LAMMPS (18 Apr 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) using 1 OpenMP thread(s) per MPI task package omp * using multi-threaded neighbor list subroutines prefer double precision OpenMP force kernels # created by fftool units real boundary p p p atom_style full bond_style harmonic angle_style harmonic dihedral_style opls special_bonds lj/coul 0.0 0.0 0.5 read_data data.0.lmp orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438) 2 by 2 by 2 MPI processor grid reading atoms ... 1090 atoms scanning bonds ... 1 = max bonds/atom scanning angles ... 10 = max angles/atom scanning dihedrals ... 12 = max dihedrals/atom reading bonds ... 729 bonds reading angles ... 377 angles reading dihedrals ... 16 dihedrals 5 = max # of 1-2 neighbors 4 = max # of 1-3 neighbors 8 = max # of 1-4 neighbors 9 = max # of special neighbors # read_restart restart.*.lmp # reset_timestep 0 pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0 pair_modify tail no kspace_style pppm 1.0e-4 pair_coeff 1 1 none # C-CO C-CO pair_coeff 1 2 none # C-CO C-D pair_coeff 1 3 none # C-CO H-D pair_coeff 1 4 none # C-CO H-H1 pair_coeff 1 5 none # C-CO OHD- pair_coeff 1 6 none # C-CO HOD- pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow pair_coeff 2 2 none # C-D C-D pair_coeff 2 3 none # C-D H-D pair_coeff 2 4 none # C-D H-H1 pair_coeff 2 5 none # C-D OHD- pair_coeff 2 6 none # C-D HOD- pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow pair_coeff 3 3 none # H-D H-D pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1 pair_coeff 3 5 none # H-D OHD- pair_coeff 3 6 none # H-D HOD- pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow pair_coeff 4 4 none # H-H1 H-H1 pair_coeff 4 5 none # H-H1 OHD- pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD- pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow pair_coeff 5 5 none # OHD- OHD- pair_coeff 5 6 none # OHD- HOD- pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow pair_coeff 6 6 none # HOD- HOD- pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow variable nsteps equal 2500000 variable nprint equal ${nsteps}/500 variable nprint equal 2500000/500 variable ndump equal ${nsteps}/100 variable ndump equal 2500000/100 # variable nrestart equal ${nsteps}/10 variable temp equal 300.0 variable press equal 1.0 neighbor 2.0 bin timestep 2.0 # velocity all create ${temp} 12345 thermo_style multi thermo ${nprint} thermo 5000 fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6 fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6 1 = # of size 2 clusters 0 = # of size 3 clusters 2 = # of size 4 clusters 360 = # of frozen angles fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500 fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500 fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500 fix fNPT all npt temp 300 300 100 iso 1 ${press} 500 fix fNPT all npt temp 300 300 100 iso 1 1 500 run 250000 PPPM initialization ... G vector (1/distance) = 0.270213 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0169033 estimated relative force accuracy = 5.09037e-05 using double precision FFTs 3d grid and FFT values/proc = 2744 