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simplify and shorten examples for fix filter/corotate and combine into a single folder

This commit is contained in:
Axel Kohlmeyer 2017-03-16 15:02:50 -04:00
parent 1995f434f3
commit bed288339e
11 changed files with 789 additions and 899 deletions
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examples/USER/misc/filter-corotate/bpti/log.lammps
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LAMMPS (26 Jan 2017)
units real
neigh_modify delay 2 every 1
include system.in.init
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data 4pti.data
orthogonal box = (-10 -10 -30) to (50 50 30)
1 by 2 by 2 MPI processor grid
reading atoms ...
892 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
906 bonds
reading angles ...
1626 angles
reading dihedrals ...
2501 dihedrals
reading impropers ...
137 impropers
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special_bonds charmm
# ------------- MINIMIZE ----------
minimize 1e-4 1e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:298)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 3549 1024
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, half, perpetual
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Memory usage per processor = 16.9693 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
241 0 -4503.3131 749.58666 -3753.7264 -29.045082
Loop time of 0.870402 on 4 procs for 241 steps with 892 atoms
98.4% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2131.73812515 -3753.43985766 -3753.72640886
Force two-norm initial, final = 1086.21 26.3688
Force max component initial, final = 310.811 3.92758
Final line search alpha, max atom move = 0.00596649 0.0234339
Iterations, force evaluations = 241 463
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26264 | 0.45712 | 0.60755 | 19.1 | 52.52
Bond | 0.0165 | 0.038426 | 0.055693 | 7.7 | 4.41
Kspace | 0.17897 | 0.34583 | 0.56313 | 24.1 | 39.73
Neigh | 0.01432 | 0.014404 | 0.014488 | 0.1 | 1.65
Comm | 0.0059164 | 0.0078539 | 0.0098884 | 1.6 | 0.90
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00677 | | | 0.78
Nlocal: 223 ave 323 max 89 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 613 ave 675 max 557 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 37222.8 ave 50005 max 20830 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 148891
Ave neighs/atom = 166.918
Ave special neighs/atom = 10.9395
Neighbor list builds = 15
Dangerous builds = 0
# ------------- RUN ---------------
thermo 100
thermo_style multi
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
velocity all create 200.0 12345678 dist uniform
dump dump1 all atom 100 4pti.dump
fix 1 all nvt temp 200 300 25
fix cor all filter/corotate m 1.0
163 = # of size 2 clusters
0 = # of size 3 clusters
25 = # of size 4 clusters
0 = # of size 5 clusters
100 = # of frozen angles
run 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 3549 1024
Memory usage per processor = 17.142 Mbytes
---------------- Step 241 ----- CPU = 0.0000 (sec) ----------------
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2593
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
---------------- Step 300 ----- CPU = 0.5825 (sec) ----------------
TotEng = -2772.9432 KinEng = 523.1156 Temp = 196.9635
PotEng = -3296.0588 E_bond = 181.3316 E_angle = 521.0952
E_dihed = 383.7103 E_impro = 36.2704 E_vdwl = -278.1519
E_coul = -808.2367 E_long = -3332.0777 Press = -53.7728
---------------- Step 400 ----- CPU = 1.5692 (sec) ----------------
TotEng = -2768.2546 KinEng = 529.1491 Temp = 199.2352
PotEng = -3297.4037 E_bond = 197.9740 E_angle = 560.5585
E_dihed = 399.0297 E_impro = 30.2332 E_vdwl = -239.0558
E_coul = -908.5701 E_long = -3337.5732 Press = -14.8873
---------------- Step 500 ----- CPU = 2.5452 (sec) ----------------
TotEng = -2807.5560 KinEng = 532.1109 Temp = 200.3504
PotEng = -3339.6669 E_bond = 187.7016 E_angle = 533.2787
E_dihed = 381.6501 E_impro = 36.0212 E_vdwl = -239.3347
E_coul = -897.2375 E_long = -3341.7463 Press = -31.1463
---------------- Step 600 ----- CPU = 3.4829 (sec) ----------------
TotEng = -2797.3491 KinEng = 545.9460 Temp = 205.5596
PotEng = -3343.2951 E_bond = 184.9046 E_angle = 548.8444
E_dihed = 385.8583 E_impro = 35.7923 E_vdwl = -236.1192
E_coul = -915.5958 E_long = -3346.9797 Press = -114.5599
---------------- Step 700 ----- CPU = 4.4101 (sec) ----------------
TotEng = -2847.1093 KinEng = 544.1043 Temp = 204.8661
PotEng = -3391.2135 E_bond = 195.4286 E_angle = 545.8848
E_dihed = 390.2441 E_impro = 35.2312 E_vdwl = -245.1111
E_coul = -977.4350 E_long = -3335.4560 Press = -75.8944
---------------- Step 800 ----- CPU = 5.3551 (sec) ----------------
TotEng = -2827.9493 KinEng = 565.6488 Temp = 212.9780
PotEng = -3393.5980 E_bond = 195.7451 E_angle = 549.0863
E_dihed = 377.8729 E_impro = 40.6960 E_vdwl = -218.5439
E_coul = -995.0702 E_long = -3343.3842 Press = -28.3879
---------------- Step 900 ----- CPU = 6.3195 (sec) ----------------
TotEng = -2851.9081 KinEng = 555.7192 Temp = 209.2393
PotEng = -3407.6272 E_bond = 180.0814 E_angle = 558.9056
E_dihed = 383.9971 E_impro = 30.1466 E_vdwl = -215.6945
E_coul = -1006.1478 E_long = -3338.9156 Press = 147.5178
---------------- Step 1000 ----- CPU = 7.3221 (sec) ----------------
TotEng = -2839.5000 KinEng = 539.5433 Temp = 203.1488
PotEng = -3379.0432 E_bond = 189.0382 E_angle = 563.1204
E_dihed = 376.6688 E_impro = 39.3375 E_vdwl = -215.4325
E_coul = -995.4610 E_long = -3336.3146 Press = -31.6144
---------------- Step 1100 ----- CPU = 8.2417 (sec) ----------------
TotEng = -2844.6804 KinEng = 556.0032 Temp = 209.3463
PotEng = -3400.6836 E_bond = 187.7618 E_angle = 559.4066
E_dihed = 363.4841 E_impro = 38.5648 E_vdwl = -238.0760
E_coul = -970.6614 E_long = -3341.1633 Press = -56.2838
---------------- Step 1200 ----- CPU = 9.1521 (sec) ----------------
TotEng = -2839.6265 KinEng = 551.6993 Temp = 207.7258
PotEng = -3391.3258 E_bond = 199.7412 E_angle = 564.9663
E_dihed = 394.3803 E_impro = 34.7852 E_vdwl = -251.8720
E_coul = -990.7418 E_long = -3342.5850 Press = -34.8501
---------------- Step 1300 ----- CPU = 10.0769 (sec) ----------------
TotEng = -2868.0625 KinEng = 572.4410 Temp = 215.5355
PotEng = -3440.5035 E_bond = 198.9955 E_angle = 566.0100
E_dihed = 370.7960 E_impro = 30.0945 E_vdwl = -236.1481
E_coul = -1035.1271 E_long = -3335.1244 Press = 19.4140
---------------- Step 1400 ----- CPU = 10.9951 (sec) ----------------
TotEng = -2800.7717 KinEng = 588.4163 Temp = 221.5505
PotEng = -3389.1880 E_bond = 210.7336 E_angle = 589.3354
E_dihed = 379.6028 E_impro = 36.7933 E_vdwl = -210.4855
E_coul = -1052.0263 E_long = -3343.1414 Press = -21.6471
---------------- Step 1500 ----- CPU = 11.9139 (sec) ----------------
TotEng = -2826.4883 KinEng = 548.8833 Temp = 206.6655
