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add lj example for fix pimd/langevin

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Yifan Li
2023-03-20 14:10:09 -04:00
parent be8c0b9835
commit 7a38f49a21
6 changed files with 1717 additions and 0 deletions
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422
examples/PACKAGES/pimd/lj/data.metalnpt01 Normal file
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LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
39 1 -10.338208372875723 -8.724519590498623 -8.445612139491281 0 -1 1
82 1 -7.5133824622188925 -6.978636164411631 -10.191775661279799 0 0 0
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8 1 -7.188384493977925 -11.000743174865285 -10.566868392413127 0 1 1
49 1 -0.45896030511450936 -8.721648062141405 -7.76988436909876 0 1 0
54 1 4.36019737005205 -9.840722628422576 -9.652200105153977 0 -1 1
114 1 3.904944042667676 -8.560258519206736 -6.227256449483399 -1 0 1
128 1 1.537670815459421 11.367557646509137 -7.44113189883349 0 0 -2
102 1 2.6467980910798623 -6.300231690446356 -10.839747469959917 1 -1 -1
157 1 6.599214138053117 -6.278630725537236 -7.389049268829837 -1 0 1
20 1 8.160418209241914 -11.236890922228888 -9.90427297873004 0 1 0
147 1 10.464052914243185 -5.834517788008704 -9.403782126876184 -1 2 0
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Velocities
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422
examples/PACKAGES/pimd/lj/data.metalnpt02 Normal file
View File

@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
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422
examples/PACKAGES/pimd/lj/data.metalnpt03 Normal file
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@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
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422
examples/PACKAGES/pimd/lj/data.metalnpt04 Normal file
View File

@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
39 1 -10.354249178970125 -8.813051919915168 -8.382969093379817 0 -1 1
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28
examples/PACKAGES/pimd/lj/in.lmp Executable file
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variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
dump dcd all custom 100 ${ibead}.xyz id type xu yu zu vx vy vz ix iy iz fx fy fz
dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

1
examples/PACKAGES/pimd/lj/run.sh Normal file
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@ -0,0 +1 @@
mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen