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 = 3.6642 (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 3.66431 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 (%) = 0.298316 (8.14112) Neigh time (%) = 0 (0) Comm time (%) = 0.770221 (21.0195) Outpt time (%) = 0 (0) Other time (%) = 2.59577 (70.8394) 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 = 4.0468 (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 4.04686 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 (%) = 0.327888 (8.10227) Neigh time (%) = 0 (0) Comm time (%) = 0.84904 (20.9802) Outpt time (%) = 0 (0) Other time (%) = 2.86993 (70.9175) 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 eb equal c_reax[1] variable ea equal c_reax[2] variable elp equal c_reax[3] variable emol equal c_reax[4] variable ev equal c_reax[5] variable ew equal c_reax[6] variable ep equal c_reax[7] variable efi equal c_reax[8] variable eqeq equal c_reax[9] thermo_style custom step temp etotal v_eb v_ea v_elp v_emol v_ev v_ew v_ep v_efi 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 eb ea elp emol ev ew ep efi eqeq 0 300 -86840.085 -141958.52 20614.164 0 0 3923.152 0.00053224591 0 0 193.78769 1 299.63584 -86840.085 -141960.32 20614.751 0 0 3923.621 0.0005317514 0 0 193.77287 2 298.65518 -86840.095 -141961.38 20615.425 0 0 3924.5261 0.00053169023 0 0 193.86029 3 297.06946 -86840.092 -141961.7 20616.182 0 0 3925.8636 0.00053206095 0 0 194.07227 4 294.89737 -86840.085 -141961.3 20617.018 0 0 3927.6276 0.00053285875 0 0 194.39496 5 292.16446 -86840.075 -141960.2 20617.929 0 0 3929.8097 0.00053407547 0 0 194.8224 6 288.90251 -86840.067 -141958.42 20618.907 0 0 3932.4001 0.00053569955 0 0 195.3431 7 285.14963 -86840.046 -141956 20619.944 0 0 3935.3866 0.00053771546 0 0 195.96503 8 280.94963 -86840.012 -141952.98 20621.031 0 0 3938.7535 0.00054010435 0 0 196.67882 9 276.35084 -86839.977 -141949.39 20622.159 0 0 3942.4839 0.00054284359 0 0 197.46381 10 271.4057 -86839.927 -141945.3 20623.318 0 0 3946.56 0.00054590664 0 0 198.32181 11 266.17001 -86839.865 -141940.76 20624.495 0 0 3950.9614 0.00054926315 0 0 199.23969 12 260.70211 -86839.787 -141935.81 20625.678 0 0 3955.6674 0.00055287915 0 0 200.20867 13 255.06218 -86839.692 -141930.53 20626.856 0 0 3960.6551 0.00055671734 0 0 201.21783 14 249.3114 -86839.58 -141924.96 20628.017 0 0 3965.8998 0.00056073779 0 0 202.25677 15 243.51104 -86839.447 -141919.18 20629.149 0 0 3971.3757 0.00056489839 0 0 203.31681 16 237.72166 -86839.294 -141913.24 20630.241 0 0 3977.0594 0.00056915552 0 0 204.38435 17 232.00212 -86839.13 -141907.21 20631.284 0 0 3982.9225 0.00057346463 0 0 205.44042 18 226.40915 -86838.932 -141901.15 20632.268 0 0 3988.9378 0.00057778086 0 0 206.497 19 220.99649 -86838.71 -141895.12 20633.185 0 0 3995.078 0.00058205946 0 0 207.53413 20 215.81399 -86838.46 -141889.18 20634.027 0 0 4001.3147 0.00058625624 0 0 208.54631 . . . . 67703 299.17164 -87329.975 -141466.73 20208.175 0 0 3128.7834 0.00053042914 0 0 234.50916 67704 299.39379 -87329.841 -141462.25 20207.573 0 0 3128.7305 0.0005308332 0 0 234.686 67705 299.61081 -87329.691 -141457.64 20206.966 0 0 3128.6778 0.00053133526 0 0 234.91695 67706 299.81959 -87329.56 -141452.9 20206.357 0 0 3128.6257 0.00053192721 0 0 235.16468 67707 300.01718 -87329.421 -141448.05 20205.746 0 0 3128.5739 0.00053260064 0 0 235.45576 67708 300.2006 -87329.276 -141443.11 20205.136 0 0 3128.5236 0.00053334713 0 0 235.78513 67709 300.36739 -87329.13 -141438.08 20204.528 0 0 3128.4755 0.00053415819 0 0 236.14682 67710 300.51545 -87328.993 -141433 20203.928 0 0 3128.4298 0.00053502557 0 0 236.52988 67711 300.64278 -87328.843 -141427.87 20203.339 0 0 3128.3867 0.00053594141 0 0 236.95213 67712 300.74777 -87328.698 -141422.71 20202.764 0 0 3128.3471 0.0005368984 0 0 237.39464 67713 300.82897 -87328.533 -141417.55 20202.208 0 0 3128.3115 0.0005378899 0 0 237.87856 67714 300.88549 -87328.366 -141412.4 20201.676 0 0 3128.2793 0.00053891035 0 0 238.38662 67715 300.91695 -87328.227 -141407.29 20201.172 0 0 3128.2508 0.00053995507 0 0 238.88419 67716 300.92318 -87328.048 -141402.23 20200.701 0 0 3128.2264 0.00054102032 0 0 239.43713 67717 300.9045 -87327.887 -141397.26 20200.266 0 0 3128.2064 0.00054210335 0 0 239.9855 67718 300.86166 -87327.731 -141392.38 20199.873 0 0 3128.1903 0.00054320219 0 0 240.53993 67719 300.79581 -87327.569 -141387.63 20199.524 0 0 3128.1773 0.00054431579 0 0 241.11092 67720 300.70829 -87327.374 -141383.02 20199.223 0 0 3128.1685 0.00054544328 0 0 241.71988 67721 300.60093 -87327.207 -141378.58 20198.973 0 0 3128.1629 0.00054658423 0 0 242.30536 67722 300.47604 -87327.037 -141374.33 20198.778 0 0 3128.1605 0.00054773847 0 0 242.89583 67723 -nan -nan -141370.28 20198.639 0 0 3128.161 0.00054890593 0 0 243.48789 67724 -nan -nan 0 -542.93434 0 0 0 0 0 0 0 67725 -nan -nan 0 -542.93434 0 0 0 0 0 0 0 67726 -nan -nan 0 -542.93434 0 0 0 0 0 0 0 67727 -nan -nan 0 -542.93434 0 0 0 0 0 0 0 67728 -nan -nan 0 -542.93434 0 0 0 0 0 0 0