PotEng = -3375.3716 E_bond = 206.2588 E_angle = 587.7388
E_dihed = 385.0180 E_impro = 35.8288 E_vdwl = -224.8238
E_coul = -1027.6650 E_long = -3337.7272 Press = 32.7176
---------------- Step 1600 ----- CPU = 12.8228 (sec) ----------------
TotEng = -2834.7829 KinEng = 585.1197 Temp = 220.3093
PotEng = -3419.9026 E_bond = 211.6949 E_angle = 580.8055
E_dihed = 375.4347 E_impro = 32.9507 E_vdwl = -216.2341
E_coul = -1065.2545 E_long = -3339.2997 Press = 29.5762
---------------- Step 1700 ----- CPU = 13.7309 (sec) ----------------
TotEng = -2862.6332 KinEng = 573.1120 Temp = 215.7881
PotEng = -3435.7452 E_bond = 206.7642 E_angle = 560.3937
E_dihed = 363.9108 E_impro = 34.2460 E_vdwl = -232.7830
E_coul = -1022.7145 E_long = -3345.5624 Press = -93.9393
---------------- Step 1800 ----- CPU = 14.6352 (sec) ----------------
TotEng = -2862.4318 KinEng = 542.3768 Temp = 204.2157
PotEng = -3404.8085 E_bond = 211.1760 E_angle = 585.2517
E_dihed = 369.7922 E_impro = 31.2026 E_vdwl = -223.1523
E_coul = -1036.4965 E_long = -3342.5822 Press = -111.5865
---------------- Step 1900 ----- CPU = 15.5415 (sec) ----------------
TotEng = -2846.9891 KinEng = 561.2261 Temp = 211.3128
PotEng = -3408.2152 E_bond = 210.0759 E_angle = 595.2289
E_dihed = 356.8271 E_impro = 34.7545 E_vdwl = -235.1305
E_coul = -1030.0427 E_long = -3339.9284 Press = -53.6864
---------------- Step 2000 ----- CPU = 16.4648 (sec) ----------------
TotEng = -2829.7971 KinEng = 565.7821 Temp = 213.0283
PotEng = -3395.5793 E_bond = 203.7783 E_angle = 595.5818
E_dihed = 359.5054 E_impro = 34.3189 E_vdwl = -236.0428
E_coul = -1005.7613 E_long = -3346.9594 Press = -4.1617
---------------- Step 2100 ----- CPU = 17.3744 (sec) ----------------
TotEng = -2840.7272 KinEng = 569.9248 Temp = 214.5881
PotEng = -3410.6521 E_bond = 208.6289 E_angle = 610.0178
E_dihed = 373.4347 E_impro = 37.0381 E_vdwl = -212.0405
E_coul = -1081.0793 E_long = -3346.6517 Press = -68.5921
---------------- Step 2200 ----- CPU = 18.2957 (sec) ----------------
TotEng = -2848.3381 KinEng = 579.8884 Temp = 218.3396
PotEng = -3428.2265 E_bond = 211.6135 E_angle = 566.1155
E_dihed = 369.3071 E_impro = 41.5661 E_vdwl = -228.6990
E_coul = -1049.2589 E_long = -3338.8709 Press = -0.6188
---------------- Step 2300 ----- CPU = 19.2318 (sec) ----------------
TotEng = -2866.6022 KinEng = 554.9055 Temp = 208.9330
PotEng = -3421.5078 E_bond = 213.4553 E_angle = 581.9918
E_dihed = 345.5661 E_impro = 29.6695 E_vdwl = -225.0851
E_coul = -1025.8102 E_long = -3341.2951 Press = -54.2678
---------------- Step 2400 ----- CPU = 20.1702 (sec) ----------------
TotEng = -2736.2120 KinEng = 619.4005 Temp = 233.2167
PotEng = -3355.6126 E_bond = 244.4505 E_angle = 626.9133
E_dihed = 367.3306 E_impro = 29.8818 E_vdwl = -222.0040
E_coul = -1058.9434 E_long = -3343.2413 Press = 110.8718
---------------- Step 2500 ----- CPU = 21.1225 (sec) ----------------
TotEng = -2813.8735 KinEng = 583.8695 Temp = 219.8385
PotEng = -3397.7429 E_bond = 226.4043 E_angle = 598.3223
E_dihed = 361.7122 E_impro = 35.8640 E_vdwl = -206.9312
E_coul = -1068.6968 E_long = -3344.4179 Press = 19.4510
---------------- Step 2600 ----- CPU = 22.1046 (sec) ----------------
TotEng = -2816.9143 KinEng = 584.2235 Temp = 219.9718
PotEng = -3401.1378 E_bond = 224.0860 E_angle = 621.4548
E_dihed = 369.5020 E_impro = 36.2512 E_vdwl = -219.2208
E_coul = -1090.6300 E_long = -3342.5809 Press = -25.4161
---------------- Step 2700 ----- CPU = 23.1427 (sec) ----------------
TotEng = -2833.9038 KinEng = 566.1402 Temp = 213.1631
PotEng = -3400.0439 E_bond = 219.4478 E_angle = 599.9801
E_dihed = 363.9691 E_impro = 35.1792 E_vdwl = -226.3864
E_coul = -1047.2322 E_long = -3345.0016 Press = 35.2272
---------------- Step 2800 ----- CPU = 24.2100 (sec) ----------------
TotEng = -2812.4818 KinEng = 609.3098 Temp = 229.4173
PotEng = -3421.7917 E_bond = 223.5342 E_angle = 606.7627
E_dihed = 378.9288 E_impro = 40.0406 E_vdwl = -213.3048
E_coul = -1115.0387 E_long = -3342.7145 Press = 30.9634
---------------- Step 2900 ----- CPU = 25.2359 (sec) ----------------
TotEng = -2805.0268 KinEng = 596.5851 Temp = 224.6262
PotEng = -3401.6119 E_bond = 208.7705 E_angle = 619.2197
E_dihed = 368.9227 E_impro = 44.4224 E_vdwl = -221.0793
E_coul = -1077.2976 E_long = -3344.5703 Press = 0.5405
---------------- Step 3000 ----- CPU = 26.2911 (sec) ----------------
TotEng = -2800.8697 KinEng = 605.6835 Temp = 228.0519
PotEng = -3406.5532 E_bond = 229.1397 E_angle = 583.6455
E_dihed = 369.8828 E_impro = 35.2221 E_vdwl = -211.6751
E_coul = -1071.0650 E_long = -3341.7031 Press = -45.7465
---------------- Step 3100 ----- CPU = 27.3100 (sec) ----------------
TotEng = -2821.0600 KinEng = 592.4503 Temp = 223.0694
PotEng = -3413.5103 E_bond = 207.5049 E_angle = 594.6270
E_dihed = 364.3845 E_impro = 39.8842 E_vdwl = -218.3073
E_coul = -1058.0689 E_long = -3343.5348 Press = 6.3405
---------------- Step 3200 ----- CPU = 28.3245 (sec) ----------------
TotEng = -2790.9473 KinEng = 595.6527 Temp = 224.2751
PotEng = -3386.6000 E_bond = 226.8372 E_angle = 625.9104
E_dihed = 364.6819 E_impro = 39.3205 E_vdwl = -212.4097
E_coul = -1090.7715 E_long = -3340.1687 Press = -15.3432
---------------- Step 3300 ----- CPU = 29.3831 (sec) ----------------
TotEng = -2796.5252 KinEng = 604.8560 Temp = 227.7403
PotEng = -3401.3812 E_bond = 244.9208 E_angle = 605.3152
E_dihed = 375.6013 E_impro = 35.8121 E_vdwl = -234.8673
E_coul = -1084.0989 E_long = -3344.0644 Press = -69.1298
---------------- Step 3400 ----- CPU = 30.4870 (sec) ----------------
TotEng = -2768.1826 KinEng = 623.6692 Temp = 234.8239
PotEng = -3391.8518 E_bond = 217.6554 E_angle = 611.2002
E_dihed = 358.2967 E_impro = 38.4652 E_vdwl = -220.0592
E_coul = -1051.5656 E_long = -3345.8445 Press = 41.0213
---------------- Step 3500 ----- CPU = 31.6175 (sec) ----------------
TotEng = -2772.6252 KinEng = 628.0355 Temp = 236.4679
PotEng = -3400.6607 E_bond = 229.9673 E_angle = 602.8571
E_dihed = 363.3657 E_impro = 40.5411 E_vdwl = -219.5383
E_coul = -1074.1100 E_long = -3343.7434 Press = 148.0665
---------------- Step 3600 ----- CPU = 32.7615 (sec) ----------------
TotEng = -2756.7832 KinEng = 635.2297 Temp = 239.1767
PotEng = -3392.0130 E_bond = 223.8752 E_angle = 629.9327
E_dihed = 381.0499 E_impro = 31.9181 E_vdwl = -202.2525
E_coul = -1115.7155 E_long = -3340.8208 Press = -170.4982
---------------- Step 3700 ----- CPU = 33.8950 (sec) ----------------
TotEng = -2745.8971 KinEng = 641.2694 Temp = 241.4507
PotEng = -3387.1665 E_bond = 236.0180 E_angle = 604.4242
E_dihed = 385.0115 E_impro = 33.4784 E_vdwl = -201.2400
E_coul = -1102.8025 E_long = -3342.0561 Press = 116.4307
---------------- Step 3800 ----- CPU = 35.0163 (sec) ----------------
TotEng = -2755.6607 KinEng = 645.3185 Temp = 242.9753
