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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
# 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
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 = 8.38576 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 1.09006 8.6791e-07
4 0.945054 0
5 1.00006 3.8639e-06
6 109.47 0.000376049
---------------- Step 5000 ----- CPU = 16.4963 (sec) ----------------
TotEng = -3314.5713 KinEng = 650.7183 Temp = 300.4163
PotEng = -3965.2896 E_bond = 0.0875 E_angle = 1.4729
E_dihed = 0.4749 E_impro = 0.0000 E_vdwl = 774.1508
E_coul = 14908.3382 E_long = -19649.8139 Press = 358.7253
Volume = 10987.1076
SHAKE stats (type/ave/delta) on step 10000
2 1.08998 2.43077e-07
4 0.944985 0
5 0.999985 4.10972e-06
6 109.47 0.000514527
---------------- Step 10000 ----- CPU = 34.0488 (sec) ----------------
TotEng = -3279.4541 KinEng = 689.4215 Temp = 318.2843
PotEng = -3968.8755 E_bond = 0.2040 E_angle = 1.8441
E_dihed = 0.1574 E_impro = 0.0000 E_vdwl = 703.3180
E_coul = 14976.4466 E_long = -19650.8457 Press = -983.5171
Volume = 10927.3524
SHAKE stats (type/ave/delta) on step 15000
2 1.09002 1.0199e-06
4 0.945017 0
5 1.00002 5.08944e-06
6 109.47 0.00042735
---------------- Step 15000 ----- CPU = 53.1541 (sec) ----------------
TotEng = -3368.2566 KinEng = 686.6827 Temp = 317.0199
PotEng = -4054.9393 E_bond = 0.4514 E_angle = 1.5194
E_dihed = 2.4125 E_impro = 0.0000 E_vdwl = 709.7507
E_coul = 14880.7025 E_long = -19649.7759 Press = -1277.1945
Volume = 10817.2760
SHAKE stats (type/ave/delta) on step 20000
2 1.09005 3.84509e-06
4 0.945044 0
5 1.00005 1.15463e-05
6 109.47 0.000893174
---------------- Step 20000 ----- CPU = 67.0658 (sec) ----------------
TotEng = -3401.0672 KinEng = 639.1818 Temp = 295.0902
PotEng = -4040.2490 E_bond = 0.8254 E_angle = 4.2422
E_dihed = 0.6223 E_impro = 0.0000 E_vdwl = 777.7799
E_coul = 14826.3237 E_long = -19650.0425 Press = -268.5153
Volume = 10911.3140
SHAKE stats (type/ave/delta) on step 25000
2 1.09 3.16085e-06
4 0.945002 0
5 1 6.82105e-06
6 109.47 0.000683982
---------------- Step 25000 ----- CPU = 83.1242 (sec) ----------------
TotEng = -3331.9648 KinEng = 658.5638 Temp = 304.0383
PotEng = -3990.5287 E_bond = 0.0504 E_angle = 4.8757
E_dihed = 0.9548 E_impro = 0.0000 E_vdwl = 742.1312
E_coul = 14907.2989 E_long = -19645.8396 Press = -803.8894
Volume = 11243.5807
SHAKE stats (type/ave/delta) on step 30000
2 1.08995 5.90921e-08
4 0.944954 0
5 0.999952 5.01043e-06
6 109.47 0.000369665
---------------- Step 30000 ----- CPU = 96.1911 (sec) ----------------
TotEng = -3321.5197 KinEng = 681.8132 Temp = 314.7718
PotEng = -4003.3328 E_bond = 0.5162 E_angle = 6.2281
E_dihed = 1.2145 E_impro = 0.0000 E_vdwl = 767.4719
E_coul = 14871.6899 E_long = -19650.4535 Press = 63.7724
Volume = 10913.5775
SHAKE stats (type/ave/delta) on step 35000
2 1.08996 3.93868e-07
4 0.944963 0
5 0.999961 4.01003e-06
6 109.47 0.000492251
---------------- Step 35000 ----- CPU = 111.1547 (sec) ----------------
TotEng = -3376.3100 KinEng = 652.5134 Temp = 301.2450
PotEng = -4028.8234 E_bond = 0.6940 E_angle = 3.8874
