ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Update to oxDNA2

Browse Source
This commit is contained in:
Oliver Henrich
2017-03-28 18:22:02 +01:00
parent 8afed61db1 3dfe4505dd
commit 604afebf6f
266 changed files with 284533 additions and 19677 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6587
examples/USER/misc/filter-corotate/data.bpti Normal file
View File

File diff suppressed because it is too large Load Diff

6531
examples/USER/misc/filter-corotate/data.peptide Normal file
View File

File diff suppressed because it is too large Load Diff

43
examples/USER/misc/filter-corotate/in.bpti Normal file
View File

@ -0,0 +1,43 @@
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
special_bonds charmm
neigh_modify delay 2 every 1
# ------------- MINIMIZE ----------
minimize 1e-4 1e-6 1000 10000
reset_timestep 0
# ------------- RUN ---------------
thermo 100
thermo_style multi
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
fix 1 all nvt temp 200 300 25
fix cor all filter/corotate m 1.0
run 1000
unfix cor
unfix 1

32
examples/USER/misc/filter-corotate/in.peptide Normal file
View File

@ -0,0 +1,32 @@
# 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
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
fix 1 all nvt temp 250.0 250.0 100.0 tchain 1
fix cor all filter/corotate m 1.0
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
examples/USER/misc/filter-corotate/log.10Mar2017.bpti.g++.4 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 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 Normal file
View File

@ -0,0 +1,146 @@
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

146
examples/USER/misc/filter-corotate/log.10Mar2017.peptide.g++.4 Normal file
View File

@ -0,0 +1,146 @@
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

1064
examples/USER/misc/grem/lj-temper/0/log.lammps.0
View File

File diff suppressed because it is too large Load Diff

1108
examples/USER/misc/grem/lj-temper/1/log.lammps.1
View File

File diff suppressed because it is too large Load Diff

1108
examples/USER/misc/grem/lj-temper/2/log.lammps.2
View File

File diff suppressed because it is too large Load Diff

1032
examples/USER/misc/grem/lj-temper/3/log.lammps.3
View File

File diff suppressed because it is too large Load Diff

180008
examples/USER/misc/momb/Ag_O1X5.5_O2X0.55.eam.fs Normal file
View File

File diff suppressed because it is too large Load Diff

20
examples/USER/misc/momb/README Normal file
View File

@ -0,0 +1,20 @@
pair_style momb example
=================
This folder contains a example of the use of pair_style momb for system
containing Ag, ethylene glycol (EG) and polyvinylpyrrolidone (PVP).
The pair_style is designed for the interaction between metals and organic
compounds. For this Ag-EG-PVP system, we use pair_style momb for the
interaction between Ag and the oxygen atom in EG and PVP, as described in
the publication listed below.
Zhou, Ya, Wissam A. Saidi, and Kristen A. Fichthorn.
"A force field for describing the polyvinylpyrrolidone-mediated solution-phase
synthesis of shape-selective Ag nanoparticles."
The Journal of Physical Chemistry C 118, no. 6 (2014): 3366-3374.
http://pubs.acs.org/doi/abs/10.1021/jp412098n
Other potentials used for this Ag-EG-PVP system includes the
EAM, Morse, and CHARMM potential. We note that the EAM potential file,
'Ag_O1X5.5_O2X0.55.eam.fs', also contains the information about the
one-way electron density donation from the oxygen atoms to Ag atoms.

195
examples/USER/misc/momb/in.system Normal file
View File

@ -0,0 +1,195 @@
# ----------------- Settings Section -----------------
units metal
boundary p p p
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
read_data system.data
pair_coeff * * eam/fs Ag_O1X5.5_O2X0.55.eam.fs NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL O1 NULL NULL NULL O2 Ag
pair_coeff 1*4 16 morse 0.00480 1.30 1.94 # HGA1, HGA2, HGA3
pair_coeff 5 16 morse 0.00722 1.14 4.85 # CG2R53
pair_coeff 6*8 16 morse 0.00244 1.01 4.92 # CG311, CG321, CG331
pair_coeff 9 16 morse 0.00230 1.03 4.92 # CG3C52
pair_coeff 10 16 morse 0.00492 1.76 3.26 # NG2R53
pair_coeff 11 16 morse 0.00325 3.34 2.65 # OG2D1
pair_coeff 12 16 morse 0.00480 1.30 1.94 # HCA2
pair_coeff 13 16 morse 0.00448 1.06 2.13 # HCP1
pair_coeff 14 16 morse 0.00216 1.26 4.99 # CC32A
pair_coeff 15 16 morse 0.00217 2.09 3.43 # OC311
pair_coeff 1*4 16 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 0.0 1.0 1.0 22.9973 2.702 # OC311
# arithmetic mixing for CHARMM pair coeffs
pair_coeff 1 1 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HRA2
pair_coeff 1 2 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HRA2 HGA1
pair_coeff 1 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HGA2
pair_coeff 1 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HRA2 HGA3
pair_coeff 1 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HRA2 CG2R53
pair_coeff 1 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HRA2 CG311
pair_coeff 1 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CG321
pair_coeff 1 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HRA2 CG331
pair_coeff 1 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HRA2 CG3C52
pair_coeff 1 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HRA2 NG2R53
pair_coeff 1 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HRA2 OG2D1
pair_coeff 1 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HCA2
pair_coeff 1 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HRA2 HCP1
pair_coeff 1 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CC32A
pair_coeff 1 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HRA2 OC311
pair_coeff 2 2 lj/charmm/coul/long 0.001950 2.387609 0.001950 2.387609 #HGA1 HGA1
pair_coeff 2 3 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HGA2
pair_coeff 2 4 lj/charmm/coul/long 0.001424 2.387609 0.001424 2.387609 #HGA1 HGA3
pair_coeff 2 5 lj/charmm/coul/long 0.001302 3.153782 0.001302 3.153782 #HGA1 CG2R53
pair_coeff 2 6 lj/charmm/coul/long 0.001646 2.975602 0.000916 2.886512 #HGA1 CG311
pair_coeff 2 7 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CG321
pair_coeff 2 8 lj/charmm/coul/long 0.002567 3.020147 0.000916 2.886512 #HGA1 CG331
pair_coeff 2 9 lj/charmm/coul/long 0.002252 2.993420 0.000916 2.886512 #HGA1 CG3C52
pair_coeff 2 10 lj/charmm/coul/long 0.004112 2.841967 0.004112 2.841967 #HGA1 NG2R53
pair_coeff 2 11 lj/charmm/coul/long 0.003184 2.708333 0.003184 2.441063 #HGA1 OG2D1
pair_coeff 2 12 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HCA2
pair_coeff 2 13 lj/charmm/coul/long 0.001970 1.393811 0.001970 1.393811 #HGA1 HCP1
pair_coeff 2 14 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CC32A
pair_coeff 2 15 lj/charmm/coul/long 0.004030 2.766240 0.004030 2.766240 #HGA1 OC311
pair_coeff 3 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HGA2
pair_coeff 3 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA2 HGA3
pair_coeff 3 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HGA2 CG2R53
pair_coeff 3 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HGA2 CG311
pair_coeff 3 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CG321
pair_coeff 3 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HGA2 CG331
