variable inp string ../mini/B-MFH.data variable med string B-g1-medium25.data variable otp string B-g1-inisat25.data variable trj string B-g1-inisat25.lammpstrj variable numden string B-g1-inisat25.dat variable rst string ./Brstt/B-g1-inisat25.*.restart variable zcen equal "xlo + 0.5*lz" variable seed equal 22222 variable T equal 298.15 variable dt equal 1.0 variable P equal 1.0 variable mu equal -10.8891 variable tfac equal 5.0/3.0 # Initialization units real atom_style full pair_style lj/cut/coul/long 12.0 pair_modify shift yes tail no bond_style harmonic angle_style harmonic dimension 3 boundary p p p kspace_style pppm 1.0e-4 neighbor 2.0 bin neigh_modify delay 0 every 1 check yes # System definition read_data ./${inp} extra/bond/per/atom 2 extra/angle/per/atom 2 extra/special/per/atom 2 #add append read_data ./../mini/B-MFH.data extra/bond/per/atom 2 extra/angle/per/atom 2 extra/special/per/atom 2 Reading data file ... orthogonal box = (0.0000000 0.0000000 0.0000000) to (36.950000 33.476100 97.965000) 1 by 1 by 1 MPI processor grid reading atoms ... 3720 atoms reading velocities ... 3720 velocities scanning bonds ... 3 = max bonds/atom reading bonds ... 240 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 = 0.002 seconds read_data CPU = 0.017 seconds molecule h2omol spcfx.txt offset 10 0 0 0 0 Read molecule template h2omol: 1 molecules 0 fragments 3 atoms with max type 12 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 single 34 27 42 mol h2omol ${seed} units box create_atoms 0 single 34 27 42 mol h2omol 22222 units box Created 3 atoms using box units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (36.950000 33.476100 97.965000) create_atoms CPU = 0.000 seconds group water type 11 12 3 atoms in group water group fluid type 5 8 9 11 12 363 atoms in group fluid # Simulation settings timestep ${dt} timestep 1 fix shak water shake 1.0e-4 200 0 b 1 a 1 t 11 12 mol h2omol 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1 = # of frozen angles find clusters CPU = 0.001 seconds variable h2ooxy atom "type==11" group gh2ooxy dynamic all var h2ooxy dynamic group gh2ooxy defined variable nO equal count(gh2ooxy) fix oxyavt all ave/time 1 1 1 v_nO file ${numden} fix oxyavt all ave/time 1 1 1 v_nO file B-g1-inisat25.dat fix prntn0 all print 1 "Current H2O number = ${nO}" screen yes thermo 1 dump dmp all atom 1 ${trj} dump dmp all atom 1 B-g1-inisat25.lammpstrj fix initgcmc water gcmc 1 100000 0 0 ${seed} ${T} ${mu} 0.1 mol h2omol tfac_insert ${tfac} shake shak full_energy fix initgcmc water gcmc 1 100000 0 0 22222 ${T} ${mu} 0.1 mol h2omol tfac_insert ${tfac} shake shak full_energy fix initgcmc water gcmc 1 100000 0 0 22222 298.15 ${mu} 0.1 mol h2omol tfac_insert ${tfac} shake shak full_energy fix initgcmc water gcmc 1 100000 0 0 22222 298.15 -10.8891 0.1 mol h2omol tfac_insert ${tfac} shake shak full_energy fix initgcmc water gcmc 1 100000 0 0 22222 298.15 -10.8891 0.1 mol h2omol tfac_insert 1.66666666666667 shake shak full_energy compute tall all temp compute_modify tall dynamic/dof yes fix nvtall all nvt temp ${T} ${T} 100.0 fix nvtall all nvt temp 298.15 ${T} 100.0 fix nvtall all nvt temp 298.15 298.15 100.0 fix_modify nvtall temp tall compute_modify thermo_temp dynamic/dof yes restart 5 ${rst} restart 5 ./Brstt/B-g1-inisat25.*.restart run 200 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:340) G vector (1/distance) = 0.23782075 grid = 18 16 40 stencil order = 7 estimated absolute RMS force accuracy = 0.021686661 estimated relative force accuracy = 6.5308736e-05 using double precision FFTW3 3d grid and FFT values/proc = 27025 11520 0 atoms in group FixGCMC:gcmc_exclusion_group:initgcmc 0 atoms in group FixGCMC:rotation_gas_atoms:initgcmc WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:627) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 6 5 14 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long/intel, perpetual attributes: half, newton on, intel pair build: half/bin/newton/intel stencil: half/bin/3d bin: intel WARNING: Inconsistent image flags (src/domain.cpp:814) Current H2O number = 1 Per MPI rank memory allocation (min/avg/max) = 52.46 | 52.46 | 52.