LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # fix gcmc example with fix shake # variables available on command line variable mu index -8.1 variable disp index 0.5 variable temp index 338.0 variable lbox index 10.0 variable spacing index 5.0 # global model settings units real atom_style full boundary p p p pair_style lj/cut/coul/long 14 pair_modify mix arithmetic tail yes kspace_style ewald 0.0001 bond_style harmonic angle_style harmonic # box, start molecules on simple cubic lattice lattice sc ${spacing} lattice sc 5.0 Lattice spacing in x,y,z = 5 5 5 region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box region box block 0 10.0 0 ${lbox} 0 ${lbox} units box region box block 0 10.0 0 10.0 0 ${lbox} units box region box block 0 10.0 0 10.0 0 10.0 units box create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 Created orthogonal box = (0 0 0) to (10 10 10) 1 by 1 by 1 MPI processor grid molecule h2omol H2O.txt Read molecule h2omol: 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 create_atoms 0 box mol h2omol 464563 units box Created 24 atoms Time spent = 0.00128841 secs # rigid SPC/E water model pair_coeff 1 1 0.15535 3.166 pair_coeff * 2 0.0000 0.0000 bond_coeff 1 1000 1.0 angle_coeff 1 100 109.47 # masses mass 1 15.9994 mass 2 1.0 # MD settings group h2o type 1 2 24 atoms in group h2o neighbor 2.0 bin neigh_modify every 1 delay 1 check yes velocity all create ${temp} 54654 velocity all create 338.0 54654 timestep 1.0 minimize 0.0 0.0 100 1000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 16 ghost atom cutoff = 16 binsize = 8, bins = 2 2 2 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) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 338 -4.1890564 9.2628112e-06 18.98377 739.06991 100 338 -36.122455 0.67828405 -12.271354 573.22675 Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4.18904713252 -34.586018764 -35.4441713339 Force two-norm initial, final = 18.0027 42.115 Force max component initial, final = 5.8993 15.4907 Final line search alpha, max atom move = 0.00127226 0.0197082 Iterations, force evaluations = 100 239 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.038526 | 0.038526 | 0.038526 | 0.0 | 83.40 Bond | 0.00031209 | 0.00031209 | 0.00031209 | 0.0 | 0.68 Kspace | 0.0019636 | 0.0019636 | 0.0019636 | 0.0 | 4.25 Neigh | 0.00055456 | 0.00055456 | 0.00055456 | 0.0 | 1.20 Comm | 0.0040288 | 0.0040288 | 0.0040288 | 0.0 | 8.72 Output | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 | 0.0 | 0.03 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007958 | | | 1.72 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2011 ave 2011 max 2011 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4921 ave 4921 max 4921 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4921 Ave neighs/atom = 205.042 Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 reset_timestep 0 # rigid constraints with thermostat fix mynvt h2o nvt temp ${temp} ${temp} 100 fix mynvt h2o nvt temp 338.0 ${temp} 100 fix mynvt h2o nvt temp 338.0 338.0 100 fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 8 = # of frozen angles # important to make temperature dofs dynamic compute_modify thermo_temp dynamic/dof yes compute_modify mynvt_temp dynamic/dof yes run 1000 Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 518.26667 -36.122455 0 -12.949638 703.43827 1000 260.39219 -55.141232 0 -43.498537 -1698.672 Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10434 | 0.10434 | 0.10434 | 0.0 | 74.33 Bond | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.09 Kspace | 0.008199 | 0.008199 | 0.008199 | 0.0 | 5.84 Neigh | 0.0061581 | 0.0061581 | 0.0061581 | 0.0 | 4.39 Comm | 0.015352 | 0.015352 | 0.015352 | 0.0 | 10.94 Output | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 | 0.0 | 0.01 Modify | 0.004544 | 0.004544 | 0.004544 | 0.0 | 3.24 Other | | 0.001639 | | | 1.17 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1776 ave 1776 max 1776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5073 ave 5073 max 5073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5073 Ave neighs/atom = 211.375 Ave special neighs/atom = 2 Neighbor list builds = 27 Dangerous builds = 0 reset_timestep 0 # gcmc variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake # atom counts variable oxygen atom "type==1" variable hydrogen atom "type==2" group oxygen dynamic all var oxygen dynamic group oxygen defined group hydrogen dynamic all var hydrogen dynamic group hydrogen defined variable nO equal count(oxygen) variable nH equal count(hydrogen) # output variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH thermo 1000 # run run 20000 Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 0 260.39219 -1699.3643 -55.141232 11.642695 0.23910963 24 0 0 0 0 8 16 1000 340.44409 -2560.1501 -280.70157 53.784356 0.80699501 81 0.054205983 0.015933081 0 0 27 54 2000 302.57602 592.41718 -310.37771 53.213377 0.89666113 90 0.030546787 0.0078577743 0 0 30 60 3000 270.18045 -817.18659 -346.75773 50.737466 0.95643854 96 0.021969243 0.0060076096 0 0 32 64 4000 334.17192 1153.3017 -335.25519 62.75449 0.95643854 96 0.016400775 0.0045269353 0 0 32 64 5000 360.36872 -647.99689 -336.2928 67.674015 0.95643854 96 0.012996731 0.0036569014 0 0 32 64 6000 282.37822 -986.51765 -341.91848 53.028098 0.95643854 96 0.010941282 0.0030159847 0 0 32 64 7000 363.01448 2952.0391 -358.72963 70.335018 0.98632724 99 0.0098923151 0.0028884203 0 0 33 66 8000 331.70391 323.34886 -382.04165 68.223498 1.0461046 105 0.0092083323 0.0025112378 0 0 35 70 9000 337.2032 -3637.5257 -390.66472 69.35457 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70 10000 373.67063 3081.3271 -380.5107 76.855041 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70 11000 336.64665 5535.9451 -405.21548 71.247059 1.0759934 108 0.0068442571 0.0018355023 0 0 36 72 12000 306.51164 1448.1757 -410.3655 64.869362 1.0759934 108 0.0062798499 0.0016809265 0 0 36 72 13000 319.03497 177.44405 -406.17113 67.519768 1.0759934 108 0.0057952448 0.0015520479 0 0 36 72 14000 309.89701 -1022.6798 -384.20239 65.585833 1.0759934 108 0.005391524 0.0014384143 0 0 36 72 15000 398.91559 2058.9251 -404.32604 84.425503 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72 16000 318.98778 873.46142 -392.13338 67.50978 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72 17000 333.16025 2347.0215 -387.73943 70.509206 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72 18000 353.23789 -2305.787 -382.1633 74.758389 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72 19000 322.70939 5619.9631 -381.81328 68.297412 1.0759934 108 0.0039877848 0.0010558436 0 0 36 72 20000 371.07261 3916.1113 -389.76357 78.532884 1.0759934 108 0.0037874635 0.0010033009 0 0 36 72 Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 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 | 38.279 | 38.279 | 38.279 | 0.0 | 15.78 Bond | 0.055672 | 0.055672 | 0.055672 | 0.0 | 0.02 Kspace | 0.60623 | 0.60623 | 0.60623 | 0.0 | 0.25 Neigh | 4.4189 | 4.4189 | 4.4189 | 0.0 | 1.82 Comm | 1.2719 | 1.2719 | 1.2719 | 0.0 | 0.52 Output | 0.00096583 | 0.00096583 | 0.00096583 | 0.0 | 0.00 Modify | 197.85 | 197.85 | 197.85 | 0.0 | 81.56 Other | | 0.1098 | | | 0.05 Nlocal: 108 ave 108 max 108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100006 ave 100006 max 100006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100006 Ave neighs/atom = 925.981 Ave special neighs/atom = 2 Neighbor list builds = 20903 Dangerous builds = 0 Total wall time: 0:04:02