00000000e+00  0.00000000e+00  xy xz yz
+
+ Atoms
+
+       1        1  1.406001e+00  8.117550e-01  2.667568e+01
+       2        1  4.218002e+00  8.117550e-01  2.667568e+01
+       3        1  0.000000e+00  3.247019e+00  2.667568e+01
+       4        1  2.812001e+00  3.247019e+00  2.667568e+01
+       5        1  0.000000e+00  1.623510e+00  2.437969e+01
+       6        1  2.812001e+00  1.623510e+00  2.437969e+01
+       7        1 -1.406001e+00  4.058774e+00  2.437969e+01
+       8        1  1.406001e+00  4.058774e+00  2.437969e+01
+       9        1  0.000000e+00  0.000000e+00  2.208370e+01
+      10        1  4.218001e+00  2.435264e+00  2.208370e+01
+      11        1  1.406001e+00  2.435264e+00  2.208370e+01
+      12        1  2.812001e+00  0.000000e+00  2.208370e+01
+      13        1  1.406001e+00  8.117550e-01  1.978771e+01  # 0 0 0
+      14        1  4.218002e+00  8.117550e-01  1.978771e+01  # 0 0 0
+      15        1  0.000000e+00  3.247019e+00  1.978771e+01  # 0 0 0
+      16        1  2.812001e+00  3.247019e+00  1.978771e+01  # 0 0 0
+      17        1  0.000000e+00  1.623510e+00  1.749172e+01  # 0 0 0
+      18        1  2.812001e+00  1.623510e+00  1.749172e+01  # 0 0 0
+      19        1 -1.406001e+00  4.058774e+00  1.749172e+01  # 0 0 0
+      20        1  1.406001e+00  4.058774e+00  1.749172e+01  # 0 0 0
+      21        1  0.000000e+00  0.000000e+00  1.519573e+01  # 0 0 0
+      22        1  4.218001e+00  2.435264e+00  1.519573e+01  # 0 0 0
+      23        1  1.406001e+00  2.435264e+00  1.519573e+01  # 0 0 0
+      24        1  2.812001e+00  0.000000e+00  1.519573e+01  # 0 0 0
+      25        2  1.406001e+00  8.117550e-01  2.853568e+01
+      26        3  1.406001e+00  8.117550e-01  2.950467e+01
+
+ Velocities
+
+       1  0.000000e+00  0.000000e+00  0.000000e+00
+       2  0.000000e+00  0.000000e+00  0.000000e+00
+       3  0.000000e+00  0.000000e+00  0.000000e+00
+       4  0.000000e+00  0.000000e+00  0.000000e+00
+       5  0.000000e+00  0.000000e+00  0.000000e+00
+       6  0.000000e+00  0.000000e+00  0.000000e+00
+       7  0.000000e+00  0.000000e+00  0.000000e+00
+       8  0.000000e+00  0.000000e+00  0.000000e+00
+       9  0.000000e+00  0.000000e+00  0.000000e+00
+      10  0.000000e+00  0.000000e+00  0.000000e+00
+      11  0.000000e+00  0.000000e+00  0.000000e+00
+      12  0.000000e+00  0.000000e+00  0.000000e+00
+      13  0.000000e+00  0.000000e+00  0.000000e+00
+      14  0.000000e+00  0.000000e+00  0.000000e+00
+      15  0.000000e+00  0.000000e+00  0.000000e+00
+      16  0.000000e+00  0.000000e+00  0.000000e+00
+      17  0.000000e+00  0.000000e+00  0.000000e+00
+      18  0.000000e+00  0.000000e+00  0.000000e+00
+      19  0.000000e+00  0.000000e+00  0.000000e+00
+      20  0.000000e+00  0.000000e+00  0.000000e+00
+      21  0.000000e+00  0.000000e+00  0.000000e+00
+      22  0.000000e+00  0.000000e+00  0.000000e+00
+      23  0.000000e+00  0.000000e+00  0.000000e+00
+      24  0.000000e+00  0.000000e+00  0.000000e+00
+      25  0.000000e+00  0.000000e+00  0.000000e+00
+      26  0.000000e+00  0.000000e+00  0.000000e+00
+
+ Masses
+
+       1  1.950780e+02 # Pt
+       2  1.599940e+01 # O
+       3  1.007940e+00 # H
+

lammps/m3gnet/lammps.lmp

@@ -0,0 +1,29 @@
+#
+# Defining the system
+#
+units         metal
+boundary      p p p
+atom_style    atomic
+pair_style    m3gnet/d3/gpu /export/compute/software/applications/NanoLabo/NanoLabo-3.0/bin/m3gnet
+read_data     lammps.dat
+pair_coeff    * * M3GNet-MP-2021.2.8-PES Pt O H
+
+group         works id 1:12 25:26
+group         atoms000 id 13:24
+velocity      atoms000 set 0.0 0.0 0.0
+fix           freeze000 atoms000 setforce 0.0 0.0 0.0
+
+#
+# Setting for output
+#
+dump          Dump all custom 10 output/lammps.dmp.* id type x y z ix iy iz vx vy vz
+thermo_style  custom step time cpu pe ke etotal enthalpy temp press vol density cella cellb cellc cellalpha cellbeta cellgamma
+thermo        5
+
+#
+# Setting to run MD or minimization
+#
+## >>> SCHEME-1
+minimize      1.0e-10 1.0e-8 10000 100000
+## <<<
+