512 Hybrid pair style last /omp style lj/cut/coul/long/soft Last active /omp style is kspace_style pppm/omp SHAKE stats (type/ave/delta) on step 0 2 1.09 4.99625e-06 4 0.945001 0 5 1 1.58341e-05 6 109.47 0.0012593 Memory usage per processor = 8.38667 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -236.7999 KinEng = 0.0000 Temp = 0.0000 PotEng = -236.7999 E_bond = 0.0000 E_angle = 0.3094 E_dihed = 0.0001 E_impro = 0.0000 E_vdwl = -192.9285 E_coul = 19402.7702 E_long = -19446.9511 Press = 406.6448 Volume = 19438.0383 SHAKE stats (type/ave/delta) on step 5000 2 1.09009 2.87398e-07 4 0.945079 0 5 1.00008 3.9811e-06 6 109.47 0.000369321 ---------------- Step 5000 ----- CPU = 11.8253 (sec) ---------------- TotEng = -3307.2904 KinEng = 658.6061 Temp = 304.0578 PotEng = -3965.8965 E_bond = 0.0083 E_angle = 0.6669 E_dihed = 0.2569 E_impro = 0.0000 E_vdwl = 734.5556 E_coul = 14945.5504 E_long = -19646.9346 Press = -401.3652 Volume = 10990.0279 SHAKE stats (type/ave/delta) on step 10000 2 1.08991 8.10164e-07 4 0.944925 0 5 0.999922 7.76553e-06 6 109.47 0.000694232 ---------------- Step 10000 ----- CPU = 23.7032 (sec) ---------------- TotEng = -3381.5340 KinEng = 646.2577 Temp = 298.3570 PotEng = -4027.7917 E_bond = 0.2113 E_angle = 1.2103 E_dihed = 0.8831 E_impro = 0.0000 E_vdwl = 807.4931 E_coul = 14812.7871 E_long = -19650.3766 Press = 1168.7845 Volume = 10591.5096 SHAKE stats (type/ave/delta) on step 15000 2 1.08988 6.96695e-07 4 0.944894 0 5 0.999889 7.87681e-06 6 109.47 0.000849755 ---------------- Step 15000 ----- CPU = 37.0159 (sec) ---------------- TotEng = -3391.4919 KinEng = 640.6926 Temp = 295.7878 PotEng = -4032.1845 E_bond = 0.3271 E_angle = 2.4027 E_dihed = 0.2102 E_impro = 0.0000 E_vdwl = 833.3641 E_coul = 14781.8806 E_long = -19650.3692 Press = 1246.1602 Volume = 10806.8631 SHAKE stats (type/ave/delta) on step 20000 2 1.09009 5.35061e-07 4 0.945076 0 5 1.00008 5.8947e-06 6 109.47 0.000481652 ---------------- Step 20000 ----- CPU = 49.5427 (sec) ---------------- TotEng = -3340.9663 KinEng = 649.0129 Temp = 299.6290 PotEng = -3989.9791 E_bond = 0.2338 E_angle = 1.4422 E_dihed = 0.7066 E_impro = 0.0000 E_vdwl = 823.4408 E_coul = 14835.4457 E_long = -19651.2482 Press = 1369.0812 Volume = 10984.3808 SHAKE stats (type/ave/delta) on step 25000 2 1.09003 1.29003e-06 4 0.945026 0 5 1.00003 5.08541e-06 6 109.47 0.000543653 ---------------- Step 25000 ----- CPU = 61.5352 (sec) ---------------- TotEng = -3350.1301 KinEng = 628.6694 Temp = 290.2370 PotEng = -3978.7994 E_bond = 0.5250 E_angle = 3.3362 E_dihed = 1.1997 E_impro = 0.0000 E_vdwl = 753.6460 E_coul = 14908.8825 E_long = -19646.3890 Press = -107.3383 Volume = 10858.4423 SHAKE stats (type/ave/delta) on step 30000 2 1.09012 2.15723e-06 4 0.945104 0 5 1.00011 7.30223e-06 6 109.47 0.000722195 ---------------- Step 30000 ----- CPU = 75.1590 (sec) ---------------- TotEng = -3291.1533 KinEng = 662.9659 Temp = 306.0706 PotEng = -3954.1192 E_bond = 0.0386 E_angle = 3.4541 E_dihed = 0.3158 E_impro = 0.0000 E_vdwl = 745.0479 E_coul = 14947.2099 E_long = -19650.1856 Press = -296.2930 Volume = 11301.5139 SHAKE stats (type/ave/delta) on step 