add harmonic/cut to python example folder. small tweaks to docs and examples
This commit is contained in:
Axel Kohlmeyer
235
examples/python/log.18Mar22.pair_python_harmonic.g++.4
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235
examples/python/log.18Mar22.pair_python_harmonic.g++.4
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LAMMPS (17 Feb 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# 3d soft repulsive particles
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units real
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atom_style atomic
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lattice fcc 5.0 origin 0.1 0.1 0.1
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Lattice spacing in x,y,z = 5 5 5
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region box block -5 5 -5 5 -5 5
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create_box 2 box
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Created orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 box
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Created 4000 atoms
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using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
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create_atoms CPU = 0.000 seconds
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set type 1 type/ratio 2 0.5 424662346
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Setting atom values ...
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2000 settings made for type/ratio
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mass * 1.0
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velocity all create 3.0 87287
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pair_style python 9.0
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pair_coeff * * py_pot.Harmonic A B
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.225 | 3.225 | 3.225 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 3 423843.22 0 423878.98 249277.9
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50 79.665061 422928.03 0 423877.66 248995.64
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100 108.5878 422583.81 0 423878.21 250822.76
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150 130.90607 422317.45 0 423877.89 251949.08
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200 120.05458 422447.24 0 423878.33 252105.09
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250 135.76605 422259.47 0 423877.84 252077.41
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Loop time of 4.70112 on 4 procs for 250 steps with 4000 atoms
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write_restart repulsive.restart
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System init for write_restart ...
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.001 seconds
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pair_style python 10.0
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pair_coeff * * py_pot.Harmonic A B
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shell rm -f python.dat
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pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
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Creating table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 9 9 9
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair python, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
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Appending to table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
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Appending to table file python.dat with DATE: 2022-03-18
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.667 | 3.667 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 135.76605 422259.47 0 423877.84 252077.41
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300 119.63404 422452.21 0 423878.28 251958.74
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350 129.35013 422336.12 0 423878 252069.99
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400 123.04377 422411.48 0 423878.19 252024.23
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450 126.01375 422375.98 0 423878.1 252019.19
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500 126.91094 422365.34 0 423878.15 252012.59
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Loop time of 6.20423 on 4 procs for 250 steps with 4000 atoms
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.001 seconds
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pair_style harmonic/cut
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pair_coeff 1 1 0.2 9.0
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pair_coeff 2 2 0.4 9.0
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shell rm -f harmonic.dat
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pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
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Creating table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair harmonic/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
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Appending to table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
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Appending to table file harmonic.dat with DATE: 2022-03-18
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.227 | 3.227 | 3.229 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 135.76605 422259.47 0 423877.84 252077.41
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300 119.63404 422452.21 0 423878.28 251958.74
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350 129.35013 422336.12 0 423878 252069.99
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400 123.04377 422411.48 0 423878.19 252024.23
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450 126.01375 422375.98 0 423878.1 252019.19
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500 126.91094 422365.34 0 423878.15 252012.59
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Loop time of 0.257048 on 4 procs for 250 steps with 4000 atoms
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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read_restart repulsive.restart
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Reading restart file ...
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restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
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restoring atom style atomic from restart
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orthogonal box = (-25 -25 -25) to (25 25 25)
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1 by 2 by 2 MPI processor grid
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pair style python stores no restart info
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4000 atoms
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read_restart CPU = 0.000 seconds
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pair_style table spline 1000
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pair_coeff 1 1 python.dat PYTH_A_A
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Reading pair table potential file python.dat with DATE: 2022-03-18
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pair_coeff 1 2 python.dat PYTH_A_B
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Reading pair table potential file python.dat with DATE: 2022-03-18
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pair_coeff 2 2 python.dat PYTH_B_B
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Reading pair table potential file python.dat with DATE: 2022-03-18
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neighbor 1.0 bin
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neigh_modify every 2 delay 4 check yes
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fix 1 all nve
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thermo 50
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run 250 post no
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generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.257 | 3.257 | 3.257 Mbytes
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Step Temp E_pair E_mol TotEng Press
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250 135.76605 422259.47 0 423877.84 252077.38
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300 119.63401 422452.21 0 423878.28 251958.73
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350 129.35009 422336.11 0 423878 252069.98
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400 123.04383 422411.48 0 423878.19 252024.21
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450 126.01378 422375.98 0 423878.1 252019.16
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500 126.91078 422365.34 0 423878.15 252012.57
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Loop time of 0.497624 on 4 procs for 250 steps with 4000 atoms
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# remove temporary files
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shell rm repulsive.restart harmonic.dat python.dat
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Total wall time: 0:00:11
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