PotEng = -3400.9792 E_bond = 226.7585 E_angle = 593.9302
E_dihed = 370.7085 E_impro = 36.8293 E_vdwl = -190.9386
E_coul = -1091.2447 E_long = -3347.0224 Press = 257.0583
---------------- Step 3900 ----- CPU = 36.1502 (sec) ----------------
TotEng = -2798.0422 KinEng = 619.8708 Temp = 233.3937
PotEng = -3417.9130 E_bond = 216.0354 E_angle = 589.9940
E_dihed = 373.7881 E_impro = 34.0169 E_vdwl = -233.6795
E_coul = -1049.2242 E_long = -3348.8435 Press = 80.2274
---------------- Step 4000 ----- CPU = 37.3067 (sec) ----------------
TotEng = -2705.8005 KinEng = 665.6801 Temp = 250.6419
PotEng = -3371.4807 E_bond = 264.5680 E_angle = 591.4868
E_dihed = 352.8245 E_impro = 33.8195 E_vdwl = -213.0503
E_coul = -1053.2507 E_long = -3347.8784 Press = 74.3631
---------------- Step 4100 ----- CPU = 38.4122 (sec) ----------------
TotEng = -2752.6654 KinEng = 636.8851 Temp = 239.8000
PotEng = -3389.5505 E_bond = 239.5334 E_angle = 590.5211
E_dihed = 378.9495 E_impro = 38.3818 E_vdwl = -220.9157
E_coul = -1067.2138 E_long = -3348.8068 Press = -107.6075
---------------- Step 4200 ----- CPU = 39.5014 (sec) ----------------
TotEng = -2765.1769 KinEng = 623.1864 Temp = 234.6421
PotEng = -3388.3633 E_bond = 223.6098 E_angle = 619.8623
E_dihed = 375.5639 E_impro = 39.6123 E_vdwl = -224.0185
E_coul = -1070.2010 E_long = -3352.7920 Press = -234.4084
---------------- Step 4300 ----- CPU = 40.6059 (sec) ----------------
TotEng = -2717.3032 KinEng = 653.4752 Temp = 246.0465
PotEng = -3370.7784 E_bond = 234.9615 E_angle = 607.5922
E_dihed = 393.9374 E_impro = 38.8199 E_vdwl = -221.7391
E_coul = -1074.8529 E_long = -3349.4974 Press = -27.5271
---------------- Step 4400 ----- CPU = 41.6876 (sec) ----------------
TotEng = -2783.5499 KinEng = 620.4917 Temp = 233.6275
PotEng = -3404.0416 E_bond = 222.1994 E_angle = 604.8699
E_dihed = 386.0154 E_impro = 36.0632 E_vdwl = -213.4643
E_coul = -1088.8703 E_long = -3350.8550 Press = 82.1988
---------------- Step 4500 ----- CPU = 42.7669 (sec) ----------------
TotEng = -2721.8812 KinEng = 660.9223 Temp = 248.8504
PotEng = -3382.8036 E_bond = 235.0157 E_angle = 623.4054
E_dihed = 361.5998 E_impro = 30.0694 E_vdwl = -196.3192
E_coul = -1087.4447 E_long = -3349.1300 Press = 6.0321
---------------- Step 4600 ----- CPU = 43.8528 (sec) ----------------
TotEng = -2719.4559 KinEng = 666.3429 Temp = 250.8914
PotEng = -3385.7988 E_bond = 219.1695 E_angle = 631.7745
E_dihed = 375.5102 E_impro = 39.6799 E_vdwl = -219.3157
E_coul = -1087.6117 E_long = -3345.0056 Press = 38.0280
---------------- Step 4700 ----- CPU = 44.9336 (sec) ----------------
TotEng = -2689.2061 KinEng = 681.8515 Temp = 256.7307
PotEng = -3371.0576 E_bond = 246.1648 E_angle = 605.1298
E_dihed = 376.2968 E_impro = 33.5041 E_vdwl = -213.1195
E_coul = -1069.0449 E_long = -3349.9887 Press = -58.9647
---------------- Step 4800 ----- CPU = 46.0101 (sec) ----------------
TotEng = -2698.1496 KinEng = 643.8263 Temp = 242.4134
PotEng = -3341.9759 E_bond = 267.0239 E_angle = 614.0844
E_dihed = 394.9058 E_impro = 42.4623 E_vdwl = -206.4540
E_coul = -1105.4257 E_long = -3348.5725 Press = 101.1932
---------------- Step 4900 ----- CPU = 47.1068 (sec) ----------------
TotEng = -2705.1842 KinEng = 666.5820 Temp = 250.9814
PotEng = -3371.7662 E_bond = 250.0471 E_angle = 632.1282
E_dihed = 385.5483 E_impro = 41.7445 E_vdwl = -211.4084
E_coul = -1122.4043 E_long = -3347.4214 Press = 133.6209
---------------- Step 5000 ----- CPU = 48.1741 (sec) ----------------
TotEng = -2690.0438 KinEng = 679.6710 Temp = 255.9097
PotEng = -3369.7148 E_bond = 243.0323 E_angle = 607.4697
E_dihed = 382.6331 E_impro = 35.4124 E_vdwl = -204.7224
E_coul = -1085.6309 E_long = -3347.9090 Press = 66.3863
---------------- Step 5100 ----- CPU = 49.1934 (sec) ----------------
TotEng = -2718.3458 KinEng = 650.7864 Temp = 245.0341
PotEng = -3369.1322 E_bond = 268.8298 E_angle = 589.1404
E_dihed = 377.7868 E_impro = 33.5961 E_vdwl = -203.6094
E_coul = -1085.7743 E_long = -3349.1017 Press = 47.6541
---------------- Step 5200 ----- CPU = 50.2147 (sec) ----------------
TotEng = -2639.5739 KinEng = 676.4342 Temp = 254.6910
PotEng = -3316.0081 E_bond = 270.2839 E_angle = 616.8283
E_dihed = 382.5201 E_impro = 32.7417 E_vdwl = -206.2442
E_coul = -1066.9338 E_long = -3345.2041 Press = 128.4308
---------------- Step 5300 ----- CPU = 51.2539 (sec) ----------------
TotEng = -2741.2287 KinEng = 646.9560 Temp = 243.5918
PotEng = -3388.1847 E_bond = 232.3573 E_angle = 599.5414
E_dihed = 373.7950 E_impro = 39.2636 E_vdwl = -190.9456
E_coul = -1094.9975 E_long = -3347.1989 Press = 39.6030
---------------- Step 5400 ----- CPU = 52.2903 (sec) ----------------
TotEng = -2667.7852 KinEng = 676.4295 Temp = 254.6892
PotEng = -3344.2147 E_bond = 248.9502 E_angle = 610.3430
E_dihed = 370.7076 E_impro = 38.4238 E_vdwl = -201.8432
E_coul = -1065.7313 E_long = -3345.0649 Press = -17.3072
---------------- Step 5500 ----- CPU = 53.3868 (sec) ----------------
TotEng = -2618.3856 KinEng = 709.8931 Temp = 267.2889
PotEng = -3328.2787 E_bond = 265.2067 E_angle = 625.4374
E_dihed = 367.5087 E_impro = 39.5594 E_vdwl = -214.1194
E_coul = -1063.8651 E_long = -3348.0062 Press = -33.5344
---------------- Step 5600 ----- CPU = 54.4341 (sec) ----------------
TotEng = -2691.7785 KinEng = 667.4646 Temp = 251.3137
PotEng = -3359.2431 E_bond = 259.9639 E_angle = 619.5561
E_dihed = 364.2642 E_impro = 36.3273 E_vdwl = -209.9347
E_coul = -1076.2202 E_long = -3353.1996 Press = -74.4756
---------------- Step 5700 ----- CPU = 55.4793 (sec) ----------------
TotEng = -2637.4348 KinEng = 679.9362 Temp = 256.0096
PotEng = -3317.3711 E_bond = 278.8708 E_angle = 631.3769
E_dihed = 369.3027 E_impro = 46.9496 E_vdwl = -220.0221
E_coul = -1075.7000 E_long = -3348.1489 Press = -70.5946
---------------- Step 5800 ----- CPU = 56.7026 (sec) ----------------
TotEng = -2639.8817 KinEng = 698.8775 Temp = 263.1413
PotEng = -3338.7593 E_bond = 269.2954 E_angle = 640.7389
E_dihed = 372.2218 E_impro = 41.3429 E_vdwl = -203.7486
E_coul = -1113.1393 E_long = -3345.4703 Press = 23.9140
---------------- Step 5900 ----- CPU = 57.8644 (sec) ----------------
TotEng = -2636.8636 KinEng = 687.3225 Temp = 258.7906
PotEng = -3324.1861 E_bond = 266.1703 E_angle = 633.7779
E_dihed = 382.5408 E_impro = 45.3265 E_vdwl = -219.9335
E_coul = -1085.6019 E_long = -3346.4662 Press = 72.7649
---------------- Step 6000 ----- CPU = 59.1325 (sec) ----------------
TotEng = -2642.0181 KinEng = 696.5373 Temp = 262.2602
PotEng = -3338.5555 E_bond = 274.6781 E_angle = 612.2951
E_dihed = 384.2396 E_impro = 38.0117 E_vdwl = -233.4111
E_coul = -1063.8623 E_long = -3350.5066 Press = -66.3283
---------------- Step 6100 ----- CPU = 60.1394 (sec) ----------------
TotEng = -2658.2404 KinEng = 698.9154 Temp = 263.1556
