LAMMPS (17 Feb 2022) # 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 2 by 2 MPI processor grid molecule h2omol H2O.txt Read molecule template h2omol: 1 molecules 0 fragments 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 using box units in orthogonal box = (0 0 0) to (10 10 10) create_atoms CPU = 0.002 seconds # 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:187) Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:340) G vector (1/distance) = 0.17044845 estimated absolute RMS force accuracy = 0.033206374 estimated relative force accuracy = 0.00010000001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 generated 0 of 1 mixed pair_coeff terms from arithmetic 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 = 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791 100 338 -15.815905 0.10936727 7.4662793 -278.75864 Loop time of 0.0318772 on 4 procs for 100 steps with 24 atoms 99.9% CPU use with 4 MPI tasks x no OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4.96106135392776 -15.6966371009978 -15.7065379926413 Force two-norm initial, final = 15.47396 4.3807065 Force max component initial, final = 5.8004229 2.0143175 Final line search alpha, max atom move = 0.0046871063 0.00944132 Iterations, force evaluations = 100 346 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0044502 | 0.008939 | 0.014884 | 4.0 | 28.04 Bond | 0.00010079 | 0.00013115 | 0.0001615 | 0.0 | 0.41 Kspace | 0.0015161 | 0.0073496 | 0.011723 | 4.3 | 23.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013957 | 0.014086 | 0.01416 | 0.1 | 44.19 Output | 1.1416e-05 | 1.2871e-05 | 1.6202e-05 | 0.0 | 0.04 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001359 | | | 4.26 Nlocal: 6 ave 8 max 3 min Histogram: 1 0 0 0 1 0 0 0 0 2 Nghost: 1722 ave 1725 max 1720 min Histogram: 2 0 0 0 0 0 1 0 0 1 Neighs: 1256.75 ave 2101 max 667 min Histogram: 1 0 1 0 1 0 0 0 0 1 Total # of neighbors = 5027 Ave neighs/atom = 209.45833 Ave special neighs/atom = 2 Neighbor list builds = 0 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 find clusters CPU = 0.001 seconds # 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:340) G vector (1/distance) = 0.17044845 estimated absolute RMS force accuracy = 0.033206374 estimated relative force accuracy = 0.00010000001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 generated 0 of 1 mixed pair_coeff terms from arithmetic mixing rule Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 518.26667 -15.815905 0 7.3569121 -385.7767 1000 240.84589 -44.723106 0 -33.954368 61.365522 Loop time of 0.0928135 on 4 procs for 1000 steps with 24 atoms Performance: 930.900 ns/day, 0.026 hours/ns, 10774.300 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0079337 | 0.014647 | 0.023202 | 4.8 | 15.78 Bond | 7.45e-05 | 9.0251e-05 | 0.00012098 | 0.0 | 0.10 Kspace | 0.0044849 | 0.012865 | 0.019419 | 5.0 | 13.86 Neigh | 0.0015513 | 0.0015789 | 0.0016063 | 0.1 | 1.70 Comm | 0.038145 | 0.038416 | 0.038704 | 0.1 | 41.39 Output | 9.084e-06 | 1.0765e-05 | 1.546e-05 | 0.0 | 0.01 Modify | 0.023572 | 0.023646 | 0.023723 | 0.0 | 25.48 Other | | 0.00156 | | | 1.68 Nlocal: 6 ave 9 max 1 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 1375.25 ave 1495 max 1251 min Histogram: 1 0 0 1 0 0 1 0 0 1 Neighs: 1263.25 ave 2045 max 122 min Histogram: 1 0 0 0 0 0 2 0 0 1 Total # of neighbors = 5053 Ave neighs/atom = 210.54167 Ave special