diff --git a/README.md b/README.md index a983946..126ae53 100644 --- a/README.md +++ b/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. diff --git a/lammps/mattersim/job.pbs b/lammps/mattersim/job.pbs new file mode 100644 index 0000000..ca16d88 --- /dev/null +++ b/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 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 + +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 diff --git a/lammps/mattersim/lammps.dat b/lammps/mattersim/lammps.dat new file mode 100644 index 0000000..94aeb41 --- /dev/null +++ b/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 diff --git a/lammps/mattersim/lammps.in b/lammps/mattersim/lammps.in new file mode 100644 index 0000000..a32cd75 --- /dev/null +++ b/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 +## <<<