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -709180.59 77.860707 -709102.72 31736.071 Current H2O number = 0 1 93.41587 -718557.09 73.439336 -716981.94 33118.442 Current H2O number = 665 2 144.50543 -721642.8 66.841148 -719094.45 32180.377 Current H2O number = 874 3 203.62269 -724077.53 65.662038 -720384.06 30122.738 Current H2O number = 1026 4 269.44658 -726172.04 73.0365 -721181.2 27366.161 Current H2O number = 1096 5 335.34969 -728284.82 85.678049 -721940.56 24406.357 Current H2O number = 1179 6 395.95236 -730153.56 99.815462 -722539.03 21238.756 Current H2O number = 1251 7 445.61894 -731606.06 111.78558 -722928.03 18305.982 Current H2O number = 1286 8 489.12947 -732559.77 119.39149 -723043.56 15951.753 Current H2O number = 1293 9 519.03061 -733392.18 119.00989 -723249.3 14134.091 Current H2O number = 1310 10 537.49505 -733981.35 110.36946 -723448.86 12646.477 Current H2O number = 1342 11 546.98016 -734345.07 101.35351 -723595.29 11419.332 Current H2O number = 1371 12 546.70433 -734651.1 100.60253 -723816.18 10604.166 Current H2O number = 1389 13 542.64129 -734748.98 110.2886 -723938.86 9922.1921 Current H2O number = 1398 14 538.84233 -734691.72 125.15843 -723960.91 9263.916 Current H2O number = 1410 15 534.87841 -734789.23 138.95623 -724081.19 8550.2489 Current H2O number = 1415 16 536.11529 -734959.38 147.37387 -724183.33 7548.1919 Current H2O number = 1413 17 542.11183 -735232.87 146.47613 -724319.43 6511.6779 Current H2O number = 1437 18 552.98369 -735629.84 134.85571 -724465.95 5447.5179 Current H2O number = 1452 19 567.29705 -736057.88 117.41304 -724592.14 4574.5818 Current H2O number = 1460 20 580.08991 -736477.84 103.74493 -724724.9 3759.033 Current H2O number = 1475 21 592.38338 -736791.48 100.49953 -724784.31 3120.8188 Current H2O number = 1475 22 601.26142 -737146.8 107.205 -724907.88 2978.9625 Current H2O number = 1496 23 604.41971 -737401.52 118.38774 -725044.45 3012.0903 Current H2O number = 1500 24 606.46722 -737474.6 128.4312 -725069.64 3522.6215 Current H2O number = 1511 25 602.35204 -737567.81 133.09423 -725198.4 4555.9341 Current H2O number = 1527 26 595.67266 -737540.65 129.4208 -725285.75 5933.8026 Current H2O number = 1533 27 584.93684 -737569.99 117.27449 -725469.05 7549.6814 Current H2O number = 1551 28 572.89063 -737562.97 101.70995 -725652.67 9515.2202 Current H2O number = 1570 29 561.95517 -737419.11 91.120311 -725724.7 11250.399 Current H2O number = 1581 30 550.88259 -737421.15 90.716038 -725890.09 12961.405 Current H2O number = 1599 31 542.19468 -737471.82 99.185431 -726048.07 14336.772 Current H2O number = 1623 32 536.51074 -737484.62 111.285 -726141.9 15374.876 Current H2O number = 1618 33 535.62506 -737551.89 121.85641 -726204.36 16181.721 Current H2O number = 1628 34 537.55148 -737705.86 126.97075 -726287.21 16614.831 Current H2O number = 1639 35 543.23154 -737910.57 123.64287 -726362.98 16632.741 Current H2O number = 1648 36 550.71717 -738215.22 112.44327 -726478.73 16330.732 Current H2O number = 1661 37 559.2733 -738559.03 99.608125 -726604.77 15811.767 Current H2O number = 1671 38 566.81164 -738905.24 93.400607 -726753.47 14794.597 Current H2O number = 1687 39 574.86852 -739195.92 98.000282 -726840.72 13563.72 Current H2O number = 1698 40 580.59886 -739576 110.82397 -727009.65 12214.787 Current H2O number = 1713 41 582.62486 -739883.46 126.09335 -727188.91 10698.812 Current H2O number = 1726 42 584.25565 -740102 138.57908 -727321.47 9150.8891 Current H2O number = 1741 43 584.23277 -740156.85 144.00401 -727367.91 7802.2974 Current H2O number = 1741 44 582.27674 -740153.65 139.79444 -727407.78 6576.5919 Current H2O number = 1751 45 576.30918 -740300.93 127.83441 -727613.76 5474.2622 Current H2O number = 1771 46 570.9315 -740307.6 116.41836 -727725.21 4486.5821 Current H2O number = 1785 47 564.72508 -740267.94 114.07717 -727806.57 3519.1124 Current H2O number = 1791 48 556.99783 -740314.28 123.07131 -727959.75 2683.7241 Current H2O number = 1800 49 550.74801 -740269.1 139.15215 -728022.59 1889.2555 Current H2O number = 1806 50 544.76264 -740309.67 155.88175 -728142.29 1399.8195 Current H2O number = 1816 51 540.03396 -740268.01 167.3438 -728186.99 843.09388 Current H2O number = 1821 52 535.42406 -740316.53 168.23448 -728310.78 623.05835 Current H2O number = 1824 53 531.68545 -740314.37 156.55547 -728387.11 621.79675 Current H2O number = 1829 54 529.42385 -740396.77 137.6354 -728500.63 863.61927 Current H2O number = 1842 55 527.11134 -740487.72 122.33715 -728629.95 1123.6616 Current H2O number = 1859 56 524.92651 -740693.17 118.73563 -728815.67 1454.184 Current H2O number = 1873 57 525.00542 -740803.17 126.92627 -728896.93 1924.6439 Current H2O number = 1881