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update examples for fix filter/corotate to comply with new CHARMM restrictions

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This commit is contained in:
Axel Kohlmeyer
2017-06-22 00:19:21 -04:00
parent de3157f720
commit b0ddabbcde
10 changed files with 778 additions and 774 deletions
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2
examples/USER/misc/filter_corotate/in.bpti
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@ -28,7 +28,7 @@ thermo 100
thermo_style multi thermo_style multi
timestep 8 timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
velocity all create 200.0 12345678 dist uniform velocity all create 200.0 12345678 dist uniform
#dump dump1 all atom 100 4pti.dump #dump dump1 all atom 100 4pti.dump

2
examples/USER/misc/filter_corotate/in.peptide
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@ -20,7 +20,7 @@ thermo 50
timestep 8 timestep 8
run_style respa 3 2 8 bond 1 pair 2 kspace 3 run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0 fix cor all filter/corotate m 1.0

240
examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1
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@ -1,240 +0,0 @@
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
examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4
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@ -1,240 +0,0 @@
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
examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1
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@ -1,146 +0,0 @@
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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LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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 allocation (min/avg/max) = 17.86 | 17.86 | 17.86 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 7.63279 on 1 procs for 241 steps with 892 atoms
32.0% 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 | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51
Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08
Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11
Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95
Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02465 | | | 0.32
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 dihedral 2 pair 2 kspace 3
Respa levels:
1 = bond angle
2 = dihedral improper 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 allocation (min/avg/max) = 19.55 | 19.55 | 19.55 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 = 8.4380 (sec) ----------------
TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802
PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893
E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577
E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640
---------------- Step 200 ----- CPU = 16.9012 (sec) ----------------
TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503
PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462
E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448
E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738
---------------- Step 300 ----- CPU = 25.3046 (sec) ----------------
TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951
PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793
E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895
E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746
---------------- Step 400 ----- CPU = 33.8063 (sec) ----------------
TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286
PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383
E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377
E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856
---------------- Step 500 ----- CPU = 42.3470 (sec) ----------------
TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090
PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256
E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927
E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471
---------------- Step 600 ----- CPU = 50.9590 (sec) ----------------
TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603
PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722
E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759
E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595
---------------- Step 700 ----- CPU = 59.4791 (sec) ----------------
TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455
PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715
E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377
E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789
---------------- Step 800 ----- CPU = 67.9330 (sec) ----------------
TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805
PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738
E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375
E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463
---------------- Step 900 ----- CPU = 76.3690 (sec) ----------------
TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961
PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658
E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498
E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343
---------------- Step 1000 ----- CPU = 84.8757 (sec) ----------------
TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691
PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104
E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182
E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649
Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms
Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76
Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09
Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89
Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24
Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05
Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00
Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66
Other | | 0.2516 | | | 0.30
Nlocal: 892 ave 892 max 892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38 ave 38 max 38 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 144068 ave 144068 max 144068 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 144068
Ave neighs/atom = 161.511
Ave special neighs/atom = 10.9395
Neighbor list builds = 190
Dangerous builds = 0
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:32

