883 lines
34 KiB
Groff
883 lines
34 KiB
Groff
LAMMPS (8 Feb 2023)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style bond
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boundary f p p
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region box block -5.000000000000001 5.000000000000001 -5 5 -5 5
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create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1
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Created orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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pair_style zero 5.0
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pair_coeff * *
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mass * 1.0
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bond_style zero
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bond_coeff * 1.0
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create_atoms 1 single -4.0 0.0 0.0
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Created 1 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.000 seconds
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create_atoms 1 single 4.0 0.0 0.0
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Created 1 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.000 seconds
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create_atoms 1 single -5.0 0.0 0.0
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Created 1 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.000 seconds
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create_atoms 1 single 5.0 0.0 0.0
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Created 1 atoms
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using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5)
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create_atoms CPU = 0.000 seconds
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create_bonds single/bond 1 3 1
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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create_bonds single/bond 1 4 2
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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group move id 1:2
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2 atoms in group move
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write_restart walltest.restart
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System init for write_restart ...
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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binsize = 3.5, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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variable name string wall-harmonic
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.001 seconds
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# log ${name}.log
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compute ea move pe/atom
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compute pe move reduce sum c_ea
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special_bonds lj/coul 1.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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1 = max # of 1-2 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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thermo_style custom step temp press ke pe etotal c_pe
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thermo 1
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thermo_modify format float %14.10g
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fix 0 move nve
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# dump 1 all custom 1 ${name}.dump id x fx
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# dump_modify 1 format float %20.15g
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fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0
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fix_modify 1 energy yes
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run 5 post no
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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binsize = 3.5, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/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) = 4.429 | 4.429 | 4.429 Mbytes
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Step Temp Press KinEng PotEng TotEng c_pe
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0 0 0 0 1800 1800 0
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1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0
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2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0
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3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
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4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
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5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
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Loop time of 7.6828e-05 on 1 procs for 5 steps with 4 atoms
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variable name string lepton-harmonic
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.000 seconds
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# log ${name}.log
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compute ea move pe/atom
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compute pe move reduce sum c_ea
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special_bonds lj/coul 1.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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1 = max # of 1-2 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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thermo_style custom step temp press ke pe etotal c_pe
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thermo 1
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thermo_modify format float %14.10g
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fix 0 move nve
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# dump 1 all custom 1 ${name}.dump id x fx
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# dump_modify 1 format float %20.15g
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fix 1 move wall/lepton xlo -5.0 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 4.0
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fix_modify 1 energy yes
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run 5 post no
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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binsize = 3.5, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/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) = 4.429 | 4.429 | 4.429 Mbytes
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Step Temp Press KinEng PotEng TotEng c_pe
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0 0 0 0 1800 1800 0
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1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0
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2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0
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3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0
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4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0
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5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0
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Loop time of 0.00134915 on 1 procs for 5 steps with 4 atoms
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variable name string bond-harmonic
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.000 seconds
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# log ${name}.log
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compute ea move pe/atom
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compute pe move reduce sum c_ea
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special_bonds lj/coul 1.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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1 = max # of 1-2 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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thermo_style custom step temp press ke pe etotal c_pe
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thermo 1
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thermo_modify format float %14.10g
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fix 0 move nve
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# dump 1 all custom 1 ${name}.dump id x fx
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# dump_modify 1 format float %20.15g
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bond_style harmonic
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bond_coeff 1 100 4.0
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run 5 post no
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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ghost atom cutoff = 7
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binsize = 3.5, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723)
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Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