PotEng = -3357.1557 E_bond = 250.1548 E_angle = 629.4120
E_dihed = 389.6450 E_impro = 40.6762 E_vdwl = -188.3455
E_coul = -1132.1292 E_long = -3346.5690 Press = -22.0575
---------------- Step 6200 ----- CPU = 61.1504 (sec) ----------------
TotEng = -2627.5121 KinEng = 675.8056 Temp = 254.4543
PotEng = -3303.3178 E_bond = 285.5432 E_angle = 649.4580
E_dihed = 367.0916 E_impro = 37.4803 E_vdwl = -205.4177
E_coul = -1089.2814 E_long = -3348.1917 Press = 65.1194
---------------- Step 6300 ----- CPU = 62.1485 (sec) ----------------
TotEng = -2649.4791 KinEng = 701.8256 Temp = 264.2514
PotEng = -3351.3047 E_bond = 245.5603 E_angle = 620.7601
E_dihed = 366.4822 E_impro = 32.2945 E_vdwl = -202.5462
E_coul = -1064.1603 E_long = -3349.6953 Press = 66.7680
---------------- Step 6400 ----- CPU = 63.1024 (sec) ----------------
TotEng = -2615.3793 KinEng = 685.3284 Temp = 258.0398
PotEng = -3300.7078 E_bond = 286.5668 E_angle = 640.5455
E_dihed = 386.7913 E_impro = 40.7469 E_vdwl = -213.7469
E_coul = -1094.8410 E_long = -3346.7704 Press = -87.4649
---------------- Step 6500 ----- CPU = 64.2024 (sec) ----------------
TotEng = -2623.5579 KinEng = 702.7035 Temp = 264.5819
PotEng = -3326.2614 E_bond = 274.2893 E_angle = 654.2571
E_dihed = 394.4634 E_impro = 45.5613 E_vdwl = -210.0465
E_coul = -1135.3767 E_long = -3349.4094 Press = -102.8119
---------------- Step 6600 ----- CPU = 65.2026 (sec) ----------------
TotEng = -2638.5775 KinEng = 701.7603 Temp = 264.2267
PotEng = -3340.3378 E_bond = 259.5340 E_angle = 632.1634
E_dihed = 375.3988 E_impro = 43.9779 E_vdwl = -230.3763
E_coul = -1074.3260 E_long = -3346.7095 Press = 37.7095
---------------- Step 6700 ----- CPU = 66.1808 (sec) ----------------
TotEng = -2600.9605 KinEng = 672.3633 Temp = 253.1582
PotEng = -3273.3237 E_bond = 282.9391 E_angle = 658.1793
E_dihed = 388.2013 E_impro = 39.8216 E_vdwl = -196.7876
E_coul = -1102.6347 E_long = -3343.0428 Press = 21.1898
---------------- Step 6800 ----- CPU = 67.2077 (sec) ----------------
TotEng = -2562.6791 KinEng = 724.5615 Temp = 272.8118
PotEng = -3287.2406 E_bond = 262.1170 E_angle = 669.0895
E_dihed = 392.0846 E_impro = 43.2389 E_vdwl = -214.8113
E_coul = -1093.8243 E_long = -3345.1350 Press = 2.2031
---------------- Step 6900 ----- CPU = 68.2164 (sec) ----------------
TotEng = -2610.2279 KinEng = 728.8392 Temp = 274.4225
PotEng = -3339.0672 E_bond = 265.7486 E_angle = 634.3539
E_dihed = 368.8325 E_impro = 44.7825 E_vdwl = -206.6867
E_coul = -1095.9447 E_long = -3350.1534 Press = 8.1500
---------------- Step 7000 ----- CPU = 69.2040 (sec) ----------------
TotEng = -2583.8942 KinEng = 723.9594 Temp = 272.5851
PotEng = -3307.8536 E_bond = 250.4931 E_angle = 674.8829
E_dihed = 364.1125 E_impro = 44.0458 E_vdwl = -209.2240
E_coul = -1078.4183 E_long = -3353.7458 Press = 60.3336
---------------- Step 7100 ----- CPU = 70.1968 (sec) ----------------
TotEng = -2671.6271 KinEng = 670.6363 Temp = 252.5079
PotEng = -3342.2633 E_bond = 251.1351 E_angle = 608.0784
E_dihed = 384.3346 E_impro = 42.1099 E_vdwl = -203.0523
E_coul = -1074.5328 E_long = -3350.3363 Press = 6.4404
---------------- Step 7200 ----- CPU = 71.2070 (sec) ----------------
TotEng = -2587.1092 KinEng = 724.3543 Temp = 272.7339
PotEng = -3311.4635 E_bond = 278.8064 E_angle = 618.7888
E_dihed = 378.5982 E_impro = 38.9323 E_vdwl = -224.0861
E_coul = -1052.8391 E_long = -3349.6641 Press = -148.3233
---------------- Step 7300 ----- CPU = 72.2566 (sec) ----------------
TotEng = -2611.3839 KinEng = 704.1644 Temp = 265.1319
PotEng = -3315.5482 E_bond = 265.3237 E_angle = 624.1887
E_dihed = 383.0346 E_impro = 33.4546 E_vdwl = -202.3121
E_coul = -1070.4710 E_long = -3348.7667 Press = 28.7777
---------------- Step 7400 ----- CPU = 73.3167 (sec) ----------------
TotEng = -2580.3735 KinEng = 731.9464 Temp = 275.5924
PotEng = -3312.3199 E_bond = 271.3923 E_angle = 653.2883
E_dihed = 387.7903 E_impro = 40.9721 E_vdwl = -216.2436
E_coul = -1099.9307 E_long = -3349.5887 Press = 40.7930
---------------- Step 7500 ----- CPU = 74.4021 (sec) ----------------
TotEng = -2561.7523 KinEng = 758.2828 Temp = 285.5086
PotEng = -3320.0351 E_bond = 250.6434 E_angle = 638.4208
E_dihed = 381.8732 E_impro = 33.3933 E_vdwl = -232.3592
E_coul = -1041.0990 E_long = -3350.9076 Press = -163.3964
---------------- Step 7600 ----- CPU = 75.4780 (sec) ----------------
TotEng = -2589.5416 KinEng = 703.7203 Temp = 264.9647
PotEng = -3293.2618 E_bond = 290.4004 E_angle = 613.3075
E_dihed = 403.2076 E_impro = 45.6446 E_vdwl = -220.7474
E_coul = -1073.5238 E_long = -3351.5508 Press = 17.4927
---------------- Step 7700 ----- CPU = 76.5394 (sec) ----------------
TotEng = -2552.9106 KinEng = 745.4133 Temp = 280.6630
PotEng = -3298.3239 E_bond = 262.1825 E_angle = 655.9648
E_dihed = 359.3331 E_impro = 39.2329 E_vdwl = -191.7072
E_coul = -1077.0139 E_long = -3346.3162 Press = 2.9227
---------------- Step 7800 ----- CPU = 77.6402 (sec) ----------------
TotEng = -2553.3323 KinEng = 716.1109 Temp = 269.6301
PotEng = -3269.4432 E_bond = 278.7606 E_angle = 673.4525
E_dihed = 386.2544 E_impro = 43.9885 E_vdwl = -194.0700
E_coul = -1107.9514 E_long = -3349.8777 Press = 217.1488
---------------- Step 7900 ----- CPU = 78.7755 (sec) ----------------
TotEng = -2539.4670 KinEng = 737.3598 Temp = 277.6307
PotEng = -3276.8268 E_bond = 281.1080 E_angle = 677.4869
E_dihed = 400.9276 E_impro = 38.0121 E_vdwl = -195.4162
E_coul = -1127.0467 E_long = -3351.8985 Press = 24.2521
---------------- Step 8000 ----- CPU = 79.9025 (sec) ----------------
TotEng = -2568.9887 KinEng = 693.7521 Temp = 261.2115
PotEng = -3262.7409 E_bond = 280.8859 E_angle = 648.7984
E_dihed = 390.2062 E_impro = 42.2797 E_vdwl = -204.2056
E_coul = -1068.2658 E_long = -3352.4398 Press = 50.7799
---------------- Step 8100 ----- CPU = 80.9714 (sec) ----------------
TotEng = -2507.6589 KinEng = 756.2905 Temp = 284.7585
PotEng = -3263.9494 E_bond = 272.3607 E_angle = 643.1893
E_dihed = 390.7346 E_impro = 43.7921 E_vdwl = -221.9076
E_coul = -1042.0029 E_long = -3350.1156 Press = 55.1611
---------------- Step 8200 ----- CPU = 82.0714 (sec) ----------------
TotEng = -2539.2889 KinEng = 731.4938 Temp = 275.4220
PotEng = -3270.7827 E_bond = 299.2908 E_angle = 633.9883
E_dihed = 407.1742 E_impro = 44.7311 E_vdwl = -226.8628
E_coul = -1082.1088 E_long = -3346.9955 Press = -195.9352
---------------- Step 8300 ----- CPU = 83.1859 (sec) ----------------
TotEng = -2539.0197 KinEng = 724.9100 Temp = 272.9431
PotEng = -3263.9297 E_bond = 283.0507 E_angle = 635.7486
E_dihed = 391.6461 E_impro = 47.4141 E_vdwl = -227.4207
E_coul = -1044.8692 E_long = -3349.4993 Press = 196.1783
---------------- Step 8400 ----- CPU = 84.3141 (sec) ----------------
TotEng = -2558.1335 KinEng = 692.8588 Temp = 260.8752