pair_coeff 3 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HGA2 CG3C52
pair_coeff 3 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HGA2 NG2R53
pair_coeff 3 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HGA2 OG2D1
pair_coeff 3 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HCA2
pair_coeff 3 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HGA2 HCP1
pair_coeff 3 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CC32A
pair_coeff 3 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HGA2 OC311
pair_coeff 4 4 lj/charmm/coul/long 0.001040 2.387609 0.001040 2.387609 #HGA3 HGA3
pair_coeff 4 5 lj/charmm/coul/long 0.000951 3.153782 0.000951 3.153782 #HGA3 CG2R53
pair_coeff 4 6 lj/charmm/coul/long 0.001202 2.975602 0.000669 2.886512 #HGA3 CG311
pair_coeff 4 7 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CG321
pair_coeff 4 8 lj/charmm/coul/long 0.001875 3.020147 0.000669 2.886512 #HGA3 CG331
pair_coeff 4 9 lj/charmm/coul/long 0.001644 2.993420 0.000669 2.886512 #HGA3 CG3C52
pair_coeff 4 10 lj/charmm/coul/long 0.003003 2.841967 0.003003 2.841967 #HGA3 NG2R53
pair_coeff 4 11 lj/charmm/coul/long 0.002326 2.708333 0.002326 2.441063 #HGA3 OG2D1
pair_coeff 4 12 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA3 HCA2
pair_coeff 4 13 lj/charmm/coul/long 0.001439 1.393811 0.001439 1.393811 #HGA3 HCP1
pair_coeff 4 14 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CC32A
pair_coeff 4 15 lj/charmm/coul/long 0.002943 2.766240 0.002943 2.766240 #HGA3 OC311
pair_coeff 5 5 lj/charmm/coul/long 0.000870 3.919954 0.000870 3.919954 #CG2R53CG2R53
pair_coeff 5 6 lj/charmm/coul/long 0.001100 3.741775 0.000612 3.652685 #CG2R53CG311
pair_coeff 5 7 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CG321
pair_coeff 5 8 lj/charmm/coul/long 0.001715 3.786320 0.000612 3.652685 #CG2R53CG331
pair_coeff 5 9 lj/charmm/coul/long 0.001504 3.759593 0.000612 3.652685 #CG2R53CG3C52
pair_coeff 5 10 lj/charmm/coul/long 0.002746 3.608140 0.002746 3.608140 #CG2R53NG2R53
pair_coeff 5 11 lj/charmm/coul/long 0.002127 3.474505 0.002127 3.207235 #CG2R53OG2D1
pair_coeff 5 12 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #CG2R53HCA2
pair_coeff 5 13 lj/charmm/coul/long 0.001316 2.159984 0.001316 2.159984 #CG2R53HCP1
pair_coeff 5 14 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CC32A
pair_coeff 5 15 lj/charmm/coul/long 0.002692 3.532413 0.002692 3.532413 #CG2R53OC311
pair_coeff 6 6 lj/charmm/coul/long 0.001390 3.563595 0.000430 3.385415 #CG311 CG311
pair_coeff 6 7 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CG321
pair_coeff 6 8 lj/charmm/coul/long 0.002168 3.608140 0.000430 3.385415 #CG311 CG331
pair_coeff 6 9 lj/charmm/coul/long 0.001901 3.581413 0.000430 3.385415 #CG311 CG3C52
pair_coeff 6 10 lj/charmm/coul/long 0.003471 3.429960 0.001931 3.340870 #CG311 NG2R53
pair_coeff 6 11 lj/charmm/coul/long 0.002688 3.296326 0.001495 2.939966 #CG311 OG2D1
pair_coeff 6 12 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #CG311 HCA2
pair_coeff 6 13 lj/charmm/coul/long 0.001663 1.981804 0.000925 1.892714 #CG311 HCP1
pair_coeff 6 14 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CC32A
pair_coeff 6 15 lj/charmm/coul/long 0.003403 3.354233 0.001893 3.265143 #CG311 OC311
pair_coeff 7 7 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CG321
pair_coeff 7 8 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG321 CG331
pair_coeff 7 9 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG321 CG3C52
pair_coeff 7 10 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #CG321 NG2R53
pair_coeff 7 11 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #CG321 OG2D1
pair_coeff 7 12 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #CG321 HCA2
