LAMMPS (6 Apr 2013) # REAX potential for AuO system # ..... units real atom_style charge boundary p p p read_data data.goldnp_hexan_nonbond_reax orthogonal box = (-13.508 -16.251 -16.154) to (70.708 70.079 69.587) 2 by 2 by 2 MPI processor grid 881 atoms #read_data auhexan_charge.data pair_style reax/c lmp_control pair_coeff * * ffield.reax C H S Au neighbor 2 bin neigh_modify every 1 delay 0 check yes #group bottom_layer id < 61 #group top_layers id > 300 group gold id < 202 201 atoms in group gold group sam id > 202 679 atoms in group sam #group Satom id = 181, 201, 221, 241, 261, 281, 301, 321, 341 #group aus_atoms union Satom bottom_layer #group top_layers subtract all aus_atoms velocity all create 300.0 4928459 dist gaussian #velocity aus_atoms zero linear variable Tinput index in.goldnp_hexan_nonbond variable input index in.goldnp_hexan_nonbond variable sname index goldnp_hexan_nonbond print ====================================================================== ====================================================================== print "500 steps CG Minimization." 500 steps CG Minimization. print ====================================================================== ====================================================================== #fix 1 aus_atoms planeforce 0.0 0.0 1.0 fix 3 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #fix 3 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq thermo 100 thermo_style multi min_style sd minimize 1.0e-4 1.0e-6 500 50000 Memory usage per processor = 5.69779 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -84830.1057 KinEng = 786.9339 Temp = 300.0000 PotEng = -85617.0396 E_bond = 0.0000 E_angle = 0.0000 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -84627.2646 E_coul = -989.7750 E_long = 0.0000 Press = 2362.3066 ---------------- Step 19 ----- CPU = 3.5580 (sec) ---------------- TotEng = -86426.6826 KinEng = 786.9339 Temp = 300.0000 PotEng = -87213.6165 E_bond = 0.0000 E_angle = 0.0000 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -86241.1696 E_coul = -972.4468 E_long = 0.0000 Press = 326.8917 Loop time of 3.55806 on 8 procs for 19 steps with 881 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -85617.039581 -87207.5575659 -87213.616458 Force two-norm initial, final = 1874.18 185.151 Force max component initial, final = 160.848 24.8678 Final line search alpha, max atom move = 7.95881e-05 0.00197918 Iterations, force evaluations = 19 48 Pair time (%) = 0.283686 (7.97307) Neigh time (%) = 0 (0) Comm time (%) = 0.72969 (20.5081) Outpt time (%) = 0 (0) Other time (%) = 2.54468 (71.5188) Nlocal: 110.125 ave 881 max 0 min Histogram: 7 0 0 0 0 0 0 0 0 1 Nghost: 118 ave 274 max 0 min Histogram: 2 1 2 0 0 0 0 0 1 2 Neighs: 10052.1 ave 80417 max 0 min Histogram: 7 0 0 0 0 0 0 0 0 1 Total # of neighbors = 80417 Ave neighs/atom = 91.2792 Neighbor list builds = 0 Dangerous builds = 0 min_style cg minimize 1.0e-4 1.0e-6 500 50000 Memory usage per processor = 5.69661 Mbytes ---------------- Step 19 ----- CPU = 0.0000 (sec) ---------------- TotEng = -86426.6826 KinEng = 786.9339 Temp = 300.0000 PotEng = -87213.6164 E_bond = 0.0000 E_angle = 0.0000 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -86241.1696 E_coul = -972.4468 E_long = 0.0000 Press = 326.8920 ---------------- Step 40 ----- CPU = 3.9181 (sec) ---------------- TotEng = -86840.0850 KinEng = 786.9339 Temp = 300.0000 PotEng = -87627.0189 E_bond = 0.0000 E_angle = 0.0000 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -86609.9744 E_coul = -1017.0444 E_long = 0.0000 Press = 8.0746 Loop time of 3.91823 on 8 procs for 21 steps with 881 atoms Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -87213.6164489 -87621.6499367 -87627.0188766 Force two-norm initial, final = 185.151 125.956 Force max component initial, final = 24.8677 29.7316 Final line search alpha, max atom move = 0.000223661 0.00664978 Iterations, force evaluations = 21 52 Pair time (%) = 0.310808 (7.93236) Neigh time (%) = 0 (0) Comm time (%) = 0.800994 (20.4428) Outpt time (%) = 0 (0) Other time (%) = 2.80643 (71.6249) Nlocal: 110.125 ave 878 max 0 min Histogram: 7 0 0 0 0 0 0 0 0 1 Nghost: 118.5 ave 275 max 3 min Histogram: 2 1 2 0 0 0 0 0 1 2 Neighs: 10073.2 ave 80334 max 0 min Histogram: 7 0 0 0 0 0 0 0 0 1 Total # of neighbors = 80586 Ave neighs/atom = 91.4711 Neighbor list builds = 0 Dangerous builds = 0 print ====================================================================== ====================================================================== print "NPT dynamics with an anisotropic pressure of 1atm along xy direction." NPT dynamics with an anisotropic pressure of 1atm along xy direction. print ====================================================================== ====================================================================== reset_timestep 0 timestep 0.1 thermo 1 thermo_style multi variable l loop 10 #number of increments #fix 4 Satom spring/self 50.0 fix 5 all nvt temp 300.0 300.0 10.0 compute reax all pair reax/c variable ew equal c_reax[11] variable ep equal c_reax[12] variable eqeq equal c_reax[14] thermo_style custom step temp etotal press vol v_ew v_ep v_eqeq #fix 5 all npt temp 300.0 300.0 10.0 x 1.0 1.0 100.0 y 1.0 1.0 100.0 dump 1 all xyz 1000 nvt_reax_${sname}.xyz dump 1 all xyz 1000 nvt_reax_goldnp_hexan_nonbond.xyz dump 5 all dcd 1000 nvt_reax_${sname}.dcd dump 5 all dcd 1000 nvt_reax_goldnp_hexan_nonbond.dcd dump_modify 5 unwrap yes restart 1000 ${sname}_nvt.restart1 ${sname}_nvt.restart2 restart 1000 goldnp_hexan_nonbond_nvt.restart1 ${sname}_nvt.restart2 restart 1000 goldnp_hexan_nonbond_nvt.restart1 goldnp_hexan_nonbond_nvt.restart2 #dump_modify 4 image yes scale yes label loop run 10000000 Memory usage per processor = 5.11151 Mbytes Step Temp TotEng Press Volume ew ep eqeq 0 300 -86840.085 8.0747043 623368.56 30830.631 -948.31496 -68.729471 1 299.63584 -86840.085 9.9268568 623368.56 30832.389 -948.61398 -68.475665 2 298.65518 -86840.095 11.489495 623368.56 30834.39 -948.94058 -68.195792 3 297.06946 -86840.092 13.054023 623368.56 30836.616 -949.27464 -67.9098 4 294.89737 -86840.085 14.467284 623368.56 30839.045 -949.6404 -67.593372 5 292.16446 -86840.075 15.720523 623368.56 30841.65 -950.01692 -67.267204 6 288.90251 -86840.067 16.826937 623368.56 30844.398 -950.40567 -66.929625 7 285.14963 -86840.046 17.763945 623368.56 30847.248 -950.79749 -66.589556 8 280.94963 -86840.012 18.520979 623368.56 30850.161 -951.20289 -66.236212 9 276.35084 -86839.977 19.173431 623368.56 30853.087 -951.62149 -65.869717 10 271.4057 -86839.927 19.640735 623368.56 30855.98 -952.03327 -65.509756 11 266.17001 -86839.865 