PotEng = -3250.9922 E_bond = 313.3163 E_angle = 639.3920
E_dihed = 396.0249 E_impro = 40.0074 E_vdwl = -210.1358
E_coul = -1078.3531 E_long = -3351.2439 Press = 4.5194
---------------- Step 8500 ----- CPU = 85.4733 (sec) ----------------
TotEng = -2502.7259 KinEng = 724.6475 Temp = 272.8442
PotEng = -3227.3734 E_bond = 284.1865 E_angle = 665.7531
E_dihed = 383.8394 E_impro = 41.2982 E_vdwl = -198.5376
E_coul = -1057.3008 E_long = -3346.6121 Press = -0.4963
---------------- Step 8600 ----- CPU = 86.6362 (sec) ----------------
TotEng = -2519.6432 KinEng = 748.8989 Temp = 281.9754
PotEng = -3268.5421 E_bond = 280.3056 E_angle = 647.5508
E_dihed = 381.5564 E_impro = 38.5243 E_vdwl = -222.0445
E_coul = -1043.5669 E_long = -3350.8679 Press = 57.4936
---------------- Step 8700 ----- CPU = 87.8342 (sec) ----------------
TotEng = -2502.4971 KinEng = 745.2389 Temp = 280.5973
PotEng = -3247.7360 E_bond = 286.5436 E_angle = 647.3502
E_dihed = 397.2023 E_impro = 40.1624 E_vdwl = -236.4788
E_coul = -1031.9453 E_long = -3350.5703 Press = -148.2869
---------------- Step 8800 ----- CPU = 89.0596 (sec) ----------------
TotEng = -2525.8157 KinEng = 770.9340 Temp = 290.2720
PotEng = -3296.7497 E_bond = 264.1415 E_angle = 658.0740
E_dihed = 382.6677 E_impro = 40.9639 E_vdwl = -205.6787
E_coul = -1087.0299 E_long = -3349.8880 Press = 95.5612
---------------- Step 8900 ----- CPU = 90.2507 (sec) ----------------
TotEng = -2546.7077 KinEng = 741.1956 Temp = 279.0749
PotEng = -3287.9033 E_bond = 278.2574 E_angle = 633.0581
E_dihed = 387.9287 E_impro = 37.9069 E_vdwl = -203.2470
E_coul = -1073.8560 E_long = -3347.9513 Press = -26.2635
---------------- Step 9000 ----- CPU = 91.4197 (sec) ----------------
TotEng = -2478.3198 KinEng = 768.2832 Temp = 289.2739
PotEng = -3246.6029 E_bond = 294.8001 E_angle = 639.8547
E_dihed = 402.1436 E_impro = 40.1159 E_vdwl = -197.3402
E_coul = -1076.9300 E_long = -3349.2471 Press = -2.0699
---------------- Step 9100 ----- CPU = 92.5984 (sec) ----------------
TotEng = -2453.2127 KinEng = 783.3521 Temp = 294.9477
PotEng = -3236.5648 E_bond = 285.7790 E_angle = 681.6460
E_dihed = 389.9879 E_impro = 38.8501 E_vdwl = -195.6240
E_coul = -1085.0324 E_long = -3352.1713 Press = -36.9688
---------------- Step 9200 ----- CPU = 93.7461 (sec) ----------------
TotEng = -2499.6290 KinEng = 780.9980 Temp = 294.0613
PotEng = -3280.6269 E_bond = 258.1971 E_angle = 656.4037
E_dihed = 415.3252 E_impro = 43.9988 E_vdwl = -197.5481
E_coul = -1107.6397 E_long = -3349.3641 Press = 2.6065
---------------- Step 9300 ----- CPU = 94.9015 (sec) ----------------
TotEng = -2483.8592 KinEng = 771.9550 Temp = 290.6565
PotEng = -3255.8142 E_bond = 251.3260 E_angle = 651.7911
E_dihed = 395.2096 E_impro = 45.8175 E_vdwl = -207.5446
E_coul = -1038.9219 E_long = -3353.4920 Press = -93.5436
---------------- Step 9400 ----- CPU = 96.0353 (sec) ----------------
TotEng = -2499.5972 KinEng = 759.6639 Temp = 286.0286
PotEng = -3259.2611 E_bond = 301.8034 E_angle = 651.2119
E_dihed = 380.7301 E_impro = 41.0984 E_vdwl = -201.0687
E_coul = -1089.2419 E_long = -3343.7943 Press = 54.1903
---------------- Step 9500 ----- CPU = 97.2038 (sec) ----------------
TotEng = -2465.0641 KinEng = 772.4729 Temp = 290.8515
PotEng = -3237.5371 E_bond = 288.0443 E_angle = 650.8313
E_dihed = 389.6729 E_impro = 41.9942 E_vdwl = -204.2369
E_coul = -1055.5641 E_long = -3348.2788 Press = 253.5358
---------------- Step 9600 ----- CPU = 98.3444 (sec) ----------------
TotEng = -2454.8975 KinEng = 775.3714 Temp = 291.9428
PotEng = -3230.2690 E_bond = 290.6612 E_angle = 667.0602
E_dihed = 397.7066 E_impro = 40.5540 E_vdwl = -199.2071
E_coul = -1079.3474 E_long = -3347.6966 Press = -125.8373
---------------- Step 9700 ----- CPU = 99.5046 (sec) ----------------
TotEng = -2474.3183 KinEng = 758.2548 Temp = 285.4980
PotEng = -3232.5731 E_bond = 288.4343 E_angle = 640.0007
E_dihed = 387.3168 E_impro = 41.1179 E_vdwl = -196.9761
E_coul = -1049.1551 E_long = -3343.3117 Press = -72.4768
---------------- Step 9800 ----- CPU = 100.6870 (sec) ----------------
TotEng = -2453.2239 KinEng = 788.4898 Temp = 296.8821
PotEng = -3241.7136 E_bond = 289.7848 E_angle = 661.9942
E_dihed = 403.1469 E_impro = 48.9315 E_vdwl = -220.4897
E_coul = -1080.7211 E_long = -3344.3602 Press = 50.2150
---------------- Step 9900 ----- CPU = 101.9692 (sec) ----------------
TotEng = -2469.0982 KinEng = 750.0546 Temp = 282.4105
PotEng = -3219.1528 E_bond = 300.4243 E_angle = 675.8282
E_dihed = 381.7571 E_impro = 45.1724 E_vdwl = -205.3894
E_coul = -1070.5857 E_long = -3346.3597 Press = 18.6819
---------------- Step 10000 ----- CPU = 103.1045 (sec) ----------------
TotEng = -2400.7511 KinEng = 802.5598 Temp = 302.1798
PotEng = -3203.3108 E_bond = 319.6964 E_angle = 669.0748
E_dihed = 388.7344 E_impro = 37.7315 E_vdwl = -213.4412
E_coul = -1054.4866 E_long = -3350.6201 Press = -0.9821
---------------- Step 10100 ----- CPU = 104.2434 (sec) ----------------
TotEng = -2445.9431 KinEng = 741.7575 Temp = 279.2865
PotEng = -3187.7006 E_bond = 312.9035 E_angle = 693.1337
E_dihed = 387.5051 E_impro = 35.2610 E_vdwl = -220.0853
E_coul = -1053.2056 E_long = -3343.2130 Press = 16.3496
---------------- Step 10200 ----- CPU = 105.3326 (sec) ----------------
TotEng = -2481.2457 KinEng = 769.3572 Temp = 289.6783
PotEng = -3250.6029 E_bond = 285.3717 E_angle = 659.7050
E_dihed = 386.7808 E_impro = 46.0416 E_vdwl = -223.7107
E_coul = -1057.4401 E_long = -3347.3513 Press = 54.9084
---------------- Step 10241 ----- CPU = 105.7807 (sec) ----------------
TotEng = -2420.1593 KinEng = 795.8536 Temp = 299.6547
PotEng = -3216.0129 E_bond = 293.2238 E_angle = 687.0481
E_dihed = 391.7794 E_impro = 42.2440 E_vdwl = -212.7813
E_coul = -1068.1771 E_long = -3349.3499 Press = -222.8824
Loop time of 105.781 on 4 procs for 10000 steps with 892 atoms
Performance: 65.342 ns/day, 0.367 hours/ns, 94.535 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 39.09 | 52.202 | 70.573 | 172.3 | 49.35
Bond | 6.9312 | 11.89 | 20.202 | 158.1 | 11.24
Kspace | 3.5986 | 3.705 | 3.7795 | 3.7 | 3.50
Neigh | 1.8 | 1.8103 | 1.8167 | 0.5 | 1.71
Comm | 6.6943 | 33.81 | 52.135 | 312.3 | 31.96
Output | 0.032599 | 0.037222 | 0.050519 | 4.0 | 0.04
Modify | 1.698 | 1.9657 | 2.4226 | 21.2 | 1.86
Other | | 0.3609 | | | 0.34
Nlocal: 223 ave 399 max 98 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 620.5 ave 721 max 506 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 34950.2 ave 53363 max 19496 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 139801
Ave neighs/atom = 156.728
Ave special neighs/atom = 10.9395
Neighbor list builds = 1683
Dangerous builds = 1
unfix cor
unfix 1
write_restart BPTI_equil
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 3549 1024
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:46