pair_coeff 7 13 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #CG321 HCP1
pair_coeff 7 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CC32A
pair_coeff 7 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CG321 OC311
pair_coeff 8 8 lj/charmm/coul/long 0.003380 3.652685 0.000430 3.385415 #CG331 CG331
pair_coeff 8 9 lj/charmm/coul/long 0.002964 3.625958 0.000430 3.385415 #CG331 CG3C52
pair_coeff 8 10 lj/charmm/coul/long 0.005413 3.474505 0.001931 3.340870 #CG331 NG2R53
pair_coeff 8 11 lj/charmm/coul/long 0.004192 3.340871 0.001495 2.939966 #CG331 OG2D1
pair_coeff 8 12 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #CG331 HCA2
pair_coeff 8 13 lj/charmm/coul/long 0.002593 2.026349 0.000925 1.892714 #CG331 HCP1
pair_coeff 8 14 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG331 CC32A
pair_coeff 8 15 lj/charmm/coul/long 0.005306 3.398778 0.001893 3.265143 #CG331 OC311
pair_coeff 9 9 lj/charmm/coul/long 0.002600 3.599231 0.000430 3.385415 #CG3C52CG3C52
pair_coeff 9 10 lj/charmm/coul/long 0.004748 3.447778 0.001931 3.340870 #CG3C52NG2R53
pair_coeff 9 11 lj/charmm/coul/long 0.003677 3.314144 0.001495 2.939966 #CG3C52OG2D1
pair_coeff 9 12 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #CG3C52HCA2
pair_coeff 9 13 lj/charmm/coul/long 0.002275 1.999622 0.000925 1.892714 #CG3C52HCP1
pair_coeff 9 14 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG3C52CC32A
pair_coeff 9 15 lj/charmm/coul/long 0.004654 3.372051 0.001893 3.265143 #CG3C52OC311
pair_coeff 10 10 lj/charmm/coul/long 0.008670 3.296325 0.008670 3.296325 #NG2R53NG2R53
pair_coeff 10 11 lj/charmm/coul/long 0.006714 3.162691 0.006714 2.895421 #NG2R53OG2D1
pair_coeff 10 12 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #NG2R53HCA2
pair_coeff 10 13 lj/charmm/coul/long 0.004154 1.848169 0.004154 1.848169 #NG2R53HCP1
pair_coeff 10 14 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #NG2R53CC32A
pair_coeff 10 15 lj/charmm/coul/long 0.008498 3.220598 0.008498 3.220598 #NG2R53OC311
pair_coeff 11 11 lj/charmm/coul/long 0.005200 3.029056 0.005200 2.494516 #OG2D1 OG2D1
pair_coeff 11 12 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #OG2D1 HCA2
pair_coeff 11 13 lj/charmm/coul/long 0.003217 1.714535 0.003217 1.447265 #OG2D1 HCP1
pair_coeff 11 14 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #OG2D1 CC32A
pair_coeff 11 15 lj/charmm/coul/long 0.006581 3.086964 0.006581 2.819694 #OG2D1 OC311
pair_coeff 12 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HCA2 HCA2
pair_coeff 12 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HCA2 HCP1
pair_coeff 12 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HCA2 CC32A
pair_coeff 12 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HCA2 OC311
pair_coeff 13 13 lj/charmm/coul/long 0.001990 0.400014 0.001990 0.400014 #HCP1 HCP1
pair_coeff 13 14 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #HCP1 CC32A
pair_coeff 13 15 lj/charmm/coul/long 0.004071 1.772443 0.004071 1.772443 #HCP1 OC311
pair_coeff 14 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CC32A CC32A
pair_coeff 14 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CC32A OC311
pair_coeff 15 15 lj/charmm/coul/long 0.008330 3.144872 0.008330 3.144872 #OC311 OC311
special_bonds charmm
# ----------------- Run Section -----------------
timestep 0.001
minimize 1.0e-3 1.0e-5 1000 10000
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
variable STEP equal step
variable PE equal pe
variable KE equal ke
variable ETOTAL equal etotal
variable TEMP equal temp
variable VOL equal vol
variable PRESS equal press
variable LX equal lx
variable LZ equal lz
variable PXX equal pxx
variable PYY equal pyy
variable PZZ equal pzz
fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100