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Step Temp Press KinEng PotEng TotEng c_pe
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0 0 27427.366 0 1800 1800 900
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1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527
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2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524
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3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
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4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
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5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417
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Loop time of 4.6572e-05 on 1 procs for 5 steps with 4 atoms
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variable name string pair-harmonic
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.000 seconds
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# log ${name}.log
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compute ea move pe/atom
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compute pe move reduce sum c_ea
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special_bonds lj/coul 1.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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1 = max # of 1-2 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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thermo_style custom step temp press ke pe etotal c_pe
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thermo 1
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thermo_modify format float %14.10g
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fix 0 move nve
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# dump 1 all custom 1 ${name}.dump id x fx
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# dump_modify 1 format float %20.15g
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pair_style harmonic/cut
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pair_coeff 1 1 100 4.0
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run 5 post no
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6
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ghost atom cutoff = 6
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binsize = 3, bins = 4 4 4
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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/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) = 4.43 | 4.43 | 4.43 Mbytes
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Step Temp Press KinEng PotEng TotEng c_pe
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0 0 27427.366 0 1800 1800 900
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1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527
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2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524
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3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952
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4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758
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5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593
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Loop time of 8.4058e-05 on 1 procs for 5 steps with 4 atoms
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variable eps index 0.02
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variable sig index 2.0
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variable name string wall-lj126
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.000 seconds
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# log ${name}.log
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compute ea move pe/atom
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compute pe move reduce sum c_ea
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special_bonds lj/coul 1.0 1.0 1.0
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 1 1 1
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special bond factors coul: 1 1 1
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1 = max # of 1-2 neighbors
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3 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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thermo_style custom step temp press ke pe etotal c_pe
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thermo 1
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thermo_modify format float %14.10g
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fix 0 move nve
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# dump 1 all custom 1 ${name}.dump id x fx
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# dump_modify 1 format float %20.15g
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fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0
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fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0
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fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0
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fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0
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fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 4.0
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fix_modify 1 energy yes
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run 5 post no
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 7
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|
ghost atom cutoff = 7
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binsize = 3.5, bins = 3 3 3
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|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
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|
(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/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) = 4.429 | 4.429 | 4.429 Mbytes
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Step Temp Press KinEng PotEng TotEng c_pe
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0 0 0 0 645.1224609 645.1224609 0
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1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0
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2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0
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3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0
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4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
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5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
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WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
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Loop time of 4.3942e-05 on 1 procs for 5 steps with 4 atoms
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variable name string lepton-lj126
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include wall.inc
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clear
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using 1 OpenMP thread(s) per MPI task
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read_restart walltest.restart
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Reading restart file ...
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restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
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restoring atom style bond from restart
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orthogonal box = (-5 -5 -5) to (5 5 5)
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1 by 1 by 1 MPI processor grid
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restoring pair style zero from restart
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restoring bond style zero from restart
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|
4 atoms
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2 bonds
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
fix 1 move wall/lepton xlo -5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0 xhi 5.0 "4.0*epsilon*((sigma/r)^12 - (sigma/r)^6);epsilon=v_eps;sigma=v_sig" 4.0
|
|
fix_modify 1 energy yes
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 7
|
|
ghost atom cutoff = 7
|
|
binsize = 3.5, bins = 3 3 3
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 0 0 645.1224609 645.1224609 0
|
|
1 178153.8707 72825.53278 1593.128544 0.2259591031 1593.354503 0
|
|
2 178262.3593 72869.88065 1594.098696 -0.02237405364 1594.076322 0
|
|
3 178259.9436 72868.89314 1594.077094 -0.003385746252 1594.073708 0
|
|
4 178259.4975 72868.71081 1594.073105 0 1594.073105 0
|
|
5 178259.4975 72868.71081 1594.073105 0 1594.073105 0
|
|
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
|
|
Loop time of 0.00298781 on 1 procs for 5 steps with 4 atoms
|
|
|
|
|
|
variable name string pair-lj126
|
|
include wall.inc
|
|
|
|
clear
|
|
using 1 OpenMP thread(s) per MPI task
|
|
read_restart walltest.restart
|
|
Reading restart file ...