10
examples/USER/misc/filter-corotate/bpti/system.in.init
View File

@ -1,10 +0,0 @@
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4

0
examples/USER/misc/filter-corotate/bpti/4pti.data → examples/USER/misc/filter-corotate/data.bpti
View File

0
examples/USER/misc/filter-corotate/peptide/data.peptide → examples/USER/misc/filter-corotate/data.peptide
View File

21
examples/USER/misc/filter-corotate/bpti/4pti.in → examples/USER/misc/filter-corotate/in.bpti
View File

@ -1,18 +1,26 @@
units real
neigh_modify delay 2 every 1
include system.in.init
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
read_data 4pti.data
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.bpti
special_bonds charmm
neigh_modify delay 2 every 1
# ------------- MINIMIZE ----------
minimize 1e-4 1e-6 1000 10000
reset_timestep 0
# ------------- RUN ---------------
@ -23,14 +31,13 @@ timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
velocity all create 200.0 12345678 dist uniform
dump dump1 all atom 100 4pti.dump
#dump dump1 all atom 100 4pti.dump
fix 1 all nvt temp 200 300 25
fix cor all filter/corotate m 1.0
run 10000
run 1000
unfix cor
unfix 1
write_restart BPTI_equil

6
examples/USER/misc/filter-corotate/peptide/in.equil → examples/USER/misc/filter-corotate/in.peptide
View File

@ -1,4 +1,4 @@
# Solvated 5-mer peptide, run for 20ps in NVT
# Solvated 5-mer peptide, run for 8ps in NVT
units real
atom_style full
@ -16,7 +16,7 @@ neighbor 2.0 bin
neigh_modify delay 5
thermo 50
dump dump1 all atom 100 peptide.dump
#dump dump1 all atom 100 peptide.dump
timestep 8
@ -24,7 +24,7 @@ run_style respa 3 2 8 bond 1 pair 2 kspace 3
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
run 2500
run 1000
unfix cor
unfix 1

240
examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.1 Normal file
View File

@ -0,0 +1,240 @@
LAMMPS (10 Mar 2017)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.bpti
orthogonal box = (-10 -10 -30) to (50 50 30)
1 by 1 by 1 MPI processor grid
reading atoms ...
892 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
906 bonds
reading angles ...
1626 angles
reading dihedrals ...
2501 dihedrals
reading impropers ...
137 impropers
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special_bonds charmm
neigh_modify delay 2 every 1
# ------------- MINIMIZE ----------
minimize 1e-4 1e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 9261 4096
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
241 0 -4503.313 749.58662 -3753.7264 -29.045104
Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2131.73812515 -3753.43984087 -3753.72636847
Force two-norm initial, final = 1086.21 26.3688
Force max component initial, final = 310.811 3.92748
Final line search alpha, max atom move = 0.00596649 0.0234333
Iterations, force evaluations = 241 463
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48
Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23
Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91
Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08
Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009358 | | | 0.28
Nlocal: 892 ave 892 max 892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 148891 ave 148891 max 148891 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 148891
Ave neighs/atom = 166.918
Ave special neighs/atom = 10.9395
Neighbor list builds = 15
Dangerous builds = 0
reset_timestep 0
# ------------- RUN ---------------
thermo 100
thermo_style multi
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
velocity all create 200.0 12345678 dist uniform
#dump dump1 all atom 100 4pti.dump
fix 1 all nvt temp 200 300 25
fix cor all filter/corotate m 1.0
163 = # of size 2 clusters
0 = # of size 3 clusters
25 = # of size 4 clusters
0 = # of size 5 clusters
100 = # of frozen angles
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 9261 4096
Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283
---------------- Step 100 ----- CPU = 3.9414 (sec) ----------------
TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014
PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317
E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451
E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662
---------------- Step 200 ----- CPU = 7.9028 (sec) ----------------
TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265
PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773
E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808
E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000
---------------- Step 300 ----- CPU = 11.8246 (sec) ----------------
TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346
PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860
E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236
E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527
---------------- Step 400 ----- CPU = 15.7990 (sec) ----------------
TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922
PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026
E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790
E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958
---------------- Step 500 ----- CPU = 19.8146 (sec) ----------------
TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568
PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605
E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657
E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200
---------------- Step 600 ----- CPU = 23.8587 (sec) ----------------
TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557
PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922
E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425
E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737
---------------- Step 700 ----- CPU = 27.8381 (sec) ----------------
TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888
PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785
E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159
E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484
---------------- Step 800 ----- CPU = 31.8039 (sec) ----------------
TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163
PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631
E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523
E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337
---------------- Step 900 ----- CPU = 35.7700 (sec) ----------------
TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776
PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664
E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389
E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720
---------------- Step 1000 ----- CPU = 39.7695 (sec) ----------------
TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490
PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543
E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030
E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910
Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms
Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 29.169 | 29.169 | 29.169 | 0.0 | 73.34
Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17
Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90
Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20
Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04
Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00
Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02
Other | | 0.1266 | | | 0.32
Nlocal: 892 ave 892 max 892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 146206 ave 146206 max 146206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 146206
Ave neighs/atom = 163.908
Ave special neighs/atom = 10.9395
Neighbor list builds = 186
Dangerous builds = 0
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:43

