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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
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