LAMMPS (23 Oct 2017) 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 2 by 2 MPI processor grid # we can load multiple molecule templates, but don't have to use them all molecule co2mol CO2.txt Read molecule co2mol: 3 atoms with 2 types 2 bonds with 1 types 1 angles with 1 types 0 dihedrals with 0 types 0 impropers with 0 types molecule h2omol H2O.txt Read molecule h2omol: 3 atoms with 2 types 2 bonds with 1 types 1 angles with 1 types 0 dihedrals with 0 types 0 impropers with 0 types create_atoms 0 box mol h2omol 464563 units box Created 24 atoms Time spent = 0.00174451 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 (../min.cpp:168) Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../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) = 11.85 | 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 -15.742442 0.14954269 7.579918 -637.49568 Loop time of 0.0566185 on 4 procs for 100 steps with 24 atoms 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -4.96106135393 -15.5388622715 -15.592899346 Force two-norm initial, final = 15.474 18.1478 Force max component initial, final = 5.80042 7.56514 Final line search alpha, max atom move = 0.00151131 0.0114333 Iterations, force evaluations = 100 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0085177 | 0.016083 | 0.026787 | 5.3 | 28.41 Bond | 0.00022459 | 0.00031394 | 0.00037575 | 0.0 | 0.55 Kspace | 0.0049062 | 0.014122 | 0.02044 | 5.0 | 24.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018515 | 0.02086 | 0.023246 | 1.2 | 36.84 Output | 2.4796e-05 | 2.6047e-05 | 2.9802e-05 | 0.0 | 0.05 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005213 | | | 9.21 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 = 209.458 Ave special neighs/atom = 2 Neighbor list builds = 0 Dangerous builds = 0 reset_timestep 0 # rigid constraints with thermostat fix mynvt all nvt temp ${temp} ${temp} 100 fix mynvt all nvt temp 338.0 ${temp} 100 fix mynvt all nvt temp 338.0 338.0 100 fix wshake all 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 # gcmc run 1000 Ewald initialization ... WARNING: Using 12-bit tables for long-range coulomb (../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) = 11.6 | 11.6 | 11.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 518.26667 -15.742442 0 7.4303753 -613.0781 1000 369.81793 -54.202686 0 -37.667331 294.98823 Loop time of 0.154891 on 4 procs for 1000 steps with 24 atoms Performance: 557.810 ns/day, 0.043 hours/ns, 6456.135 timesteps/s 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0154 | 0.028993 | 0.040525 | 5.5 | 18.72 Bond | 0.00016999 | 0.0001902 | 0.00023293 | 0.0 | 0.12 Kspace | 0.019093 | 0.028112 | 0.038976 | 4.3 | 18.15 Neigh | 0.0020263 | 0.0022184 | 0.002408 | 0.4 | 1.43 Comm | 0.04947 | 0.053627 | 0.058009 | 1.4 | 34.62 Output | 2.5749e-05 | 2.7537e-05 | 3.2187e-05 | 0.0 | 0.02 Modify | 0.035275 | 0.036815 | 0.038425 | 0.7 | 23.77 Other | | 0.004909 | | | 3.17 Nlocal: 6 ave 8 max 3 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 1331.5 ave 1369 max 1290 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 1259.75 ave 1642 max 428 min Histogram: 1 0 0 0 0 0 0 1 0 2 Total # of neighbors = 5039 Ave neighs/atom = 209.958 Ave special neighs/atom = 2 Neighbor list builds = 27 Dangerous builds = 0 variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) fix mygcmc all gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc all gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc all gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake fix mygcmc all 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) compute_modify thermo_temp dynamic/dof yes 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 ... WARNING: Using 12-bit tables for long-range coulomb (../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 (../fix_gcmc.cpp:445) 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 (../neighbor.cpp:472) 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 1000 369.81793 295.32434 -54.202686 16.535355 0.23910963 24 0 0 0 0 8 16 2000 84.544466 -2810.9047 -344.81664 14.364627 0.86677242 87 0.052198354 0.0099581757 0 0 29 58 3000 75.188527 -3688.256 -425.02228 14.567977 0.98632724 99 0.030546787 0.0049111089 0 0 33 66 4000 75.019396 -5669.3063 -427.69454 14.535207 0.98632724 99 0.019972039 0.0033375609 0 0 33 66 5000 90.415371 -2141.7596 -434.65925 17.518218 0.98632724 99 0.014909796 0.002514964 0 0 33 66 6000 78.212628 -943.75125 -428.80584 15.153904 0.98632724 99 0.01181521 0.0020316119 0 0 33 66 7000 71.754139 -2028.5122 -435.2139 13.902555 0.98632724 99 0.0099466198 0.0016755471 0 0 33 66 8000 84.446231 -1969.1657 -428.27313 16.361681 0.98632724 99 0.0084791272 0.0014442102 0 0 33 66 9000 70.952348 -2476.9812 -446.33824 14.170197 1.0162159 102 0.0077150892 0.0012556189 0 0 34 68 10000 71.418543 -1875.7083 -443.7214 14.263302 1.0162159 102 0.0068355714 0.0011197957 0 0 34 68 11000 86.094994 -4508.7581 -444.82687 17.194399 1.0162159 102 0.0061494515 0.0010082475 0 0 34 68 12000 81.906091 -1547.8105 -442.36719 16.357815 1.0162159 102 0.0055834729 0.00091775114 0 0 34 68 13000 57.221548 -4607.6222 -448.30939 11.42796 1.0162159 102 0.0051230355 0.00084046326 0 0 34 68 14000 61.288344 -2518.1779 -445.70636 12.240157 1.0162159 102 0.0047276997 0.00077602396 0 0 34 68 15000 85.787669 -2407.7111 -443.3834 17.133022 1.0162159 102 0.0043983485 0.00071920715 0 0 34 68 16000 74.845939 -3288.3403 -445.8247 14.947802 1.0162159 102 0.0042321884 0.00080654918 0 0 34 68 17000 73.835431 -1926.9566 -445.67476 14.745989 1.0162159 102 0.0039751059 0.00075470749 0 0 34 68 18000 72.634985 -3997.552 -447.2351 14.506243 1.0162159 102 0.0037395847 0.00071063946 0 0 34 68 19000 96.776472 -714.44132 -453.65552 19.904587 1.0461046 105 0.0036487876 0.00066993446 0 0 35 70 20000 75.470786 183.16972 -464.04688 15.522521 1.0461046 105 0.0034630763 0.00063350614 0 0 35 70 21000 65.658309 -773.41266 -466.27068 13.504331 1.0461046 105 0.003289113 0.00060198052 0 0 35 70 Loop time of 84.4085 on 4 procs for 20000 steps with 105 atoms Performance: 20.472 ns/day, 1.172 hours/ns, 236.943 timesteps/s 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3571 | 9.7574 | 13.984 | 90.7 | 11.56 Bond | 0.026374 | 0.031321 | 0.035482 | 2.1 | 0.04 Kspace | 0.57402 | 4.7894 | 8.1754 | 129.0 | 5.67 Neigh | 0.34952 | 0.34987 | 0.35021 | 0.1 | 0.41 Comm | 2.4028 | 2.4228 | 2.4372 | 0.9 | 2.87 Output | 0.0012269 | 0.0012826 | 0.0014355 | 0.2 | 0.00 Modify | 66.819 | 66.828 | 66.837 | 0.1 | 79.17 Other | | 0.2281 | | | 0.27 Nlocal: 26.25 ave 31 max 22 min Histogram: 1 0 1 0 0 0 1 0 0 1 Nghost: 6049.25 ave 6133 max 5962 min Histogram: 1 0 0 0 1 0 1 0 0 1 Neighs: 23613 ave 35083 max 14025 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 94452 Ave neighs/atom = 899.543 Ave special neighs/atom = 2 Neighbor list builds = 20428 Dangerous builds = 0 Total wall time: 0:01:24