240
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LAMMPS (10 Mar 2017)
using 1 OpenMP thread(s) per MPI task
units real
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.bpti
orthogonal box = (-10 -10 -30) to (50 50 30)
1 by 2 by 2 MPI processor grid
reading atoms ...
892 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
906 bonds
reading angles ...
1626 angles
reading dihedrals ...
2501 dihedrals
reading impropers ...
137 impropers
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special_bonds charmm
neigh_modify delay 2 every 1
# ------------- MINIMIZE ----------
minimize 1e-4 1e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302)
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 3549 1024
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
241 0 -4503.3131 749.58666 -3753.7264 -29.045153
Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2131.73812515 -3753.43983927 -3753.72640137
Force two-norm initial, final = 1086.21 26.3688
Force max component initial, final = 310.811 3.92751
Final line search alpha, max atom move = 0.00596649 0.0234334
Iterations, force evaluations = 241 463
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34267 | 0.63792 | 0.90268 | 25.2 | 50.39
Bond | 0.025776 | 0.063318 | 0.095631 | 10.8 | 5.00
Kspace | 0.21904 | 0.51601 | 0.84895 | 31.3 | 40.76
Neigh | 0.023185 | 0.023363 | 0.023538 | 0.1 | 1.85
Comm | 0.012025 | 0.014189 | 0.016335 | 1.4 | 1.12
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01114 | | | 0.88
Nlocal: 223 ave 323 max 89 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 613 ave 675 max 557 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 37222.8 ave 50005 max 20830 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 148891
Ave neighs/atom = 166.918
Ave special neighs/atom = 10.9395
Neighbor list builds = 15
Dangerous builds = 0
reset_timestep 0
# ------------- RUN ---------------
thermo 100
thermo_style multi
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
velocity all create 200.0 12345678 dist uniform
#dump dump1 all atom 100 4pti.dump
fix 1 all nvt temp 200 300 25
fix cor all filter/corotate m 1.0
163 = # of size 2 clusters
0 = # of size 3 clusters
25 = # of size 4 clusters
0 = # of size 5 clusters
100 = # of frozen angles
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.203272
grid = 16 16 16
stencil order = 5
estimated absolute RMS force accuracy = 0.0316399
estimated relative force accuracy = 9.52826e-05
using double precision FFTs
3d grid and FFT values/proc = 3549 1024
Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000
PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2592
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2282
---------------- Step 100 ----- CPU = 1.5457 (sec) ----------------
TotEng = -2718.9184 KinEng = 538.6205 Temp = 202.8014
PotEng = -3257.5389 E_bond = 203.3365 E_angle = 566.5311
E_dihed = 397.6202 E_impro = 34.6621 E_vdwl = -248.7451
E_coul = -874.5326 E_long = -3336.4111 Press = 135.8435
---------------- Step 200 ----- CPU = 3.0720 (sec) ----------------
TotEng = -2660.1146 KinEng = 626.3474 Temp = 235.8323
PotEng = -3286.4620 E_bond = 209.5168 E_angle = 591.7735
E_dihed = 388.9615 E_impro = 29.5000 E_vdwl = -243.5840
E_coul = -923.4998 E_long = -3339.1299 Press = 88.8857
---------------- Step 300 ----- CPU = 4.5597 (sec) ----------------
TotEng = -2669.7442 KinEng = 619.3625 Temp = 233.2023
PotEng = -3289.1067 E_bond = 203.4405 E_angle = 569.5281
E_dihed = 378.3314 E_impro = 38.2880 E_vdwl = -221.1904
E_coul = -915.3396 E_long = -3342.1646 Press = 79.3780
---------------- Step 400 ----- CPU = 5.9808 (sec) ----------------
TotEng = -2618.9975 KinEng = 644.6145 Temp = 242.7102
PotEng = -3263.6119 E_bond = 209.5864 E_angle = 618.8954
E_dihed = 401.3798 E_impro = 39.9064 E_vdwl = -212.1271
E_coul = -977.1589 E_long = -3344.0940 Press = -7.8938
---------------- Step 500 ----- CPU = 7.4159 (sec) ----------------
TotEng = -2579.7486 KinEng = 666.4643 Temp = 250.9371
PotEng = -3246.2129 E_bond = 219.2549 E_angle = 620.3474
E_dihed = 388.4395 E_impro = 41.4499 E_vdwl = -225.9686
E_coul = -949.3689 E_long = -3340.3672 Press = 113.2543
---------------- Step 600 ----- CPU = 8.9252 (sec) ----------------
TotEng = -2535.8235 KinEng = 708.5919 Temp = 266.7990
PotEng = -3244.4154 E_bond = 243.9451 E_angle = 606.0866
E_dihed = 400.0562 E_impro = 33.9708 E_vdwl = -223.1319
E_coul = -964.9940 E_long = -3340.3482 Press = -102.4475
---------------- Step 700 ----- CPU = 10.4022 (sec) ----------------
TotEng = -2552.6681 KinEng = 702.3080 Temp = 264.4330
PotEng = -3254.9761 E_bond = 250.8834 E_angle = 639.0977
E_dihed = 386.4014 E_impro = 42.3004 E_vdwl = -224.4816
E_coul = -1011.8551 E_long = -3337.3222 Press = 10.6424
---------------- Step 800 ----- CPU = 11.8699 (sec) ----------------
TotEng = -2423.5415 KinEng = 772.1254 Temp = 290.7206
PotEng = -3195.6670 E_bond = 238.5831 E_angle = 640.9180
E_dihed = 377.7994 E_impro = 40.3135 E_vdwl = -216.5705
E_coul = -935.1087 E_long = -3341.6019 Press = -38.2479
---------------- Step 900 ----- CPU = 13.3548 (sec) ----------------
TotEng = -2394.4779 KinEng = 766.6895 Temp = 288.6739
PotEng = -3161.1673 E_bond = 284.8428 E_angle = 671.0959
E_dihed = 380.3406 E_impro = 51.2975 E_vdwl = -219.5211
E_coul = -990.6305 E_long = -3338.5925 Press = -15.2279
---------------- Step 1000 ----- CPU = 14.7908 (sec) ----------------
TotEng = -2340.1471 KinEng = 799.0198 Temp = 300.8469
PotEng = -3139.1669 E_bond = 271.0389 E_angle = 683.8278
E_dihed = 407.0795 E_impro = 39.6209 E_vdwl = -230.5355
E_coul = -974.2981 E_long = -3335.9003 Press = -94.3420
Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms
Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4184 | 7.5543 | 10.133 | 74.2 | 51.07
Bond | 0.94027 | 1.9781 | 2.7492 | 54.4 | 13.37
Kspace | 0.45487 | 0.45887 | 0.46343 | 0.4 | 3.10
Neigh | 0.28145 | 0.28339 | 0.28539 | 0.3 | 1.92
Comm | 0.7515 | 4.1484 | 8.3861 | 135.5 | 28.05
Output | 0.00049973 | 0.00055474 | 0.00066924 | 0.0 | 0.00
Modify | 0.26165 | 0.31142 | 0.35023 | 6.7 | 2.11
Other | | 0.05572 | | | 0.38
Nlocal: 223 ave 313 max 122 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 584.5 ave 605 max 553 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 35448 ave 42093 max 25175 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 141792
Ave neighs/atom = 158.96
Ave special neighs/atom = 10.9395
Neighbor list builds = 186
Dangerous builds = 0
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:16

146
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LAMMPS (10 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
thermo 50
#dump dump1 all atom 100 peptide.dump
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
19 = # of size 2 clusters
0 = # of size 3 clusters
3 = # of size 4 clusters
0 = # of size 5 clusters
646 = # of frozen angles
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891
100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465
150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489
200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332
250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345
300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757
350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063
400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091
450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559
500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032
550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399
600 249.05313 -7509.6729 741.48104 -5281.2046 992.87
650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176
700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021
750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421
800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565
850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478
900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228
950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117
1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659
Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms
Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14
Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72
Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35
Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91
Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13
Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00
Modify | 2 | 2 | 2 | 0.0 | 1.33
Other | | 0.6352 | | | 0.42
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11197 ave 11197 max 11197 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 707779 ave 707779 max 707779 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 707779
Ave neighs/atom = 353.183
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 200
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:30

