From 2e5bc2f6b7a379a1996cf7d83f9e028ee7434954 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 23 Feb 2023 01:09:44 -0500 Subject: [PATCH] add test example for validating custom potentials --- examples/wall/in.wall.lepton | 110 ++ examples/wall/in.wall.table | 129 ++ examples/wall/log.23Feb23.wall.lepton.g++.1 | 894 ++++++++++++++ examples/wall/log.23Feb23.wall.lepton.g++.4 | 894 ++++++++++++++ examples/wall/log.23Feb23.wall.table.g++.1 | 1131 +++++++++++++++++ examples/wall/log.23Feb23.wall.table.g++.4 | 1131 +++++++++++++++++ examples/wall/wall.inc | 16 + examples/wall/walltab.dat | 1212 +++++++++++++++++++ tools/tabulate/wall_multi_tabulate.py | 4 +- 9 files changed, 5519 insertions(+), 2 deletions(-) create mode 100644 examples/wall/in.wall.lepton create mode 100644 examples/wall/in.wall.table create mode 100644 examples/wall/log.23Feb23.wall.lepton.g++.1 create mode 100644 examples/wall/log.23Feb23.wall.lepton.g++.4 create mode 100644 examples/wall/log.23Feb23.wall.table.g++.1 create mode 100644 examples/wall/log.23Feb23.wall.table.g++.4 create mode 100644 examples/wall/wall.inc create mode 100644 examples/wall/walltab.dat diff --git a/examples/wall/in.wall.lepton b/examples/wall/in.wall.lepton new file mode 100644 index 0000000000..76d8e71f01 --- /dev/null +++ b/examples/wall/in.wall.lepton @@ -0,0 +1,110 @@ +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +create_atoms 1 single 4.0 0.0 0.0 +create_atoms 1 single -5.0 0.0 0.0 +create_atoms 1 single 5.0 0.0 0.0 +create_bonds single/bond 1 3 1 +create_bonds single/bond 1 4 2 + +group move id 1:2 +write_restart walltest.restart + +variable name string wall-harmonic +include wall.inc + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-harmonic +include wall.inc + +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 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-harmonic +include wall.inc + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no + +variable name string pair-harmonic +include wall.inc + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-lj126 +include wall.inc + +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 + +variable name string pair-lj126 +include wall.inc + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_modify shift yes +run 5 post no + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string lepton-morse +include wall.inc + +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 + +variable name string bond-morse +include wall.inc + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +run 5 post no + +variable name string pair-morse +include wall.inc + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_modify shift yes +run 5 post no + +shell rm -f walltest.restart diff --git a/examples/wall/in.wall.table b/examples/wall/in.wall.table new file mode 100644 index 0000000000..f5b8232ef8 --- /dev/null +++ b/examples/wall/in.wall.table @@ -0,0 +1,129 @@ +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +create_atoms 1 single 4.0 0.0 0.0 +create_atoms 1 single -5.0 0.0 0.0 +create_atoms 1 single 5.0 0.0 0.0 +create_bonds single/bond 1 3 1 +create_bonds single/bond 1 4 2 + +group move id 1:2 +write_restart walltest.restart + +variable name string wall-harmonic +include wall.inc + +fix 1 move wall/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-harmonic +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-harmonic +include wall.inc + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-harmonic +include wall.inc + +bond_style harmonic +bond_coeff 1 100 4.0 +run 5 post no + +variable name string pair-harmonic +include wall.inc + +pair_style harmonic/cut +pair_coeff 1 1 100 4.0 +run 5 post no + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +fix 1 move wall/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-lj126 +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-lj126 +include wall.inc + +fix 1 move wall/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string pair-lj126 +include wall.inc + +pair_style lj/cut 4.0 +pair_coeff 1 1 ${eps} ${sig} +pair_modify shift yes +run 5 post no + +variable d0 index 20.0 +variable al index 2.0 +variable r0 index 1.2 + +variable name string wall-morse +include wall.inc + +fix 1 move wall/morse xlo -5.0 ${d0} ${al} ${r0} 4.0 xhi 5.0 ${d0} ${al} ${r0} 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string table-morse +include wall.inc + +fix 1 move wall/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string spline-morse +include wall.inc + +fix 1 move wall/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +fix_modify 1 energy yes +run 5 post no + +variable name string bond-morse +include wall.inc + +bond_style morse +bond_coeff 1 ${d0} ${al} ${r0} +run 5 post no + +variable name string pair-morse +include wall.inc + +pair_style morse 4.0 +pair_coeff 1 1 ${d0} ${al} ${r0} +pair_modify shift yes +run 5 post no + +shell rm -f walltest.restart diff --git a/examples/wall/log.23Feb23.wall.lepton.g++.1 b/examples/wall/log.23Feb23.wall.lepton.g++.1 new file mode 100644 index 0000000000..91fb3a3a53 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.lepton.g++.1 @@ -0,0 +1,894 @@ +LAMMPS (8 Feb 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +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 +create_bonds