19.919613 623368.56 30858.788 -952.44261 -65.151633 12 260.70211 -86839.787 20.102895 623368.56 30861.458 -952.85184 -64.792713 13 255.06218 -86839.692 20.149648 623368.56 30863.939 -953.24277 -64.450831 14 249.3114 -86839.58 20.031122 623368.56 30866.177 -953.62114 -64.119933 15 243.51104 -86839.447 19.768497 623368.56 30868.123 -953.98843 -63.798249 16 237.72166 -86839.294 19.275545 623368.56 30869.729 -954.3469 -63.48319 17 232.00212 -86839.13 18.742632 623368.56 30870.95 -954.66445 -63.206545 18 226.40915 -86838.932 17.951919 623368.56 30871.746 -954.95899 -62.950148 19 220.99649 -86838.71 17.033618 623368.56 30872.08 -955.22087 -62.723389 20 215.81399 -86838.46 16.017953 623368.56 30871.924 -955.45807 -62.518117 21 210.90719 -86838.192 14.77143 623368.56 30871.253 -955.65266 -62.352018 22 206.31678 -86837.894 13.327992 623368.56 30870.05 -955.82291 -62.206733 23 202.07815 -86837.57 11.859661 623368.56 30868.305 -955.94879 -62.102131 24 198.22105 -86837.217 10.3814 623368.56 30866.016 -956.02838 -62.040065 25 194.76935 -86836.836 8.7477473 623368.56 30863.187 -956.07622 -62.005998 26 191.74096 -86836.441 7.0629116 623368.56 30859.832 -956.09 -62.002245 27 189.14757 -86836.004 5.3653168 623368.56 30855.97 -956.05706 -62.041495 28 186.99474 -86835.536 3.6529106 623368.56 30851.629 -955.98722 -62.114056 29 185.28207 -86835.035 1.9083621 623368.56 30846.844 -955.8795 -62.221024 30 184.00335 -86834.501 0.2014242 623368.56 30841.658 -955.73394 -62.362534 31 183.14667 -86833.937 -1.5200002 623368.56 30836.117 -955.55016 -62.539187 32 182.69466 -86833.339 -3.2275406 623368.56 30830.275 -955.3519 -62.727517 33 182.62496 -86832.709 -4.8874359 623368.56 30824.192 -955.12405 -62.942891 34 182.91058 -86832.044 -6.5203829 623368.56 30817.93 -954.86364 -63.188565 35 183.51952 -86831.344 -8.0640943 623368.56 30811.557 -954.57814 -63.457405 36 184.41703 -86830.611 -9.5707197 623368.56 30805.139 -954.27474 -63.742547 37 185.56606 -86829.841 -10.980756 623368.56 30798.748 -953.96485 -64.032968 38 186.92607 -86829.038 -12.195566 623368.56 30792.456 -953.65579 -64.321713 39 188.45454 -86828.201 -13.333756 623368.56 30786.333 -953.32349 -64.633164 40 190.10769 -86827.332 -14.298565 623368.56 30780.45 -952.98665 -64.949026 41 191.84122 -86826.432 -15.117913 623368.56 30774.873 -952.65407 -65.260866 42 193.6112 -86825.504 -15.812822 623368.56 30769.668 -952.34084 -65.553945 43 195.37494 -86824.545 -16.447753 623368.56 30764.895 -952.03699 -65.838563 44 197.09194 -86823.568 -17.147725 623368.56 30760.609 -951.72934 -66.128174 45 198.72459 -86822.57 -18.086097 623368.56 30756.861 -951.44885 -66.392158 46 200.23896 -86821.557 -19.157203 623368.56 30753.695 -951.18581 -66.640457 47 201.60512 -86820.53 -20.71637 623368.56 30751.148 -950.93931 -66.874219 48 202.79727 -86819.489 -22.591336 623368.56 30749.252 -950.71674 -67.086242 49 203.79393 -86818.449 -24.80194 623368.56 30748.029 -950.53111 -67.263713 50 204.57805 -86817.403 -27.309154 623368.56 30747.495 -950.36813 -67.421001 51 205.13694 -86816.364 -30.110323 623368.56 30747.658 -950.23055 -67.555455 52 205.46323 -86815.331 -32.991387 623368.56 30748.517 -950.12558 -67.659915 53 205.55507 -86814.303 -35.945379 623368.56 30750.063 -950.04605 -67.741541 54 205.41547 -86813.288 -38.87164 623368.56 30752.278 -949.99433 -67.797935 55 