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LAMMPS (10 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
thermo 50
#dump dump1 all atom 100 peptide.dump
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
19 = # of size 2 clusters
0 = # of size 3 clusters
3 = # of size 4 clusters
0 = # of size 5 clusters
646 = # of frozen angles
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891
100 242.81819 -7125.5629 416.08082 -5259.7209 15525.244
150 235.94928 -7531.9186 932.50658 -5190.6621 -14842.431
200 255.85551 -7254.4065 568.8803 -5157.9249 8936.8651
250 247.8705 -7607.4583 858.06087 -5269.4711 -9926.0442
300 257.64176 -7267.424 618.5573 -5110.6004 5173.3307
350 251.65439 -7572.3806 821.15745 -5248.7049 -7092.327
400 256.87927 -7414.2145 655.33178 -5225.169 4119.4095
450 257.12393 -7576.5541 853.39773 -5187.9819 -5224.8823
500 242.42371 -7524.705 705.75357 -5371.5455 2111.3878
550 248.97188 -7541.076 792.86994 -5261.7038 -2278.4185
600 249.81862 -7592.0499 767.17722 -5333.3149 -1149.4759
650 253.31349 -7578.2665 813.75975 -5252.0827 -2915.5706
700 256.61152 -7588.1475 761.03356 -5294.9988 -747.88089
750 248.3606 -7660.457 837.71615 -5339.8883 -3072.8311
800 253.81464 -7638.6089 782.4229 -5340.7698 -1025.909
850 245.69185 -7660.9036 795.66792 -5398.3172 -2717.5851
900 249.13156 -7589.4769 806.43464 -5295.5867 -761.63361
950 251.11482 -7691.4981 869.34937 -5322.852 -3282.3031
1000 241.9195 -7630.9899 828.59107 -5358.0033 -95.962685
Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms
Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 35.545 | 36.674 | 38.004 | 15.8 | 80.51
Bond | 0.51302 | 0.67796 | 0.86345 | 18.6 | 1.49
Kspace | 0.66031 | 0.68459 | 0.70506 | 2.1 | 1.50
Neigh | 1.5605 | 1.5627 | 1.5649 | 0.1 | 3.43
Comm | 3.4611 | 4.9841 | 6.294 | 47.2 | 10.94
Output | 0.00079799 | 0.00086641 | 0.0010369 | 0.0 | 0.00
Modify | 0.67341 | 0.69059 | 0.71186 | 1.7 | 1.52
Other | | 0.2762 | | | 0.61
Nlocal: 501 ave 523 max 473 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 6643.25 ave 6708 max 6566 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 176977 ave 185765 max 164931 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 707908
Ave neighs/atom = 353.248
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 200
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:45

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examples/USER/misc/filter-corotate/peptide/log.lammps
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LAMMPS (26 Jan 2017)
# Solvated 5-mer peptide, run for 20ps in NVT
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
thermo 50
dump dump1 all atom 100 peptide.dump
timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3
Respa levels:
1 = bond angle dihedral improper
2 = pair
3 = kspace
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
19 = # of size 2 clusters
0 = # of size 3 clusters
3 = # of size 4 clusters
0 = # of size 5 clusters
646 = # of frozen angles
run 2500
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:317)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, half, perpetual
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Memory usage per processor = 17.8588 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821
50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891
100 242.8184 -7125.5635 416.08033 -5259.7208 15525.272
150 235.96512 -7531.8759 932.41522 -5190.6162 -14839.782
200 257.35102 -7247.5781 567.90676 -5143.141 8513.9733
250 247.35399 -7601.041 853.30194 -5270.8966 -8894.9042
300 238.39155 -7288.613 630.94229 -5234.3391 5570.9342
350 257.06739 -7568.1232 879.98206 -5153.3042 -7285.87
400 247.83949 -7471.1145 708.16434 -5283.209 3868.2834
450 252.55473 -7611.3166 851.78998 -5251.6328 -5460.3887
500 250.22449 -7513.0592 781.53558 -5237.5427 2201.7135
550 247.41884 -7677.3706 837.98176 -5362.1592 -4052.9427
600 250.37286 -7549.0586 757.06856 -5297.1232 559.74437
650 247.46682 -7653.5193 821.44119 -5354.562 -1717.7384
700 256.63169 -7672.6713 840.65 -5299.7857 -2922.6855
750 250.74235 -7638.8231 805.19765 -5336.5526 -1391.7887
800 249.192 -7638.156 802.5243 -5347.8152 -1882.0832
850 250.46499 -7607.8867 848.33053 -5264.1393 -1223.6763
900 241.12036 -7659.1054 848.18521 -5371.296 -2484.5958
950 248.08095 -7649.5224 853.94078 -5314.3988 -702.75135
1000 250.91296 -7658.3307 844.91335 -5315.3259 -1692.5939
1050 246.73851 -7713.0602 872.22591 -5367.6665 -1480.8398
1100 252.23301 -7742.3279 900.71873 -5335.6362 -1867.4031
1150 247.26614 -7672.9686 855.72245 -5340.9282 -1393.7358
1200 239.19944 -7733.9801 867.1273 -5438.6975 -2648.0668
1250 251.45165 -7752.8724 879.96452 -5371.6001 -1986.4684
1300 250.38401 -7751.9707 862.79267 -5394.2447 -1845.5444
1350 253.93283 -7801.2241 851.58306 -5433.5192 -2584.0105
1400 245.32436 -7720.3887 860.22548 -5395.4388 -2070.4882
1450 241.28817 -7701.2839 882.28435 -5378.3735 -850.62889
1500 250.37265 -7730.7213 903.63057 -5332.2251 -1356.525
1550 251.89349 -7763.3915 862.06926 -5397.3764 -134.50239
1600 251.13013 -7748.6889 907.21595 -5342.0848 -966.47349
1650 242.6259 -7810.6283 919.82972 -5442.1855 -1748.0311
1700 253.825 -7755.9582 883.21577 -5357.2644 -2116.3693
1750 255.50339 -7795.9448 910.24763 -5360.1982 -1959.9545
1800 246.79851 -7797.6035 878.7576 -5445.3199 -1665.5912
1850 249.49648 -7768.6601 932.69007 -5346.3356 -3294.8304
1900 247.68068 -7715.6737 910.66693 -5326.2138 504.55752
1950 249.31864 -7801.0719 930.9931 -5381.5063 -2806.6965
2000 252.99295 -7748.0016 895.00182 -5342.4896 -289.4189
2050 249.41601 -7815.8807 872.03861 -5454.6882 -1468.7262
2100 258.65142 -7808.6779 907.04932 -5357.3341 65.360616
2150 245.76718 -7810.1657 951.69975 -5391.0976 -3632.8405
2200 247.53005 -7779.7673 887.2345 -5414.6392 -1490.7467
2250 248.00828 -7788.7784 873.20488 -5434.8246 -1956.1633
2300 244.25241 -7798.9373 920.21778 -5420.3952 -1605.2485
2350 241.95391 -7773.5907 943.11124 -5385.8785 -1070.6519
2400 245.38073 -7815.2976 920.48267 -5429.7539 -1819.1152
2450 262.54741 -7927.234 907.81937 -5451.8589 -2727.1674
2500 249.5176 -7863.2466 904.52129 -5468.965 -1285.4951
Loop time of 76.5028 on 4 procs for 2500 steps with 2004 atoms
Performance: 22.587 ns/day, 1.063 hours/ns, 32.679 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 62.256 | 63.223 | 64.078 | 9.6 | 82.64
Bond | 0.85178 | 1.0305 | 1.2337 | 17.4 | 1.35
Kspace | 1.1172 | 1.126 | 1.1346 | 0.6 | 1.47
Neigh | 2.4852 | 2.4867 | 2.4876 | 0.1 | 3.25
Comm | 5.6095 | 6.6778 | 7.5121 | 30.5 | 8.73
Output | 0.011705 | 0.013602 | 0.019284 | 2.8 | 0.02
Modify | 1.3646 | 1.3807 | 1.3911 | 0.9 | 1.80
Other | | 0.5647 | | | 0.74
Nlocal: 501 ave 529 max 488 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 6628.25 ave 6688 max 6557 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177188 ave 191445 max 170612 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 708754
Ave neighs/atom = 353.67
Ave special neighs/atom = 2.34032
Neighbor list builds = 500
Dangerous builds = 500
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:16