single/bond 1 4 2 +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 + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +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 + +variable name string wall-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 = 0.001 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/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 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 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 5.837e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 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 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.00343046 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 harmonic +bond_coeff 1 100 4.0 +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 +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +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 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 6.3996e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 harmonic/cut +pair_coeff 1 1 100 4.0 +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 harmonic/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 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 5.4513e-05 on 1 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 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 5.3398e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 "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 0.0051554 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 5.4716e-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 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 + 1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0 + 2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0 + 3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0 + 4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0 + 5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0 +Loop time of 4.8727e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string lepton-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 0.00478609 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 3.7914e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 +Loop time of 4.2699e-05 on 1 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.lepton.g++.4 b/examples/wall/log.23Feb23.wall.lepton.g++.4 new file mode 100644 index 0000000000..ba630cc5d8 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.lepton.g++.4 @@ -0,0 +1,894 @@ +LAMMPS (8 Feb 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.001 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +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 +create_bonds single/bond 1 4 2 +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 + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +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 + +variable name string wall-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.000225045 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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 "k*(r-rc)^2;k=100.0" 4.0 xhi 5.0 "k*(r-rc)^2;k=100.0" 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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.00491331 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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 harmonic +bond_coeff 1 100 4.0 +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 +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 0.000214841 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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 harmonic/cut +pair_coeff 1 1 100 4.0 +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 harmonic/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) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 0.000212697 on 4 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 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) = 4.32 | 4.379 | 4.559 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 0.000207412 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 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 0.00958101 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.38 | 4.56 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 0.00016574 on 4 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 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0 + 2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0 + 3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0 + 4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0 + 5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0 +Loop time of 0.000162994 on 4 procs for 5 steps with 4 atoms + + +variable name string lepton-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 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 0.00780516 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 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 0.000141974 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.38 | 4.56 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 +Loop time of 0.000196232 on 4 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.table.g++.1 b/examples/wall/log.23Feb23.wall.table.g++.1 new file mode 100644 index 0000000000..c03bc61f23 --- /dev/null +++ b/examples/wall/log.23Feb23.wall.table.g++.1 @@ -0,0 +1,1131 @@ +LAMMPS (8 Feb 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 1 by 1 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +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 +create_bonds single/bond 1 4 2 +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 + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +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 + +variable name string wall-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 = 0.001 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/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 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 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 7.7442e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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 1800.000356 1800.000356 0 + 1 16146.37291 6600.295604 144.3878119 1652.527723 1796.915535 0 + 2 59294.04011 24238.149 530.232812 1258.437853 1788.670665 0 + 3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0 + 4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0 + 5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0 +Loop time of 7.9176e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 7.4164e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 harmonic +bond_coeff 1 100 4.0 +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 +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +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 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 7.4638e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 harmonic/cut +pair_coeff 1 1 100 4.0 +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 harmonic/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 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 7.6049e-05 on 1 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 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 6.7788e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +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 0 645.2141852 645.2141852 0 + 1 178212.5398 72849.51549 1593.653189 0.2256644171 1593.878854 0 + 2 178320.9331 72893.82438 1594.622489 -0.02236253394 1594.600126 0 + 3 178318.518 72892.83712 1594.600891 -0.0033818408 1594.597509 0 + 4 178318.0722 72892.6549 1594.596905 0 1594.596905 0 + 5 178318.0722 72892.6549 1594.596905 0 1594.596905 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 7.0625e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +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 0 645.3361317 645.3361317 0 + 1 161871.9611 66169.83266 1447.528705 0.3353251002 1447.86403 0 + 2 162015.342 66228.44376 1448.810879 -0.02581160308 1448.785068 0 + 3 162012.784 66227.39811 1448.788005 -0.004635008226 1448.78337 0 + 4 162012.2554 66227.18201 1448.783278 0 1448.783278 0 + 5 162012.2554 66227.18201 1448.783278 0 1448.783278 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 7.8628e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 5.1616e-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 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 + 1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0 + 2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0 + 3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0 + 4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0 + 5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0 +Loop time of 3.8086e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string table-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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 -30.0282104 -30.0282104 0 + 1 146.0967469 59.72125889 1.306459954 -31.40033773 -30.09387777 0 + 2 485.8417772 198.6018386 4.344606156 -34.55851819 -30.21391203 0 + 3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0 + 4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0 + 5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0 +Loop time of 3.7571e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string spline-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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 -30.02905657 -30.02905657 0 + 1 146.0893531 59.71823647 1.306393836 -31.40065068 -30.09425684 0 + 2 485.809133 198.5884944 4.344314238 -34.55987846 -30.21556422 0 + 3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0 + 4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0 + 5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0 +Loop time of 4.1369e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 = 0.001 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 5.8418e-05 on 1 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 +Loop time of 6.2323e-05 on 1 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/log.23Feb23.wall.table.g++.4 b/examples/wall/log.23Feb23.wall.table.g++.4 new file mode 100644 index 0000000000..d8329f739e --- /dev/null +++ b/examples/wall/log.23Feb23.wall.table.g++.4 @@ -0,0 +1,1131 @@ +LAMMPS (8 Feb 2023) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +units real +atom_style bond +boundary f p p +region box block -5.000000000000001 5.000000000000001 -5 5 -5 5 +create_box 1 box bond/types 1 extra/bond/per/atom 1 extra/special/per/atom 1 +Created orthogonal box = (-5 -5 -5) to (5 5 5) + 1 by 2 by 2 MPI processor grid + +pair_style zero 5.0 +pair_coeff * * +mass * 1.0 +bond_style zero +bond_coeff * 1.0 + +create_atoms 1 single -4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 4.