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LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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 allocation (min/avg/max) = 16.97 | 17.2 | 17.52 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3075.6498 943.91164 -2131.7381 -380.67776
241 0 -4503.3131 749.58665 -3753.7264 -29.044989
Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms
31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2131.73812515 -3753.4398752 -3753.72640446
Force two-norm initial, final = 1086.21 26.3687
Force max component initial, final = 310.811 3.92765
Final line search alpha, max atom move = 0.0059665 0.0234343
Iterations, force evaluations = 241 463
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.91458 | 1.6235 | 2.2701 | 38.2 | 53.00
Bond | 0.055164 | 0.13173 | 0.19487 | 15.1 | 4.30
Kspace | 0.48966 | 1.1993 | 1.9847 | 48.7 | 39.15
Neigh | 0.053297 | 0.053442 | 0.053576 | 0.0 | 1.74
Comm | 0.031677 | 0.035006 | 0.038061 | 1.5 | 1.14
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02021 | | | 0.66
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 dihedral 2 pair 2 kspace 3
Respa levels:
1 = bond angle
2 = dihedral improper 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 allocation (min/avg/max) = 17.14 | 17.63 | 18.14 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 = 345.2593
E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339
E_coul = -886.3622 E_long = -3326.2088 Press = 83.2284
---------------- Step 100 ----- CPU = 3.4639 (sec) ----------------
TotEng = -2718.4266 KinEng = 539.6246 Temp = 203.1794
PotEng = -3258.0513 E_bond = 203.2306 E_angle = 566.1887
E_dihed = 397.6756 E_impro = 34.7695 E_vdwl = -248.6577
E_coul = -874.8446 E_long = -3336.4135 Press = 135.8653
---------------- Step 200 ----- CPU = 6.8898 (sec) ----------------
TotEng = -2662.0450 KinEng = 625.0178 Temp = 235.3317
PotEng = -3287.0628 E_bond = 208.1691 E_angle = 590.8259
E_dihed = 389.1424 E_impro = 30.5879 E_vdwl = -240.5397
E_coul = -926.3110 E_long = -3338.9375 Press = 103.4843
---------------- Step 300 ----- CPU = 10.2791 (sec) ----------------
TotEng = -2661.8829 KinEng = 623.0352 Temp = 234.5852
PotEng = -3284.9181 E_bond = 203.0274 E_angle = 573.6583
E_dihed = 383.0124 E_impro = 41.9015 E_vdwl = -218.0696
E_coul = -926.5806 E_long = -3341.8675 Press = 45.6868
---------------- Step 400 ----- CPU = 13.5874 (sec) ----------------
TotEng = -2594.5220 KinEng = 672.8693 Temp = 253.3487
PotEng = -3267.3914 E_bond = 201.3378 E_angle = 612.7099
E_dihed = 410.1920 E_impro = 44.0201 E_vdwl = -217.9714
E_coul = -971.6203 E_long = -3346.0595 Press = -121.1015
---------------- Step 500 ----- CPU = 16.9047 (sec) ----------------
TotEng = -2603.9306 KinEng = 668.2122 Temp = 251.5952
PotEng = -3272.1428 E_bond = 238.1081 E_angle = 578.3310
E_dihed = 399.1305 E_impro = 41.4314 E_vdwl = -216.9664
E_coul = -969.4047 E_long = -3342.7729 Press = 156.7851
---------------- Step 600 ----- CPU = 20.1970 (sec) ----------------
TotEng = -2531.1096 KinEng = 728.1698 Temp = 274.1705
PotEng = -3259.2794 E_bond = 232.8396 E_angle = 621.3323
E_dihed = 398.1952 E_impro = 37.0914 E_vdwl = -241.6350
E_coul = -963.1540 E_long = -3343.9488 Press = 58.6784
---------------- Step 700 ----- CPU = 23.4360 (sec) ----------------
TotEng = -2499.9495 KinEng = 742.1211 Temp = 279.4234
PotEng = -3242.0705 E_bond = 240.5622 E_angle = 582.9270
E_dihed = 396.6246 E_impro = 36.6510 E_vdwl = -228.4925
E_coul = -926.8734 E_long = -3343.4695 Press = -60.7458
---------------- Step 800 ----- CPU = 26.6709 (sec) ----------------
TotEng = -2426.0217 KinEng = 760.1083 Temp = 286.1959
PotEng = -3186.1300 E_bond = 266.5863 E_angle = 652.3401
E_dihed = 380.7407 E_impro = 34.6861 E_vdwl = -225.3729
E_coul = -953.2382 E_long = -3341.8721 Press = -57.9824
---------------- Step 900 ----- CPU = 29.8152 (sec) ----------------
TotEng = -2419.4636 KinEng = 780.8361 Temp = 294.0004
PotEng = -3200.2996 E_bond = 269.3237 E_angle = 665.7171
E_dihed = 408.3527 E_impro = 43.7811 E_vdwl = -254.0696
E_coul = -1002.0694 E_long = -3331.3352 Press = -52.0169
---------------- Step 1000 ----- CPU = 32.8748 (sec) ----------------
TotEng = -2398.7244 KinEng = 811.9856 Temp = 305.7288
PotEng = -3210.7099 E_bond = 258.2207 E_angle = 639.3671
E_dihed = 379.3353 E_impro = 41.7602 E_vdwl = -207.2654
E_coul = -983.9330 E_long = -3338.1948 Press = 89.4870
Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms
Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s
31.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.449 | 19.023 | 24.612 | 99.6 | 57.86
Bond | 1.4547 | 2.8768 | 3.9098 | 61.4 | 8.75
Kspace | 1.0537 | 1.0778 | 1.0992 | 2.1 | 3.28
Neigh | 0.67542 | 0.67994 | 0.68323 | 0.3 | 2.07
Comm | 1.8602 | 8.4515 | 16.516 | 182.9 | 25.71
Output | 0.000839 | 0.00147 | 0.003293 | 2.7 | 0.00
Modify | 0.56658 | 0.63186 | 0.69304 | 6.8 | 1.92
Other | | 0.133 | | | 0.40
Nlocal: 223 ave 339 max 136 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 590 ave 626 max 552 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 36488.2 ave 41965 max 29054 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 145953
Ave neighs/atom = 163.624
Ave special neighs/atom = 10.9395
Neighbor list builds = 189
Dangerous builds = 0
unfix cor
unfix 1
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:36