360
examples/USER/misc/momb/log.17Mar2017.system.g++.1 Normal file
View File

@ -0,0 +1,360 @@
LAMMPS (17 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# ----------------- Settings Section -----------------
units metal
boundary p p p
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
read_data system.data
orthogonal box = (0 0 0) to (53.6198 53.6198 160)
1 by 1 by 1 MPI processor grid
reading atoms ...
18146 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
13 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
12694 bonds
reading angles ...
19786 angles
reading dihedrals ...
29690 dihedrals
reading impropers ...
5 impropers
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
23 = max # of special neighbors
pair_coeff * * eam/fs Ag_O1X5.5_O2X0.55.eam.fs NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL O1 NULL NULL NULL O2 Ag
pair_coeff 1*4 16 morse 0.00480 1.30 1.94 # HGA1, HGA2, HGA3
pair_coeff 5 16 morse 0.00722 1.14 4.85 # CG2R53
pair_coeff 6*8 16 morse 0.00244 1.01 4.92 # CG311, CG321, CG331
pair_coeff 9 16 morse 0.00230 1.03 4.92 # CG3C52
pair_coeff 10 16 morse 0.00492 1.76 3.26 # NG2R53
pair_coeff 11 16 morse 0.00325 3.34 2.65 # OG2D1
pair_coeff 12 16 morse 0.00480 1.30 1.94 # HCA2
pair_coeff 13 16 morse 0.00448 1.06 2.13 # HCP1
pair_coeff 14 16 morse 0.00216 1.26 4.99 # CC32A
pair_coeff 15 16 morse 0.00217 2.09 3.43 # OC311
pair_coeff 1*4 16 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 0.0 1.0 1.0 22.9973 2.702 # OC311
# arithmetic mixing for CHARMM pair coeffs
pair_coeff 1 1 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HRA2
pair_coeff 1 2 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HRA2 HGA1
pair_coeff 1 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HGA2
pair_coeff 1 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HRA2 HGA3
pair_coeff 1 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HRA2 CG2R53
pair_coeff 1 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HRA2 CG311
pair_coeff 1 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CG321
pair_coeff 1 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HRA2 CG331
pair_coeff 1 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HRA2 CG3C52
pair_coeff 1 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HRA2 NG2R53
pair_coeff 1 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HRA2 OG2D1
pair_coeff 1 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HCA2
pair_coeff 1 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HRA2 HCP1
pair_coeff 1 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CC32A
pair_coeff 1 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HRA2 OC311
pair_coeff 2 2 lj/charmm/coul/long 0.001950 2.387609 0.001950 2.387609 #HGA1 HGA1
pair_coeff 2 3 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HGA2
pair_coeff 2 4 lj/charmm/coul/long 0.001424 2.387609 0.001424 2.387609 #HGA1 HGA3
pair_coeff 2 5 lj/charmm/coul/long 0.001302 3.153782 0.001302 3.153782 #HGA1 CG2R53
pair_coeff 2 6 lj/charmm/coul/long 0.001646 2.975602 0.000916 2.886512 #HGA1 CG311
pair_coeff 2 7 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CG321
pair_coeff 2 8 lj/charmm/coul/long 0.002567 3.020147 0.000916 2.886512 #HGA1 CG331
pair_coeff 2 9 lj/charmm/coul/long 0.002252 2.993420 0.000916 2.886512 #HGA1 CG3C52
pair_coeff 2 10 lj/charmm/coul/long 0.004112 2.841967 0.004112 2.841967 #HGA1 NG2R53
pair_coeff 2 11 lj/charmm/coul/long 0.003184 2.708333 0.003184 2.441063 #HGA1 OG2D1
pair_coeff 2 12 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HCA2
pair_coeff 2 13 lj/charmm/coul/long 0.001970 1.393811 0.001970 1.393811 #HGA1 HCP1
pair_coeff 2 14 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CC32A
pair_coeff 2 15 lj/charmm/coul/long 0.004030 2.766240 0.004030 2.766240 #HGA1 OC311
pair_coeff 3 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HGA2
pair_coeff 3 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA2 HGA3
pair_coeff 3 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HGA2 CG2R53
pair_coeff 3 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HGA2 CG311
pair_coeff 3 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CG321
pair_coeff 3 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HGA2 CG331
pair_coeff 3 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HGA2 CG3C52
pair_coeff 3 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HGA2 NG2R53
pair_coeff 3 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HGA2 OG2D1
pair_coeff 3 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HCA2
pair_coeff 3 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HGA2 HCP1
pair_coeff 3 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CC32A
pair_coeff 3 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HGA2 OC311