E_dihed = 0.6796 E_impro = 0.0000 E_vdwl = 811.7936
E_coul = 14803.9468 E_long = -19649.8247 Press = 957.3673
Volume = 10810.8812
SHAKE stats (type/ave/delta) on step 40000
2 1.08993 1.84911e-06
4 0.944937 0
5 0.999934 4.48159e-06
6 109.47 0.000423379
---------------- Step 40000 ----- CPU = 127.8336 (sec) ----------------
TotEng = -3342.5048 KinEng = 641.0827 Temp = 295.9678
PotEng = -3983.5875 E_bond = 1.4592 E_angle = 3.3579
E_dihed = 0.1250 E_impro = 0.0000 E_vdwl = 714.5090
E_coul = 14945.5914 E_long = -19648.6299 Press = -1146.3509
Volume = 10993.6945
SHAKE stats (type/ave/delta) on step 45000
2 1.09004 2.52413e-06
4 0.945038 0
5 1.00004 7.30752e-06
6 109.47 0.000660905
---------------- Step 45000 ----- CPU = 141.7030 (sec) ----------------
TotEng = -3368.5223 KinEng = 640.7082 Temp = 295.7949
PotEng = -4009.2305 E_bond = 0.0226 E_angle = 2.7492
E_dihed = 0.8929 E_impro = 0.0000 E_vdwl = 820.3025
E_coul = 14817.6347 E_long = -19650.8325 Press = 388.8981
Volume = 11292.9397
SHAKE stats (type/ave/delta) on step 50000
2 1.09006 2.89749e-06
4 0.945051 0
5 1.00006 6.08927e-06
6 109.47 0.000779845
---------------- Step 50000 ----- CPU = 156.2936 (sec) ----------------
TotEng = -3253.6028 KinEng = 683.0893 Temp = 315.3610
PotEng = -3936.6921 E_bond = 0.4303 E_angle = 5.1773
E_dihed = 1.1538 E_impro = 0.0000 E_vdwl = 722.3282
E_coul = 14982.9162 E_long = -19648.6979 Press = -338.7238
Volume = 11230.1507
SHAKE stats (type/ave/delta) on step 55000
2 1.09007 9.95472e-07
4 0.945062 0
5 1.00007 3.93786e-06
6 109.47 0.000436645
---------------- Step 55000 ----- CPU = 176.2674 (sec) ----------------
TotEng = -3332.0820 KinEng = 662.9270 Temp = 306.0527
PotEng = -3995.0090 E_bond = 0.8395 E_angle = 1.9527
E_dihed = 1.0770 E_impro = 0.0000 E_vdwl = 750.6359
E_coul = 14899.3802 E_long = -19648.8943 Press = -498.7755
Volume = 11082.6763
SHAKE stats (type/ave/delta) on step 60000
2 1.09006 7.79087e-08
4 0.945052 1.22125e-15
5 1.00006 3.87615e-06
6 109.47 0.000355506
---------------- Step 60000 ----- CPU = 193.3379 (sec) ----------------
TotEng = -3296.5834 KinEng = 679.6746 Temp = 313.7845
PotEng = -3976.2580 E_bond = 2.4610 E_angle = 2.9231
E_dihed = 0.8719 E_impro = 0.0000 E_vdwl = 803.1348
E_coul = 14863.3163 E_long = -19648.9651 Press = 1009.2429
Volume = 11125.1736
SHAKE stats (type/ave/delta) on step 65000
2 1.09003 1.05995e-06
4 0.945023 1.22125e-15
5 1.00003 4.3471e-06
6 109.47 0.000511365
---------------- Step 65000 ----- CPU = 210.3194 (sec) ----------------
TotEng = -3322.0496 KinEng = 666.5091 Temp = 307.7064
PotEng = -3988.5587 E_bond = 0.8728 E_angle = 5.7476
E_dihed = 0.9783 E_impro = 0.0000 E_vdwl = 743.8165
E_coul = 14910.0426 E_long = -19650.0166 Press = -421.7167
Volume = 10902.5998
SHAKE stats (type/ave/delta) on step 70000
2 1.0901 1.09831e-06
4 0.94509 0
5 1.0001 3.59309e-06
6 109.47 0.000361318
---------------- Step 70000 ----- CPU = 228.7878 (sec) ----------------
TotEng = -3395.7912 KinEng = 667.4514 Temp = 308.1414
PotEng = -4063.2426 E_bond = 0.6965 E_angle = 5.1350
E_dihed
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