|
|
restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
|
|
restoring atom style bond from restart
|
|
orthogonal box = (-5 -5 -5) to (5 5 5)
|
|
1 by 1 by 1 MPI processor grid
|
|
restoring pair style zero from restart
|
|
restoring bond style zero from restart
|
|
4 atoms
|
|
2 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
1 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
pair_style lj/cut 4.0
|
|
pair_coeff 1 1 ${eps} ${sig}
|
|
pair_coeff 1 1 0.02 ${sig}
|
|
pair_coeff 1 1 0.02 2.0
|
|
pair_modify shift yes
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 6
|
|
ghost atom cutoff = 6
|
|
binsize = 3, bins = 4 4 4
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair lj/cut, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 178343.7047 0 645.1224609 645.1224609 322.5612305
|
|
1 178153.8707 72925.96146 1593.128544 0.2259591031 1593.354503 0.1129795516
|
|
2 178262.3593 72867.28485 1594.098696 -0.02237405364 1594.076322 -0.01118702682
|
|
3 178260.8147 72867.80305 1594.084884 -0.007499601847 1594.077384 -0.005806728722
|
|
4 176007.6835 72778.53677 1573.936415 2.772305717 1576.708721 2.772305717
|
|
5 1.132219912e+27 4.628275436e+26 1.012479748e+25 3.761972158e+12 1.012479748e+25 3.761972158e+12
|
|
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936)
|
|
Loop time of 4.4455e-05 on 1 procs for 5 steps with 4 atoms
|
|
|
|
|
|
variable d0 index 20.0
|
|
variable al index 2.0
|
|
variable r0 index 1.2
|
|
|
|
variable name string wall-morse
|
|
include wall.inc
|
|
|
|
clear
|
|
using 1 OpenMP thread(s) per MPI task
|
|
read_restart walltest.restart
|
|
Reading restart file ...
|
|
restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
|
|
restoring atom style bond from restart
|
|
orthogonal box = (-5 -5 -5) to (5 5 5)
|
|
1 by 1 by 1 MPI processor grid
|
|
restoring pair style zero from restart
|
|
restoring bond style zero from restart
|
|
4 atoms
|
|
2 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
1 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 2.0 ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 ${al} ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 ${r0} 4.0
|
|
fix 1 move wall/morse xlo -5.0 20.0 2.0 1.2 4.0 xhi 5.0 20.0 2.0 1.2 4.0
|
|
fix_modify 1 energy yes
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 7
|
|
ghost atom cutoff = 7
|
|
binsize = 3.5, bins = 3 3 3
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 0 0 -30.02905654 -30.02905654 0
|
|
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
|
|
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
|
|
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
|
|
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
|
|
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
|
|
Loop time of 7.6505e-05 on 1 procs for 5 steps with 4 atoms
|
|
|
|
|
|
variable name string lepton-morse
|
|
include wall.inc
|
|
|
|
clear
|
|
using 1 OpenMP thread(s) per MPI task
|
|
read_restart walltest.restart
|
|
Reading restart file ...
|
|
restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
|
|
restoring atom style bond from restart
|
|
orthogonal box = (-5 -5 -5) to (5 5 5)
|
|
1 by 1 by 1 MPI processor grid
|
|
restoring pair style zero from restart
|
|
restoring bond style zero from restart
|
|
4 atoms
|
|
2 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
1 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
fix 1 move wall/lepton xlo -5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0 xhi 5.0 "d0*(-1.0 + (1.0 - ralpha) * (1.0 - ralpha));ralpha=exp(-alpha*(r-r0));d0=v_d0;alpha=v_al;r0=v_r0" 4.0
|
|
fix_modify 1 energy yes
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 7
|
|
ghost atom cutoff = 7
|
|
binsize = 3.5, bins = 3 3 3
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 0 0 -30.02905654 -30.02905654 0
|
|
1 146.0893547 59.71823711 1.30639385 -31.40065042 -30.09425657 0
|
|
2 485.8091411 198.5884977 4.34431431 -34.55987817 -30.21556386 0
|
|
3 822.0828974 336.0500941 7.351418888 -37.63613582 -30.28471693 0
|
|
4 1018.806679 416.4666136 9.110607565 -39.39265114 -30.28204357 0
|
|
5 1050.331347 429.3532307 9.392514704 -39.63687095 -30.24435625 0
|
|
Loop time of 0.00266357 on 1 procs for 5 steps with 4 atoms
|
|
|
|
|
|
variable name string bond-morse
|
|
include wall.inc
|
|
|
|
clear
|
|
using 1 OpenMP thread(s) per MPI task
|
|
read_restart walltest.restart
|
|
Reading restart file ...