pair_coeff 4 4 lj/charmm/coul/long 0.001040 2.387609 0.001040 2.387609 #HGA3 HGA3
pair_coeff 4 5 lj/charmm/coul/long 0.000951 3.153782 0.000951 3.153782 #HGA3 CG2R53
pair_coeff 4 6 lj/charmm/coul/long 0.001202 2.975602 0.000669 2.886512 #HGA3 CG311
pair_coeff 4 7 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CG321
pair_coeff 4 8 lj/charmm/coul/long 0.001875 3.020147 0.000669 2.886512 #HGA3 CG331
pair_coeff 4 9 lj/charmm/coul/long 0.001644 2.993420 0.000669 2.886512 #HGA3 CG3C52
pair_coeff 4 10 lj/charmm/coul/long 0.003003 2.841967 0.003003 2.841967 #HGA3 NG2R53
pair_coeff 4 11 lj/charmm/coul/long 0.002326 2.708333 0.002326 2.441063 #HGA3 OG2D1
pair_coeff 4 12 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA3 HCA2
pair_coeff 4 13 lj/charmm/coul/long 0.001439 1.393811 0.001439 1.393811 #HGA3 HCP1
pair_coeff 4 14 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CC32A
pair_coeff 4 15 lj/charmm/coul/long 0.002943 2.766240 0.002943 2.766240 #HGA3 OC311
pair_coeff 5 5 lj/charmm/coul/long 0.000870 3.919954 0.000870 3.919954 #CG2R53CG2R53
pair_coeff 5 6 lj/charmm/coul/long 0.001100 3.741775 0.000612 3.652685 #CG2R53CG311
pair_coeff 5 7 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CG321
pair_coeff 5 8 lj/charmm/coul/long 0.001715 3.786320 0.000612 3.652685 #CG2R53CG331
pair_coeff 5 9 lj/charmm/coul/long 0.001504 3.759593 0.000612 3.652685 #CG2R53CG3C52
pair_coeff 5 10 lj/charmm/coul/long 0.002746 3.608140 0.002746 3.608140 #CG2R53NG2R53
pair_coeff 5 11 lj/charmm/coul/long 0.002127 3.474505 0.002127 3.207235 #CG2R53OG2D1
pair_coeff 5 12 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #CG2R53HCA2
pair_coeff 5 13 lj/charmm/coul/long 0.001316 2.159984 0.001316 2.159984 #CG2R53HCP1
pair_coeff 5 14 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CC32A
pair_coeff 5 15 lj/charmm/coul/long 0.002692 3.532413 0.002692 3.532413 #CG2R53OC311
pair_coeff 6 6 lj/charmm/coul/long 0.001390 3.563595 0.000430 3.385415 #CG311 CG311
pair_coeff 6 7 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CG321
pair_coeff 6 8 lj/charmm/coul/long 0.002168 3.608140 0.000430 3.385415 #CG311 CG331
pair_coeff 6 9 lj/charmm/coul/long 0.001901 3.581413 0.000430 3.385415 #CG311 CG3C52
pair_coeff 6 10 lj/charmm/coul/long 0.003471 3.429960 0.001931 3.340870 #CG311 NG2R53
pair_coeff 6 11 lj/charmm/coul/long 0.002688 3.296326 0.001495 2.939966 #CG311 OG2D1
pair_coeff 6 12 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #CG311 HCA2
pair_coeff 6 13 lj/charmm/coul/long 0.001663 1.981804 0.000925 1.892714 #CG311 HCP1
pair_coeff 6 14 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CC32A
pair_coeff 6 15 lj/charmm/coul/long 0.003403 3.354233 0.001893 3.265143 #CG311 OC311
pair_coeff 7 7 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CG321
pair_coeff 7 8 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG321 CG331
pair_coeff 7 9 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG321 CG3C52
pair_coeff 7 10 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #CG321 NG2R53
pair_coeff 7 11 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #CG321 OG2D1
pair_coeff 7 12 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #CG321 HCA2
pair_coeff 7 13 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #CG321 HCP1
pair_coeff 7 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CC32A
pair_coeff 7 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CG321 OC311
pair_coeff 8 8 lj/charmm/coul/long 0.003380 3.652685 0.000430 3.385415 #CG331 CG331
pair_coeff 8 9 lj/charmm/coul/long 0.002964 3.625958 0.000430 3.385415 #CG331 CG3C52
pair_coeff 8 10 lj/charmm/coul/long 0.005413 3.474505 0.001931 3.340870 #CG331 NG2R53
pair_coeff 8 11 lj/charmm/coul/long 0.004192 3.340871 0.001495 2.939966 #CG331 OG2D1
pair_coeff 8 12 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #CG331 HCA2
pair_coeff 8 13 lj/charmm/coul/long 0.002593 2.026349 0.000925 1.892714 #CG331 HCP1
pair_coeff 8 14 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG331 CC32A
pair_coeff 8 15 lj/charmm/coul/long 0.005306 3.398778 0.001893 3.265143 #CG331 OC311
pair_coeff 9 9 lj/charmm/coul/long 0.002600 3.599231 0.000430 3.385415 #CG3C52CG3C52
pair_coeff 9 10 lj/charmm/coul/long 0.004748 3.447778 0.001931 3.340870 #CG3C52NG2R53
pair_coeff 9 11 lj/charmm/coul/long 0.003677 3.314144 0.001495 2.939966 #CG3C52OG2D1
pair_coeff 9 12 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #CG3C52HCA2
pair_coeff 9 13 lj/charmm/coul/long 0.002275 1.999622 0.000925 1.892714 #CG3C52HCP1
pair_coeff 9 14 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG3C52CC32A
pair_coeff 9 15 lj/charmm/coul/long 0.004654 3.372051 0.001893 3.265143 #CG3C52OC311
pair_coeff 10 10 lj/charmm/coul/long 0.008670 3.296325 0.008670 3.296325 #NG2R53NG2R53