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single -5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_atoms 1 single 5.0 0.0 0.0 +Created 1 atoms + using lattice units in orthogonal box = (-5 -5 -5) to (5 5 5) + create_atoms CPU = 0.000 seconds +create_bonds single/bond 1 3 1 +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 +create_bonds single/bond 1 4 2 +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 + +group move id 1:2 +2 atoms in group move +write_restart walltest.restart +System init for write_restart ... +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 + +variable name string wall-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/harmonic xlo -5.0 100 0.0 4.0 xhi 5.0 100 1.0 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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.000226889 on 4 procs for 5 steps with 4 atoms + + +variable name string table-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table linear 1000 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800.000356 1800.000356 0 + 1 16146.37291 6600.295604 144.3878119 1652.527723 1796.915535 0 + 2 59294.04011 24238.149 530.232812 1258.437853 1788.670665 0 + 3 115302.7492 47133.32419 1031.086781 746.8824148 1777.969196 0 + 4 165817.4572 67782.66799 1482.811029 285.5061521 1768.317181 0 + 5 194283.6024 79419.02582 1737.367544 25.51090543 1762.878449 0 +Loop time of 0.000222504 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table spline 200 xlo -5.0 walltab.dat HARMONIC 4.0 xhi 5.0 walltab.dat HARMONIC 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 1800 1800 0 + 1 16146.37291 6600.295604 144.3878119 1652.527054 1796.914866 0 + 2 59294.04011 24238.149 530.232812 1258.437705 1788.670517 0 + 3 115302.7492 47133.32419 1031.086781 746.8819904 1777.968771 0 + 4 165817.4572 67782.66799 1482.811029 285.5057515 1768.31678 0 + 5 194283.6024 79419.02582 1737.367544 25.51012833 1762.877672 0 +Loop time of 0.000211631 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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 harmonic +bond_coeff 1 100 4.0 +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 +WARNING: Communication cutoff 7 is shorter than a bond length based estimate of 8. This may lead to errors. (src/comm.cpp:723) +Per MPI rank memory allocation (min/avg/max) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 194283.6024 91313.53086 1737.367544 25.51012833 1762.877672 12.75506417 +Loop time of 0.00017705 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-harmonic +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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 harmonic/cut +pair_coeff 1 1 100 4.0 +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 harmonic/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) = 4.32 | 4.38 | 4.56 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 27427.366 0 1800 1800 900 + 1 16146.37291 36178.74173 144.3878119 1652.527054 1796.914866 826.263527 + 2 59294.04011 58444.6962 530.232812 1258.437705 1788.670517 629.2188524 + 3 115302.7492 83661.44348 1031.086781 746.8819904 1777.968771 373.4409952 + 4 165817.4572 98424.89283 1482.811029 285.5057515 1768.31678 142.7528758 + 5 170540.4005 97560.47089 1525.045619 190.8165235 1715.862142 178.0614593 +Loop time of 0.000186388 on 4 procs for 5 steps with 4 atoms + + +variable eps index 0.02 +variable sig index 2.0 +variable name string wall-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/lj126 xlo -5.0 ${eps} ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 ${sig} 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 ${eps} ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 ${sig} 4.0 +fix 1 move wall/lj126 xlo -5.0 0.02 2.0 4.0 xhi 5.0 0.02 2.0 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) = 4.32 | 4.379 | 4.559 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 0.000258277 on 4 procs for 5 steps with 4 atoms + + +variable name string table-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table linear 1000 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.2141852 645.2141852 0 + 1 178212.5398 72849.51549 1593.653189 0.2256644171 1593.878854 0 + 2 178320.9331 72893.82438 1594.622489 -0.02236253394 1594.600126 0 + 3 178318.518 72892.83712 1594.600891 -0.0033818408 1594.597509 0 + 4 178318.0722 72892.6549 1594.596905 0 1594.596905 0 + 5 178318.0722 72892.6549 1594.596905 0 1594.596905 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000230164 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table spline 200 xlo -5.0 walltab.dat LJ126 4.0 xhi 5.0 walltab.dat LJ126 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +WARNING: 1 of 400 force values in table are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/fix_wall_table.cpp:244) +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 645.3361317 645.3361317 0 + 1 161871.9611 66169.83266 1447.528705 0.3353251002 1447.86403 0 + 2 162015.342 66228.44376 1448.810879 -0.02581160308 1448.785068 0 + 3 162012.784 66227.39811 1448.788005 -0.004635008226 1448.78337 0 + 4 162012.2554 66227.18201 1448.783278 0 1448.783278 0 + 5 162012.2554 66227.18201 1448.783278 0 1448.783278 0 +WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:936) +Loop time of 0.000182437 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-lj126 +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.38 | 4.56 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 0.000170205 on 4 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 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905654 -30.02905654 0 + 1 144.4114716 59.032354 1.291389498 -31.40065042 -30.10926092 0 + 2 471.9742076 192.9330696 4.220596384 -34.53885647 -30.31826008 0 + 3 784.0772455 320.5141877 7.011556 -37.58109301 -30.56953701 0 + 4 961.8950756 393.2023542 8.601679525 -39.34691775 -30.74523823 0 + 5 996.609681 407.3929504 8.91211246 -39.66353245 -30.75141999 0 +Loop time of 0.000141964 on 4 procs for 5 steps with 4 atoms + + +variable name string table-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table linear 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.0282104 -30.0282104 0 + 1 146.0967469 59.72125889 1.306459954 -31.40033773 -30.09387777 0 + 2 485.8417772 198.6018386 4.344606156 -34.55851819 -30.21391203 0 + 3 822.1558136 336.0799007 7.352070936 -37.63533573 -30.28326479 0 + 4 1018.904947 416.5067832 9.111486314 -39.39200056 -30.28051425 0 + 5 1050.436268 429.3961205 9.393452958 -39.63643565 -30.24298269 0 +Loop time of 0.000146935 on 4 procs for 5 steps with 4 atoms + + +variable name string spline-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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/table spline 1000 xlo -5.0 walltab.dat MORSE 4.0 xhi 5.0 walltab.dat MORSE 4.0 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +Reading fix wall/table table potential file walltab.dat with DATE: 2023-02-23 +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) = 4.32 | 4.379 | 4.559 Mbytes + Step Temp Press KinEng PotEng TotEng c_pe + 0 0 0 0 -30.02905657 -30.02905657 0 + 1 146.0893531 59.71823647 1.306393836 -31.40065068 -30.09425684 0 + 2 485.809133 198.5884944 4.344314238 -34.55987846 -30.21556422 0 + 3 822.0828818 336.0500877 7.351418748 -37.63613601 -30.28471726 0 + 4 1018.80666 416.4666056 9.110607389 -39.39265128 -30.28204389 0 + 5 1050.331328 429.353223 9.392514534 -39.63687099 -30.24435645 0 +Loop time of 0.000143113 on 4 procs for 5 steps with 4 atoms + + +variable name string bond-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.379 | 4.559 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 0.000130547 on 4 procs for 5 steps with 4 atoms + + +variable name string pair-morse +include wall.inc + +clear +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + 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 2 by 2 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 = 0.001 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) = 4.32 | 4.38 | 4.56 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 +Loop time of 0.000136551 on 4 procs for 5 steps with 4 atoms + + +shell rm -f walltest.restart +Total wall time: 0:00:00 diff --git a/examples/wall/wall.inc b/examples/wall/wall.inc new file mode 100644 index 0000000000..1b36f2c38e --- /dev/null +++ b/examples/wall/wall.inc @@ -0,0 +1,16 @@ + +clear +read_restart walltest.restart +# 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 + +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 diff --git a/examples/wall/walltab.dat b/examples/wall/walltab.dat new file mode 100644 index 0000000000..53b2b42700 --- /dev/null +++ b/examples/wall/walltab.dat @@ -0,0 +1,1212 @@ +# DATE: 2023-02-23 UNITS: real +HARMONIC +N 400 FP 199.99999998802 200.000000002102 + + 1 0.01 1592.01 798 + 2 0.02 1584.04 796 + 3 0.03 1576.09 794 + 4 0.04 1568.16 792 + 5 0.05 1560.25 790 + 6 0.06 1552.36 788 + 7 0.07 1544.49 786 + 8 0.08 1536.64 784 + 9 0.09 1528.81 782 + 10 0.1 1521 780 + 11 0.11 1513.21 778 + 12 0.12 1505.44 776 + 13 0.13 1497.69 774 + 14 0.14 1489.96 772 + 15 0.15 1482.25 770 + 16 0.16 1474.56 768 + 17 0.17 1466.89 766 + 18 0.18 1459.24 764 + 19 0.19 1451.61 762 + 20 0.2 1444 760 + 21 0.21 1436.41 758 + 22 0.22 1428.84 756 + 23 0.23 1421.29 754 + 24 0.24 1413.76 752 + 25 0.25 1406.25 750 + 26 0.26 1398.76 748 + 27 0.27 1391.29 746 + 28 0.28 1383.84 744 + 29 0.29 1376.41 742 + 30 0.3 1369 740 + 31 0.31 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-0.325605579013906 + 396 3.96 -0.159912981328916 -0.319184089948422 + 397 3.97 -0.156752721271987 -0.312888738023495 + 398 3.98 -0.153654794309244 -0.306717065428139 + 399 3.99 -0.150617975739817 -0.30066666145589 + 400 4 -0.147641064738004 -0.29473516163338 diff --git a/tools/tabulate/wall_multi_tabulate.py b/tools/tabulate/wall_multi_tabulate.py index b1b4aa6cbf..576889cf75 100755 --- a/tools/tabulate/wall_multi_tabulate.py +++ b/tools/tabulate/wall_multi_tabulate.py @@ -51,9 +51,9 @@ if __name__ == "__main__": sys.argv.append('--filename') sys.argv.append(fname) sys.argv.append('--num-points') - sys.argv.append('100') + sys.argv.append('400') sys.argv.append('--inner') - sys.argv.append('0.04') + sys.argv.append('0.01') sys.argv.append('--outer') sys.argv.append('4.0') wtable = WallTabulate(harmonic_energy, harmonic_force, units='real')