205.05281 -86812.288 -41.760614 623368.56 30755.138 -949.9807 -67.818752 56 204.48047 -86811.304 -44.649064 623368.56 30758.609 -949.99335 -67.815677 57 203.71682 -86810.337 -47.328687 623368.56 30762.65 -950.02752 -67.793309 58 202.78489 -86809.387 -49.864481 623368.56 30767.215 -950.08716 -67.747523 59 201.71153 -86808.461 -52.243467 623368.56 30772.249 -950.16719 -67.683188 60 200.52704 -86807.549 -54.482807 623368.56 30777.693 -950.25974 -67.607915 61 199.26455 -86806.655 -56.598924 623368.56 30783.485 -950.37162 -67.514639 62 197.95942 -86805.779 -58.537955 623368.56 30789.557 -950.51903 -67.386912 63 196.64862 -86804.919 -60.328883 623368.56 30795.838 -950.67423 -67.252143 64 195.36991 -86804.075 -61.886353 623368.56 30802.257 -950.82454 -67.122677 65 194.16133 -86803.243 -63.359757 623368.56 30808.742 -950.96912 -66.999042 66 193.06055 -86802.426 -64.68034 623368.56 30815.22 -951.14742 -66.841546 67 192.10397 -86801.62 -65.802637 623368.56 30821.619 -951.29989 -66.709328 68 191.32618 -86800.82 -66.762424 623368.56 30827.872 -951.45933 -66.56935 69 190.75932 -86800.03 -67.538034 623368.56 30833.912 -951.61392 -66.433132 70 190.43244 -86799.246 -68.002528 623368.56 30839.679 -951.75052 -66.313527 71 190.37098 -86798.459 -68.371433 623368.56 30845.115 -951.86552 -66.213894 72 190.59627 -86797.679 -68.516147 623368.56 30850.17 -951.9723 -66.120674 73 191.1252 -86796.897 -68.454438 623368.56 30854.8 -952.05895 -66.045557 74 191.96978 -86796.113 -68.175158 623368.56 30858.967 -952.1318 -65.982081 75 193.13696 -86795.314 -67.677479 623368.56 30862.642 -952.17727 -65.943685 76 194.62838 -86794.52 -66.950247 623368.56 30865.803 -952.20071 -65.924949 77 196.44031 -86793.717 -65.974009 623368.56 30868.435 -952.18684 -65.941095 78 198.56362 -86792.903 -64.809595 623368.56 30870.533 -952.15689 -65.970911 79 200.98392 -86792.08 -63.440503 623368.56 30872.098 -952.11088 -66.014418 80 203.68168 -86791.243 -61.868061 623368.56 30873.14 -952.04963 -66.070892 81 206.63257 -86790.393 -60.124991 623368.56 30873.676 -951.97021 -66.143347 82 209.8077 -86789.529 -58.245029 623368.56 30873.732 -951.85872 -66.245804 83 213.17421 -86788.649 -56.254625 623368.56 30873.337 -951.72421 -66.369425 84 216.69566 -86787.753 -54.159167 623368.56 30872.528 -951.57492 -66.506169 85 220.33258 -86786.842 -51.947975 623368.56 30871.349 -951.41933 -66.647815 86 224.04312 -86785.915 -49.591633 623368.56 30869.845 -951.26765 -66.784425 87 227.7837 -86784.973 -47.181735 623368.56 30868.065 -951.08234 -66.953722 88 231.50974 -86784.016 -44.746143 623368.56 30866.064 -950.89421 -67.125254 89 235.17631 -86783.043 -42.30865 623368.56 30863.894 -950.70462 -67.297932 90 238.73858 -86782.059 -39.914733 623368.56 30861.61 -950.52843 -67.457222 91 242.15312 -86781.062 -37.572237 623368.56 30859.267 -950.35186 -67.61717 92 245.37862 -86780.056 -35.323151 623368.56 30856.918 -950.18927 -67.76371 93 248.37597 -86779.04 -33.200553 623368.56 30854.615 -950.03712 -67.900653 94 251.10916 -86778.019 -31.231417 623368.56 30852.405 -949.88212 -68.041516 95 253.54583 -86776.99 -29.474727 623368.56 30850.332 -949.74561 -68.165229 96 255.65759 -86775.956 -28.024915 623368.56 30848.435 -949.62727 -68.272321 97 257.42069 -86774.92 -26.793128 623368.56 30846.75 -949.52945 -68.36062 98 258.8165 -86773.883 -25.957322 623368.56 