LAMMPS: Difference between revisions

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LAMMPS (view source)

Revision as of 19:53, 25 March 2022

750 bytes removed ,  2 years ago
update sample jobs to StdEnv/2020
m (add categories Software and BiomolecularSimulation)
(update sample jobs to StdEnv/2020)
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The input file below can be used with either of the example job scripts.
The input file below can be used with either of the example job scripts.


<!--T:25-->
<tabs>
<tabs>


<!--T:26-->
<!--T:26-->
<tab name="INPUT">
<tab name="INPUT">
</translate>
{{File
{{File
   |name=lammps.in
   |name=lammps.in
   |lang="txt"
   |lang="txt"
   |contents=
   |contents=
# 3d Lennard-Jones melt
# 3d Lennard-Jones melt / fusion


<!--T:27-->
units          lj
units          lj
atom_style      atomic
atom_style      atomic


<!--T:28-->
lattice        fcc 0.8442
lattice        fcc 0.8442
region          box block 0 15 0 15 0 15
region          box block 0 15 0 15 0 15
Line 118: Line 117:
mass            1 1.0
mass            1 1.0


<!--T:29-->
velocity        all create 1.44 87287 loop geom
velocity        all create 1.44 87287 loop geom


<!--T:30-->
pair_style      lj/cut 2.5
pair_style      lj/cut 2.5
pair_coeff      1 1 1.0 1.0 2.5
pair_coeff      1 1 1.0 1.0 2.5
Line 127: Line 124:
neigh_modify    delay 5 every 1
neigh_modify    delay 5 every 1


<!--T:31-->
fix            1 all nve
fix            1 all nve
thermo          5
thermo          5
Line 133: Line 129:
write_data    config.end_sim
write_data    config.end_sim


<!--T:32-->
# End input / Fin d'input
# End of the Input file.
}}
}}
</tab>
</tab>


<translate>
<!--T:33-->
<!--T:33-->
<tab name="Serial job">
<tab name="Serial job">
</translate>
{{File
{{File
   |name=run_lmp_serial.sh
   |name=run_lmp_serial.sh
Line 145: Line 143:
   |contents=
   |contents=
#!/bin/bash
#!/bin/bash
<!--T:34-->
#SBATCH --ntasks=1
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=2500M     # memory; default unit is megabytes.
#SBATCH --mem-per-cpu=2500M
#SBATCH --time=0-00:30           # time (DD-HH:MM).
#SBATCH --time=0-00:30
 
<!--T:35-->
# Load the module:
 
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module load nixpkgs/16.09  intel/2016.4  openmpi/2.1.1 lammps-omp/20170811
 
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echo "Starting run at: `date`"
 
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lmp_exec=lmp_icc_openmpi
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"


<!--T:39-->
module load StdEnv/2020 intel/2020.1.217 openmpi/4.0.3 lammps-omp/20210929
${lmp_exec} < ${lmp_input} > ${lmp_output}


<!--T:40-->
lmp < lammps.in > lammps_output.txt
echo "Program finished with exit code $? at: `date`"
}}
}}
</tab>
</tab>


<translate>
<!--T:41-->
<!--T:41-->
<tab name="MPI job">
<tab name="MPI job">
</translate>
{{File
{{File
   |name=run_lmp_mpi.sh
   |name=run_lmp_mpi.sh
Line 180: Line 163:
   |contents=
   |contents=
#!/bin/bash
#!/bin/bash
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=2500M
#SBATCH --time=0-00:30


<!--T:42-->
module load StdEnv/2020 intel/2020.1.217 openmpi/4.0.3 lammps-omp/20210929
#SBATCH --ntasks=4              # number of MPI processes.
#SBATCH --mem-per-cpu=2500M      # memory; default unit is megabytes.
#SBATCH --time=0-00:30          # time (DD-HH:MM).
 
<!--T:43-->
# Load the module:
 
<!--T:44-->
module load nixpkgs/16.09  intel/2016.4  openmpi/2.1.1 lammps-omp/20170811


<!--T:45-->
srun lmp < lammps.in > lammps_output.txt
echo "Starting run at: `date`"
 
<!--T:46-->
lmp_exec=lmp_icc_openmpi
lmp_input="lammps.in"
lmp_output="lammps_lj_output.txt"
 
<!--T:47-->
srun ${lmp_exec} < ${lmp_input} > ${lmp_output}
 
<!--T:48-->
echo "Program finished with exit code $? at: `date`"
}}
}}
</tab>
</tab>


<!--T:49-->
</tabs>
</tabs>
<translate>


= Performance = <!--T:50-->
= Performance = <!--T:50-->
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