neighs/atom = 2 Neighbor list builds = 30 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:340) G vector (1/distance) = 0.17044845 estimated absolute RMS force accuracy = 0.033206374 estimated relative force accuracy = 0.00010000001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 generated 0 of 1 mixed pair_coeff terms from arithmetic mixing rule WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:486) 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:635) Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 0 240.84589 61.724018 -44.723106 10.768738 0.23910963 24 0 0 0 0 8 16 1000 345.18281 -1439.9493 -275.72969 56.590842 0.83688372 84 0.054205983 0.013941446 0 0 28 56 2000 345.18939 -1776.1886 -334.1935 66.88136 0.98632724 99 0.03258324 0.0068755525 0 0 33 66 3000 371.00685 1611.457 -344.8868 71.883561 0.98632724 99 0.021303508 0.0046725853 0 0 33 66 4000 333.39448 -779.09163 -363.7251 66.583637 1.0162159 102 0.016400775 0.0035209497 0 0 34 68 5000 313.43793 1752.7257 -366.08712 62.598028 1.0162159 102 0.012996731 0.0028442566 0 0 34 68 6000 372.34785 3089.6885 -378.09103 74.36318 1.0162159 102 0.011272836 0.0026808753 0 0 34 68 7000 393.56304 1095.6551 -359.16911 78.600157 1.0162159 102 0.0096096775 0.0023107363 0 0 34 68 8000 378.04525 -1933.9224 -346.54153 75.501032 1.0162159 102 0.0084617108 0.0020089902 0 0 34 68 9000 297.05101 4804.6743 -367.61786 59.325326 1.0162159 102 0.0074970783 0.0017916732 0 0 34 68 10000 379.5212 -951.43658 -368.99713 78.058362 1.0461046 105 0.0069429291 0.0016131959 0 0 35 70 11000 308.54229 1335.2452 -378.61796 63.459711 1.0461046 105 0.006303921 0.0014684018 0 0 35 70 12000 375.19931 2791.9525 -368.98209 79.406248 1.0759934 108 0.0059493315 0.0013447412 0 0 36 72 13000 392.21002 4857.5806 -386.58586 83.006354 1.0759934 108 0.005490232 0.0012416383 0 0 36 72 14000 327.23916 3472.146 -393.65093 69.256081 1.0759934 108 0.0051077595 0.0011507314 0 0 36 72 15000 330.63194 5995.4662 -389.36253 69.974121 1.0759934 108 0.004761212 0.0010753989 0 0 36 72 16000 329.25034 694.90103 -387.21725 69.681723 1.0759934 108 0.0044719941 0.0010062767 0 0 36 72 17000 368.22282 -3340.8134 -399.58632 77.929761 1.0759934 108 0.0042070328 0.00094751928 0 0 36 72 18000 270.78376 1831.8085 -388.15376 57.308002 1.0759934 108 0.0039804956 0.00089324594 0 0 36 72 19000 337.54827 1211.6625 -387.9744 71.437877 1.0759934 108 0.0037779014 0.00084467485 0 0 36 72 20000 382.5465 5070.3639 -399.03603 83.241787 1.1058821 111 0.0036877934 0.00080264069 0 0 37 74 Loop time of 47.6346 on 4 procs for 20000 steps with 111 atoms Performance: 36.276 ns/day, 0.662 hours/ns, 419.863 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3783 | 5.9819 | 7.7932 | 52.3 | 12.56 Bond | 0.014825 | 0.015376 | 0.016097 | 0.4 | 0.03 Kspace | 0.27624 | 2.0815 | 3.68 | 88.4 | 4.37 Neigh | 0.60717 | 0.60731 | 0.60741 | 0.0 | 1.27 Comm | 1.6019 | 1.6072 | 1.6116 | 0.3 | 3.37 Output | 0.00049839 | 0.00055603 | 0.00072798 | 0.0 | 0.00 Modify | 37.253 | 37.253 | 37.253 | 0.0 | 78.21 Other | | 0.08782 | | | 0.18 Nlocal: 27.75 ave 31 max 26 min Histogram: 2 0 0 0 1 0 0 0 0 1 Nghost: 6387 ave 6439 max 6327 min Histogram: 1 0 0 1 0 0 0 0 1 1 Neighs: 26407 ave 33738 max 18362 min Histogram: 1 0 0 0 0 2 0 0 0 1 Total # of neighbors = 105628 Ave neighs/atom = 951.6036 Ave special neighs/atom = 2 Neighbor list builds = 20923 Dangerous builds = 0 Total wall time: 0:00:47