35000 2 1.08998 1.28162e-06 4 0.944981 0 5 0.999982 8.25561e-06 6 109.47 0.000790911 ---------------- Step 35000 ----- CPU = 86.8870 (sec) ---------------- TotEng = -3370.6689 KinEng = 637.0075 Temp = 294.0864 PotEng = -4007.6763 E_bond = 0.2585 E_angle = 2.7426 E_dihed = 0.2288 E_impro = 0.0000 E_vdwl = 766.3429 E_coul = 14871.1344 E_long = -19648.3835 Press = -434.1739 Volume = 11077.2342 SHAKE stats (type/ave/delta) on step 40000 2 1.09005 3.30799e-07 4 0.945044 0 5 1.00005 4.39187e-06 6 109.47 0.000367325 ---------------- Step 40000 ----- CPU = 102.1257 (sec) ---------------- TotEng = -3318.0442 KinEng = 694.3948 Temp = 320.5803 PotEng = -4012.4390 E_bond = 0.3986 E_angle = 4.3594 E_dihed = 1.0551 E_impro = 0.0000 E_vdwl = 716.6662 E_coul = 14914.0530 E_long = -19648.9712 Press = -1177.4188 Volume = 11087.6184 SHAKE stats (type/ave/delta) on step 45000 2 1.08997 7.63663e-06 4 0.944973 0 5 0.999973 2.30441e-05 6 109.47 0.00155851 ---------------- Step 45000 ----- CPU = 119.3648 (sec) ---------------- TotEng = -3371.5332 KinEng = 660.1645 Temp = 304.7773 PotEng = -4031.6977 E_bond = 1.3352 E_angle = 2.6760 E_dihed = 1.0255 E_impro = 0.0000 E_vdwl = 734.4320 E_coul = 14878.0777 E_long = -19649.2440 Press = -978.3955 Volume = 11108.5059 SHAKE stats (type/ave/delta) on step 50000 2 1.09015 1.28872e-06 4 0.945128 0 5 1.00014 5.27234e-06 6 109.47 0.000408939 ---------------- Step 50000 ----- CPU = 132.4029 (sec) ---------------- TotEng = -3345.1117 KinEng = 660.2366 Temp = 304.8106 PotEng = -4005.3482 E_bond = 0.9878 E_angle = 3.3427 E_dihed = 0.4740 E_impro = 0.0000 E_vdwl = 763.3350 E_coul = 14874.5886 E_long = -19648.0763 Press = 257.8221 Volume = 10750.8743 SHAKE stats (type/ave/delta) on step 55000 2 1.09006 1.79853e-06 4 0.945055 0 5 1.00006 8.96473e-06 6 109.47 0.000604022 ---------------- Step 55000 ----- CPU = 144.3965 (sec) ---------------- TotEng = -3329.0112 KinEng = 639.1918 Temp = 295.0949 PotEng = -3968.2030 E_bond = 0.3779 E_angle = 4.2627 E_dihed = 0.1647 E_impro = 0.0000 E_vdwl = 775.0143 E_coul = 14900.7482 E_long = -19648.7708 Press = 384.3466 Volume = 10943.9465 SHAKE stats (type/ave/delta) on step 60000 2 1.09006 5.76725e-07 4 0.94505 0 5 1.00005 4.15938e-06 6 109.47 0.000456895 ---------------- Step 60000 ----- CPU = 158.9285 (sec) ---------------- TotEng = -3337.6373 KinEng = 686.3391 Temp = 316.8613 PotEng = -4023.9764 E_bond = 0.1951 E_angle = 3.2295 E_dihed = 0.2227 E_impro = 0.0000 E_vdwl = 803.8460 E_coul = 14822.5916 E_long = -19654.0613 Press = 343.2839 Volume = 11053.5476 SHAKE stats (type/ave/delta) on step 65000 2 1.08992 1.92627e-06 4 0.944928 0 5 0.999925 9.65284e-06 6 109.47 0.000982037 ---------------- Step 65000 ----- CPU = 171.6679 (sec) ---------------- TotEng = -3286.1431 KinEng = 655.6296 Temp = 302.6837 PotEng = -3941.7726 E_bond = 0.8912 E_angle = 5.2439 E_dihed = 1.0392 E_impro = 0.0000 E_vdwl = 723.8338 E_coul = 14977.3056 E_long = -19650.0863 Press = -610.8426 Volume = 11125.9793 SHAKE stats (type/ave/delta) on step 70000 2 1.08995 3.49023e-07 4 0.944954 0 5 0.999952 3.62092e-06 6 109.47 0.000402967 ---------------- Step 70000 ----- CPU