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LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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 dihedral 2 pair 2 kspace 3
Respa levels:
1 = bond angle
2 = dihedral improper 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 allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122
100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011
150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894
200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563
250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359
300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021
350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665
400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811
450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859
500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769
550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227
600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352
650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309
700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651
750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372
800 251.73191 -7315.2457 839.59859 -4972.666 952.56448
850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823
900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166
950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267
1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136
Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms
Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80
Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25
Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10
Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48
Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90
Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00
Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10
Other | | 1.289 | | | 0.36
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11191 ave 11191 max 11191 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708610 ave 708610 max 708610 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708610
Ave neighs/atom = 353.598
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: 0:05:57

147
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LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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 dihedral 2 pair 2 kspace 3
Respa levels:
1 = bond angle
2 = dihedral improper 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 allocation (min/avg/max) = 16.87 | 17.05 | 17.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984
50 239.47667 -7205.1005 1092.7664 -4682.5237 -23733.122
100 244.63889 -6788.1152 422.96733 -4904.5161 16457.756
150 239.36917 -7258.7053 967.87775 -4861.6589 -13526.261
200 255.14702 -6864.0525 604.58036 -4736.1009 11013.1
250 252.72919 -7303.0966 898.11178 -4896.0494 -8480.8766
300 250.66477 -6989.2603 652.83649 -4839.8141 6209.3375
350 243.30794 -7218.8575 838.31977 -4927.8525 -5180.4928
400 256.3573 -7090.677 706.24197 -4853.8377 3302.577
450 246.15776 -7274.574 834.31676 -4970.557 -3427.971
500 256.28473 -7082.1447 735.42828 -4816.5524 2846.086
550 251.32327 -7341.739 812.64934 -5028.5484 -1786.9277
600 254.57737 -7152.3448 740.52534 -4891.8494 825.91675
650 244.95305 -7207.1136 790.67659 -4953.9295 -520.79769
700 249.4984 -7204.2699 779.06969 -4935.5544 -940.75384
750 248.46962 -7232.1037 791.6642 -4956.9361 -548.12171
800 260.2974 -7293.1982 793.23282 -4945.8435 -1171.26
850 249.79023 -7258.3759 823.56789 -4943.4198 -499.76275
900 249.97237 -7267.0584 784.57992 -4990.0028 -271.33531
950 251.29018 -7261.0642 823.467 -4937.2534 -538.7168
1000 246.05777 -7285.0948 847.90892 -4968.0826 -2613.1854
Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms
Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s
37.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 33.389 | 78.508 | 94.639 | 294.1 | 82.92
Bond | 0.39957 | 1.104 | 1.4443 | 40.6 | 1.17
Kspace | 0.53324 | 1.2631 | 1.5137 | 37.5 | 1.33
Neigh | 1.2668 | 3.011 | 3.5942 | 58.0 | 3.18
Comm | 3.4563 | 8.8707 | 11.494 | 107.9 | 9.37
Output | 0.000435 | 0.0017425 | 0.004136 | 3.4 | 0.00
Modify | 0.59335 | 1.4123 | 1.6921 | 39.8 | 1.49
Other | | 0.5129 | | | 0.54
Nlocal: 501 ave 515 max 476 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6681.5 ave 6740 max 6634 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 176872 ave 182642 max 168464 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 707486
Ave neighs/atom = 353.037
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: 0:01:53