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update PIMD examples

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This commit is contained in:
Axel Kohlmeyer
2023-01-26 18:48:30 -05:00
parent ba0d24d028
commit 3be1dd0488
4 changed files with 12 additions and 10 deletions
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7
examples/PACKAGES/pimd/para-h2/in.scp
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@ -15,13 +15,14 @@ pair_coeff 1 * pair.table PAIR_H2
timestep 0.001
thermo_style custom step temp pe etotal pzz
thermo ${out_freq}
velocity all create 1.0 1985 rot yes dist gaussian
fix 1 all pimd method nmpimd fmass 1.0 temp 25.0 nhc 4
thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
thermo ${out_freq}
#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2

2
examples/PACKAGES/pimd/para-h2/run.sh
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@ -1 +1 @@
mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log logfile/log.lammps -screen screen/screen
mpirun -np 64 lmp_mpi -partition 8x8 -in in.scp -log log.lammps -screen none

11
examples/PACKAGES/pimd/prot-hairpin/in.scp
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@ -14,18 +14,19 @@ pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data system.data
#read_restart restart/system_${ibead}.rest1
#read_restart system_${ibead}.rest1
special_bonds charmm
fix 1 all pimd method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
thermo 10
thermo_style custom step temp pe etotal
thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3]
thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
timestep 0.08
restart 100 restart/system_${ibead}.rest1 restart/system_${ibead}.rest2
# restart 100 system_${ibead}.rest1 system_${ibead}.rest2
group prot id <= 256
dump 1 prot dcd 100 dcd/prot_${ibead}.dcd
# dump 1 prot dcd 100 prot_${ibead}.dcd
run 2000000
run 200

2
examples/PACKAGES/pimd/prot-hairpin/run.sh
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@ -1 +1 @@
mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log logfile/log.lammps -screen screen/screen
mpirun -np 8 lmp_mpi -partition 8x1 -in in.scp -log log.lammps -screen none