pair_coeff 10 11 lj/charmm/coul/long 0.006714 3.162691 0.006714 2.895421 #NG2R53OG2D1
pair_coeff 10 12 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #NG2R53HCA2
pair_coeff 10 13 lj/charmm/coul/long 0.004154 1.848169 0.004154 1.848169 #NG2R53HCP1
pair_coeff 10 14 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #NG2R53CC32A
pair_coeff 10 15 lj/charmm/coul/long 0.008498 3.220598 0.008498 3.220598 #NG2R53OC311
pair_coeff 11 11 lj/charmm/coul/long 0.005200 3.029056 0.005200 2.494516 #OG2D1 OG2D1
pair_coeff 11 12 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #OG2D1 HCA2
pair_coeff 11 13 lj/charmm/coul/long 0.003217 1.714535 0.003217 1.447265 #OG2D1 HCP1
pair_coeff 11 14 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #OG2D1 CC32A
pair_coeff 11 15 lj/charmm/coul/long 0.006581 3.086964 0.006581 2.819694 #OG2D1 OC311
pair_coeff 12 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HCA2 HCA2
pair_coeff 12 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HCA2 HCP1
pair_coeff 12 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HCA2 CC32A
pair_coeff 12 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HCA2 OC311
pair_coeff 13 13 lj/charmm/coul/long 0.001990 0.400014 0.001990 0.400014 #HCP1 HCP1
pair_coeff 13 14 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #HCP1 CC32A
pair_coeff 13 15 lj/charmm/coul/long 0.004071 1.772443 0.004071 1.772443 #HCP1 OC311
pair_coeff 14 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CC32A CC32A
pair_coeff 14 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CC32A OC311
pair_coeff 15 15 lj/charmm/coul/long 0.008330 3.144872 0.008330 3.144872 #OC311 OC311
special_bonds charmm
# ----------------- Run Section -----------------
timestep 0.001
minimize 1.0e-3 1.0e-5 1000 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 8 23
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/charmm/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair momb, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) pair morse, perpetual, copy from (3)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, 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) = 99.82 | 99.82 | 99.82 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10035.476 218.18376 -9817.2917 -1066.914
9 0 -10244.892 211.35072 -10033.541 -3283.8636
Loop time of 2.6765 on 1 procs for 9 steps with 18146 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9817.29174185 -10023.887559 -10033.5413886
Force two-norm initial, final = 76.9233 27.3547
Force max component initial, final = 11.8658 7.37882
Final line search alpha, max atom move = 0.0472944 0.348977
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3191 | 2.3191 | 2.3191 | 0.0 | 86.65
Bond | 0.084626 | 0.084626 | 0.084626 | 0.0 | 3.16
Kspace | 0.2622 | 0.2622 | 0.2622 | 0.0 | 9.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0033448 | 0.0033448 | 0.0033448 | 0.0 | 0.12
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.007261 | | | 0.27
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 29277 ave 29277 max 29277 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 439189 ave 439189 max 439189 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 439189
Ave neighs/atom = 24.2031
Ave special neighs/atom = 5.92362
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
variable STEP equal step
variable PE equal pe
variable KE equal ke
variable ETOTAL equal etotal
variable TEMP equal temp
variable VOL equal vol
variable PRESS equal press
variable LX equal lx
variable LZ equal lz
variable PXX equal pxx
variable PYY equal pyy
variable PZZ equal pzz
fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 79764 46656
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Per MPI rank memory allocation (min/avg/max) = 96.44 | 96.44 | 96.44 Mbytes
Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
Loop time of 18.5289 on 1 procs for 100 steps with 18146 atoms
Performance: 0.466 ns/day, 51.469 hours/ns, 5.397 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 | 14.326 | 14.326 | 14.326 | 0.0 | 77.31
Bond | 0.65294 | 0.65294 | 0.65294 | 0.0 | 3.52
Kspace | 2.2291 | 2.2291 | 2.2291 | 0.0 | 12.03
Neigh | 1.2037 | 1.2037 | 1.2037 | 0.0 | 6.50
Comm | 0.038561 | 0.038561 | 0.038561 | 0.0 | 0.21
Output | 0.0022585 | 0.0022585 | 0.0022585 | 0.0 | 0.01
Modify | 0.058746 | 0.058746 | 0.058746 | 0.0 | 0.32
Other | | 0.018 | | | 0.10
Nlocal: 18146 ave 18146 max 18146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 29127 ave 29127 max 29127 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 441898 ave 441898 max 441898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 441898
Ave neighs/atom = 24.3524
Ave special neighs/atom = 5.92362
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:22

