SOF-7806: add LAMMPS+MatterSim example

README.md

@@ -16,6 +16,7 @@ VASP              | [vasp/](vasp/job.pbs)                            | Self-cons
 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.
+LAMMPS+MatterSim  | [lammps/mattersim](lammps/mattersim/job.pbs)     | LAMMPS using MatterSim 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.

lammps/mattersim/job.pbs

@@ -0,0 +1,45 @@
+#!/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 mattersim
+#PBS -j oe
+#PBS -l nodes=1
+#PBS -l ppn=12
+#PBS -l walltime=00:01:00:00
+#PBS -q GOF
+##PBS -m abe
+##PBS -M [email protected]
+#
+## 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>
+
+if [ -d output ]; then rm -rf output; fi
+mkdir output
+
+export OMP_NUM_THREADS=$PBS_NP
+
+export APPTAINERENV_PREPEND_PATH=/export/compute/software/libraries/nvhpc-25.3-cuda-12.8/Linux_x86_64/25.3/cuda/bin
+export APPTAINERENV_LD_LIBRARY_PATH=/export/compute/software/libraries/nvhpc-25.3-cuda-12.8/Linux_x86_64/25.3/cuda/lib64:\${LD_LIBRARY_PATH}
+
+apptainer exec --nv --bind /export,/cluster-001-share /export/compute/software/applications/nanolabo-mattersim.sif lammps_gnnp -i lammps.in

lammps/mattersim/lammps.dat

@@ -0,0 +1,74 @@
+# This file is created by Advance/NanoLabo.
+
+      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/mattersim/lammps.in

@@ -0,0 +1,28 @@
+#
+# Defining the system
+#
+units         metal
+boundary      p p p
+atom_style    atomic
+pair_style    gnnp/d3/gpu
+read_data     lammps.dat
+pair_coeff    * * mattersim MatterSim-v1.0.0-1M 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
+## <<<