|
|
restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
|
|
restoring atom style bond from restart
|
|
orthogonal box = (-5 -5 -5) to (5 5 5)
|
|
1 by 1 by 1 MPI processor grid
|
|
restoring pair style zero from restart
|
|
restoring bond style zero from restart
|
|
4 atoms
|
|
2 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
1 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
bond_style morse
|
|
bond_coeff 1 ${d0} ${al} ${r0}
|
|
bond_coeff 1 20.0 ${al} ${r0}
|
|
bond_coeff 1 20.0 2.0 ${r0}
|
|
bond_coeff 1 20.0 2.0 1.2
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 7
|
|
ghost atom cutoff = 7
|
|
binsize = 3.5, bins = 3 3 3
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair zero, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.429 | 4.429 | 4.429 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 2683.187147 0 9.675661328 9.675661328 4.837830664
|
|
1 146.0893547 2514.939772 1.30639385 8.304067455 9.610461305 4.152033728
|
|
2 485.8091411 2063.804037 4.34431431 5.144839701 9.489154012 2.572419851
|
|
3 822.0828974 1456.368913 7.351418888 2.06858205 9.420000938 1.034291025
|
|
4 1018.806679 823.4383177 9.110607565 0.3120667313 9.422674297 0.1560333657
|
|
5 1050.331347 253.0262957 9.392514704 0.06784692056 9.460361624 0.03392346028
|
|
Loop time of 0.000120428 on 1 procs for 5 steps with 4 atoms
|
|
|
|
|
|
variable name string pair-morse
|
|
include wall.inc
|
|
|
|
clear
|
|
using 1 OpenMP thread(s) per MPI task
|
|
read_restart walltest.restart
|
|
Reading restart file ...
|
|
restart file = 8 Feb 2023, LAMMPS = 8 Feb 2023
|
|
restoring atom style bond from restart
|
|
orthogonal box = (-5 -5 -5) to (5 5 5)
|
|
1 by 1 by 1 MPI processor grid
|
|
restoring pair style zero from restart
|
|
restoring bond style zero from restart
|
|
4 atoms
|
|
2 bonds
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0 0 0
|
|
special bond factors coul: 0 0 0
|
|
1 = max # of 1-2 neighbors
|
|
0 = max # of 1-3 neighbors
|
|
0 = max # of 1-4 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
read_restart CPU = 0.000 seconds
|
|
# log ${name}.log
|
|
|
|
compute ea move pe/atom
|
|
compute pe move reduce sum c_ea
|
|
special_bonds lj/coul 1.0 1.0 1.0
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 1 1 1
|
|
special bond factors coul: 1 1 1
|
|
1 = max # of 1-2 neighbors
|
|
3 = max # of special neighbors
|
|
special bonds CPU = 0.000 seconds
|
|
|
|
thermo_style custom step temp press ke pe etotal c_pe
|
|
thermo 1
|
|
thermo_modify format float %14.10g
|
|
|
|
fix 0 move nve
|
|
# dump 1 all custom 1 ${name}.dump id x fx
|
|
# dump_modify 1 format float %20.15g
|
|
|
|
pair_style morse 4.0
|
|
pair_coeff 1 1 ${d0} ${al} ${r0}
|
|
pair_coeff 1 1 20.0 ${al} ${r0}
|
|
pair_coeff 1 1 20.0 2.0 ${r0}
|
|
pair_coeff 1 1 20.0 2.0 1.2
|
|
pair_modify shift yes
|
|
run 5 post no
|
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 6
|
|
ghost atom cutoff = 6
|
|
binsize = 3, bins = 4 4 4
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair morse, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes
|
|
Step Temp Press KinEng PotEng TotEng c_pe
|
|
0 0 2683.187147 0 -30.02905654 -30.02905654 -15.01452827
|
|
1 146.0893547 2514.939772 1.30639385 -31.40065042 -30.09425657 -15.70032521
|
|
2 485.8091411 2063.804037 4.34431431 -34.55987817 -30.21556386 -17.27993908
|
|
3 822.0828974 1456.368913 7.351418888 -37.63613582 -30.28471693 -18.81806791
|
|
4 1018.806679 823.4383177 9.110607565 -39.39265114 -30.28204357 -19.69632557
|
|
5 1050.331347 253.0262957 9.392514704 -39.63687095 -30.24435625 -19.81843547
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Loop time of 3.6356e-05 on 1 procs for 5 steps with 4 atoms
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shell rm -f walltest.restart
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Total wall time: 0:00:00
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