30845.305 -949.46975 -68.412726 99 259.83144 -86772.845 -25.554403 623368.56 30844.122 -949.4124 -68.464467 100 260.45721 -86771.809 -25.742205 623368.56 30843.219 -949.37301 -68.500335 101 260.6911 -86770.775 -26.213572 623368.56 30842.604 -949.35483 -68.517157 102 260.53624 -86769.744 -27.268175 623368.56 30842.282 -949.38513 -68.487722 103 260.00162 -86768.722 -28.713712 623368.56 30842.249 -949.43617 -68.43972 104 259.10226 -86767.701 -30.464233 623368.56 30842.494 -949.51048 -68.370562 105 257.85913 -86766.687 -32.443636 623368.56 30843.002 -949.58581 -68.30241 106 256.29878 -86765.679 -34.571135 623368.56 30843.751 -949.69033 -68.206996 107 254.45267 -86764.677 -36.795866 623368.56 30844.712 -949.81187 -68.096357 108 252.35651 -86763.681 -39.09213 623368.56 30845.85 -949.95545 -67.965308 109 250.04938 -86762.691 -41.506717 623368.56 30847.129 -950.11891 -67.815814 110 247.57306 -86761.716 -44.024684 623368.56 30848.506 -950.29722 -67.652686 111 244.97128 -86760.721 -46.610426 623368.56 30849.936 -950.47497 -67.491076 112 242.28899 -86759.747 -49.378952 623368.56 30851.37 -950.64831 -67.334594 113 239.57182 -86758.775 -52.303312 623368.56 30852.759 -950.82733 -67.172918 114 236.86534 -86757.808 -55.346225 623368.56 30854.054 -951.02431 -66.993526 115 234.21459 -86756.855 -58.621871 623368.56 30855.206 -951.22072 -66.814673 116 231.66336 -86755.904 -62.030029 623368.56 30856.166 -951.40209 -66.650552 117 229.25362 -86754.94 -65.574654 623368.56 30856.89 -951.55633 -66.512986 118 227.02498 -86753.973 -69.220565 623368.56 30857.334 -951.71113 -66.374114 119 225.01403 -86753.005 -72.92622 623368.56 30857.46 -951.87206 -66.228163 120 223.25407 -86752.045 -76.706177 623368.56 30857.235 -952.02075 -66.09328 121 221.77459 -86751.068 -80.527876 623368.56 30856.628 -952.13438 -65.992065 122 220.60065 -86750.084 -84.258023 623368.56 30855.619 -952.22772 -65.909654 123 219.75269 -86749.092 -87.910886 623368.56 30854.189 -952.30031 -65.846393 124 219.24616 -86748.092 -91.478009 623368.56 30852.33 -952.3568 -65.797547 125 219.09131 -86747.082 -94.922203 623368.56 30850.039 -952.39776 -65.762508 126 219.29308 -86746.057 -98.200152 623368.56 30847.321 -952.41353 -65.750916 127 219.85084 -86745.033 -101.38271 623368.56 30844.188 -952.39376 -65.773107 128 220.75861 -86743.985 -104.26983 623368.56 30840.659 -952.35451 -65.813128 129 222.00509 -86742.924 -106.94829 623368.56 30836.76 -952.30017 -65.866691 130 223.57368 -86741.847 -109.4262 623368.56 30832.526 -952.23391 -65.930737 131 225.44289 -86740.758 -111.55069 623368.56 30827.995 -952.14914 -66.012034 132 227.58657 -86739.649 -113.38595 623368.56 30823.213 -952.04609 -66.110515 133 229.97421 -86738.523 -114.85937 623368.56 30818.231 -951.91355 -66.237605 134 232.57144 -86737.383 -116.00235 623368.56 30813.106 -951.78643 -66.358692 135 235.34051 -86736.226 -116.82935 623368.56 30807.896 -951.65205 -66.486693 136 238.24107 -86735.064 -117.21755 623368.56 30802.664 -951.50861 -66.623699 137 241.2307 -86733.871 -117.27988 623368.56 30797.476 -951.35938 -66.766731 138 244.26546 -86732.671 -116.99777 623368.56 30792.397 -951.21774 -66.902734 139 247.30055 -86731.454 -116.35142 623368.56 30787.494 -951.08162 -67.03409 140 250.29027 -86730.231 -115.40092 623368.56 30782.833 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