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LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package gpu 0
# 3d soft repulsive particles
units real
atom_style atomic
lattice fcc 5.0 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 5 5 5
region box block -5 5 -5 5 -5 5
create_box 2 box
Created orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
create_atoms CPU = 0.000 seconds
set type 1 type/ratio 2 0.5 424662346
Setting atom values ...
2000 settings made for type/ratio
mass * 1.0
velocity all create 3.0 87287
pair_style python 9.0
pair_coeff * * py_pot.Harmonic A B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- GPU package (short-range, long-range and three-body potentials):
@Article{Brown11,
author = {W. M. Brown, P. Wang, S. J. Plimpton, A. N. Tharrington},
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Short Range Forces},
journal = {Comp.~Phys.~Comm.},
year = 2011,
volume = 182,
pages = {898--911}
}
@Article{Brown12,
author = {W. M. Brown, A. Kohlmeyer, S. J. Plimpton, A. N. Tharrington},
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh},
journal = {Comp.~Phys.~Comm.},
year = 2012,
volume = 183,
pages = {449--459}
}
@Article{Brown13,
author = {W. M. Brown, Y. Masako},
title = {Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials},
journal = {Comp.~Phys.~Comm.},
year = 2013,
volume = 184,
pages = {2785--2793}
}
@Article{Trung15,
author = {T. D. Nguyen, S. J. Plimpton},
title = {Accelerating dissipative particle dynamics simulations for soft matter systems},
journal = {Comput.~Mater.~Sci.},
year = 2015,
volume = 100,
pages = {173--180}
}
@Article{Trung17,
author = {T. D. Nguyen},
title = {GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations},
journal = {Comp.~Phys.~Comm.},
year = 2017,
volume = 212,
pages = {113--122}
}
@Article{Nikolskiy19,
author = {V. Nikolskiy, V. Stegailov},
title = {GPU acceleration of four-site water models in LAMMPS},
journal = {Proceeding of the International Conference on Parallel Computing (ParCo 2019), Prague, Czech Republic},
year = 2019
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 423789.56 0 423825.32 249259.3
50 75.889551 422919.46 0 423824.08 248893.24
100 105.20972 422570.47 0 423824.6 250756.6
150 132.08764 422249.71 0 423824.23 251894.29
200 118.14116 422416.43 0 423824.7 252088.96
250 128.40086 422293.71 0 423824.28 252057.16
Loop time of 21.1837 on 1 procs for 250 steps with 4000 atoms
write_restart repulsive.restart
System init for write_restart ...
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package gpu 0
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
Creating table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: full/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.451 | 5.451 | 5.451 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.16
300 119.72871 422397.4 0 423824.6 251985.11
350 124.88375 422335.77 0 423824.42 252051.28
400 121.76143 422373.11 0 423824.53 252006.39
450 125.29847 422330.9 0 423824.49 251997.23
500 126.87408 422312.08 0 423824.45 252053.51
Loop time of 28.5184 on 1 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package gpu 0
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
Creating table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair harmonic/cut, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: full/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.16
300 119.72871 422397.4 0 423824.6 251985.11
350 124.88375 422335.77 0 423824.42 252051.28
400 121.76143 422373.11 0 423824.53 252006.39
450 125.29847 422330.9 0 423824.49 251997.23
500 126.87408 422312.08 0 423824.45 252053.51
Loop time of 1.1146 on 1 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
package gpu 0
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style table spline 1000
pair_coeff 1 1 python.dat PYTH_A_A
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 1 2 python.dat PYTH_A_B
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 2 2 python.dat PYTH_B_B
Reading pair table potential file python.dat with DATE: 2022-03-18
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.14
300 119.72876 422397.4 0 423824.6 251985.09
350 124.88381 422335.77 0 423824.42 252051.26
400 121.76148 422373.11 0 423824.53 252006.37
450 125.29841 422330.9 0 423824.49 251997.2
500 126.87418 422312.08 0 423824.45 252053.48
Loop time of 0.389958 on 1 procs for 250 steps with 4000 atoms
# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat
Total wall time: 0:00:54
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