Loading examples/gcmc/data.spce 0 → 100644 +17322 −0 File added.File size exceeds preview limit. View file examples/gcmc/in.widom.spce 0 → 100644 +38 −0 Original line number Diff line number Diff line units real dimension 3 boundary p p p atom_style full pair_style lj/cut/coul/long 10.0 bond_style harmonic angle_style harmonic read_data data.spce molecule h2omol H2O.txt ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### pair_coeff 1 1 0.1502629 3.1169 pair_coeff 1 2 0.0341116368 2.04845 pair_coeff 2 2 0.00774378 0.98 bond_coeff 1 176.864 0.9611 angle_coeff 1 42.1845 109.4712 kspace_style pppm 1.0e-4 fix mywidom all widom 10 20 0 29494 298 mol h2omol fix 2 all nvt temp 298.0 298.0 100.0 neighbor 2.0 bin neigh_modify delay 10 every 2 check yes #run variables timestep 0.5 thermo 10 thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3] run 100 examples/gcmc/log.30Jun20.widom.spce.g++.1 0 → 100644 +133 −0 Original line number Diff line number Diff line LAMMPS (30 Jun 2020) using 1 OpenMP thread(s) per MPI task units real dimension 3 boundary p p p atom_style full pair_style lj/cut/coul/long 10.0 bond_style harmonic angle_style harmonic read_data data.spce orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533) 1 by 1 by 1 MPI processor grid reading atoms ... 8640 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 5760 bonds reading angles ... 2880 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.008 seconds read_data CPU = 0.028 seconds molecule h2omol H2O.txt Read molecule template h2omol: 1 molecules 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### pair_coeff 1 1 0.1502629 3.1169 pair_coeff 1 2 0.0341116368 2.04845 pair_coeff 2 2 0.00774378 0.98 bond_coeff 1 176.864 0.9611 angle_coeff 1 42.1845 109.4712 kspace_style pppm 1.0e-4 fix mywidom all widom 10 20 0 29494 298 mol h2omol fix 2 all nvt temp 298.0 298.0 100.0 neighbor 2.0 bin neigh_modify delay 10 every 2 check yes #run variables timestep 0.5 thermo 10 thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3] run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:330) G vector (1/distance) = 0.2690183 grid = 24 24 24 stencil order = 5 estimated absolute RMS force accuracy = 0.024843102 estimated relative force accuracy = 7.4814263e-05 using double precision FFTW3 3d grid and FFT values/proc = 29791 13824 WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297) 0 atoms in group FixWidom:widom_exclusion_group:mywidom 0 atoms in group FixWidom:rotation_gas_atoms:mywidom WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487) Neighbor list info ... update every 2 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116 10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116 20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116 30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116 40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116 50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116 60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116 70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116 80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116 90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116 100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116 Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23 Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02 Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47 Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09 Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03 Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00 Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15 Other | | 0.003614 | | | 0.00 Nlocal: 8640.00 ave 8640 max 8640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23499.0 ave 23499 max 23499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3273800 Ave neighs/atom = 378.91204 Ave special neighs/atom = 2.0000000 Neighbor list builds = 220 Dangerous builds = 0 Total wall time: 0:02:44 Loading
examples/gcmc/in.widom.spce 0 → 100644 +38 −0 Original line number Diff line number Diff line units real dimension 3 boundary p p p atom_style full pair_style lj/cut/coul/long 10.0 bond_style harmonic angle_style harmonic read_data data.spce molecule h2omol H2O.txt ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### pair_coeff 1 1 0.1502629 3.1169 pair_coeff 1 2 0.0341116368 2.04845 pair_coeff 2 2 0.00774378 0.98 bond_coeff 1 176.864 0.9611 angle_coeff 1 42.1845 109.4712 kspace_style pppm 1.0e-4 fix mywidom all widom 10 20 0 29494 298 mol h2omol fix 2 all nvt temp 298.0 298.0 100.0 neighbor 2.0 bin neigh_modify delay 10 every 2 check yes #run variables timestep 0.5 thermo 10 thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3] run 100
examples/gcmc/log.30Jun20.widom.spce.g++.1 0 → 100644 +133 −0 Original line number Diff line number Diff line LAMMPS (30 Jun 2020) using 1 OpenMP thread(s) per MPI task units real dimension 3 boundary p p p atom_style full pair_style lj/cut/coul/long 10.0 bond_style harmonic angle_style harmonic read_data data.spce orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533) 1 by 1 by 1 MPI processor grid reading atoms ... 8640 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 5760 bonds reading angles ... 2880 angles 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.008 seconds read_data CPU = 0.028 seconds molecule h2omol H2O.txt Read molecule template h2omol: 1 molecules 3 atoms with max type 2 2 bonds with max type 1 1 angles with max type 1 0 dihedrals with max type 0 0 impropers with max type 0 ### Flexible SPC/E Potential Parameters ### ### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ### pair_coeff 1 1 0.1502629 3.1169 pair_coeff 1 2 0.0341116368 2.04845 pair_coeff 2 2 0.00774378 0.98 bond_coeff 1 176.864 0.9611 angle_coeff 1 42.1845 109.4712 kspace_style pppm 1.0e-4 fix mywidom all widom 10 20 0 29494 298 mol h2omol fix 2 all nvt temp 298.0 298.0 100.0 neighbor 2.0 bin neigh_modify delay 10 every 2 check yes #run variables timestep 0.5 thermo 10 thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3] run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:330) G vector (1/distance) = 0.2690183 grid = 24 24 24 stencil order = 5 estimated absolute RMS force accuracy = 0.024843102 estimated relative force accuracy = 7.4814263e-05 using double precision FFTW3 3d grid and FFT values/proc = 29791 13824 WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297) 0 atoms in group FixWidom:widom_exclusion_group:mywidom 0 atoms in group FixWidom:rotation_gas_atoms:mywidom WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487) Neighbor list info ... update every 2 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3] 0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116 10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116 20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116 30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116 40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116 50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116 60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116 70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116 80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116 90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116 100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116 Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23 Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02 Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47 Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09 Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03 Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00 Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15 Other | | 0.003614 | | | 0.00 Nlocal: 8640.00 ave 8640 max 8640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 23499.0 ave 23499 max 23499 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 3273800 Ave neighs/atom = 378.91204 Ave special neighs/atom = 2.0000000 Neighbor list builds = 220 Dangerous builds = 0 Total wall time: 0:02:44