360
examples/USER/misc/momb/log.17Mar2017.system.g++.4 Normal file
View File

@ -0,0 +1,360 @@
LAMMPS (17 Mar 2017)
using 1 OpenMP thread(s) per MPI task
# ----------------- Settings Section -----------------
units metal
boundary p p p
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5
kspace_style pppm 1e-5
# ----------------- Atom Definition Section -----------------
read_data system.data
orthogonal box = (0 0 0) to (53.6198 53.6198 160)
1 by 1 by 4 MPI processor grid
reading atoms ...
18146 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
13 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
12694 bonds
reading angles ...
19786 angles
reading dihedrals ...
29690 dihedrals
reading impropers ...
5 impropers
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
20 = max # of 1-4 neighbors
23 = max # of special neighbors
pair_coeff * * eam/fs Ag_O1X5.5_O2X0.55.eam.fs NULL NULL NULL NULL NULL NULL NULL NULL NULL NULL O1 NULL NULL NULL O2 Ag
pair_coeff 1*4 16 morse 0.00480 1.30 1.94 # HGA1, HGA2, HGA3
pair_coeff 5 16 morse 0.00722 1.14 4.85 # CG2R53
pair_coeff 6*8 16 morse 0.00244 1.01 4.92 # CG311, CG321, CG331
pair_coeff 9 16 morse 0.00230 1.03 4.92 # CG3C52
pair_coeff 10 16 morse 0.00492 1.76 3.26 # NG2R53
pair_coeff 11 16 morse 0.00325 3.34 2.65 # OG2D1
pair_coeff 12 16 morse 0.00480 1.30 1.94 # HCA2
pair_coeff 13 16 morse 0.00448 1.06 2.13 # HCP1
pair_coeff 14 16 morse 0.00216 1.26 4.99 # CC32A
pair_coeff 15 16 morse 0.00217 2.09 3.43 # OC311
pair_coeff 1*4 16 momb 0.0 1.0 1.0 10.2847 2.361 # H
pair_coeff 5*9 16 momb 0.0 1.0 1.0 36.3619 2.812 # C
pair_coeff 10 16 momb 0.0 1.0 1.0 30.4846 2.757 # N
pair_coeff 11 16 momb 0.0 1.0 1.0 22.9973 2.702 # O
pair_coeff 12 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCA2
pair_coeff 13 16 momb 0.0 1.0 1.0 10.2847 2.361 # HCP1
pair_coeff 14 16 momb 0.0 1.0 1.0 36.3619 2.812 # CC32A
pair_coeff 15 16 momb 0.0 1.0 1.0 22.9973 2.702 # OC311
# arithmetic mixing for CHARMM pair coeffs
pair_coeff 1 1 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HRA2
pair_coeff 1 2 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HRA2 HGA1
pair_coeff 1 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HGA2
pair_coeff 1 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HRA2 HGA3
pair_coeff 1 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HRA2 CG2R53
pair_coeff 1 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HRA2 CG311
pair_coeff 1 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CG321
pair_coeff 1 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HRA2 CG331
pair_coeff 1 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HRA2 CG3C52
pair_coeff 1 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HRA2 NG2R53
pair_coeff 1 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HRA2 OG2D1
pair_coeff 1 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HRA2 HCA2
pair_coeff 1 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HRA2 HCP1
pair_coeff 1 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HRA2 CC32A
pair_coeff 1 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HRA2 OC311
pair_coeff 2 2 lj/charmm/coul/long 0.001950 2.387609 0.001950 2.387609 #HGA1 HGA1
pair_coeff 2 3 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HGA2
pair_coeff 2 4 lj/charmm/coul/long 0.001424 2.387609 0.001424 2.387609 #HGA1 HGA3
pair_coeff 2 5 lj/charmm/coul/long 0.001302 3.153782 0.001302 3.153782 #HGA1 CG2R53
pair_coeff 2 6 lj/charmm/coul/long 0.001646 2.975602 0.000916 2.886512 #HGA1 CG311
pair_coeff 2 7 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CG321
pair_coeff 2 8 lj/charmm/coul/long 0.002567 3.020147 0.000916 2.886512 #HGA1 CG331
pair_coeff 2 9 lj/charmm/coul/long 0.002252 2.993420 0.000916 2.886512 #HGA1 CG3C52
pair_coeff 2 10 lj/charmm/coul/long 0.004112 2.841967 0.004112 2.841967 #HGA1 NG2R53
pair_coeff 2 11 lj/charmm/coul/long 0.003184 2.708333 0.003184 2.441063 #HGA1 OG2D1
pair_coeff 2 12 lj/charmm/coul/long 0.001722 2.387609 0.001722 2.387609 #HGA1 HCA2
pair_coeff 2 13 lj/charmm/coul/long 0.001970 1.393811 0.001970 1.393811 #HGA1 HCP1
pair_coeff 2 14 lj/charmm/coul/long 0.002177 2.984511 0.000916 2.886512 #HGA1 CC32A
pair_coeff 2 15 lj/charmm/coul/long 0.004030 2.766240 0.004030 2.766240 #HGA1 OC311
pair_coeff 3 3 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HGA2
pair_coeff 3 4 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA2 HGA3
pair_coeff 3 5 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #HGA2 CG2R53
pair_coeff 3 6 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #HGA2 CG311
pair_coeff 3 7 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CG321
pair_coeff 3 8 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #HGA2 CG331
pair_coeff 3 9 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #HGA2 CG3C52
pair_coeff 3 10 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #HGA2 NG2R53
pair_coeff 3 11 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #HGA2 OG2D1
pair_coeff 3 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HGA2 HCA2
pair_coeff 3 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HGA2 HCP1
pair_coeff 3 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HGA2 CC32A
pair_coeff 3 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HGA2 OC311
pair_coeff 4 4 lj/charmm/coul/long 0.001040 2.387609 0.001040 2.387609 #HGA3 HGA3
pair_coeff 4 5 lj/charmm/coul/long 0.000951 3.153782 0.000951 3.153782 #HGA3 CG2R53
pair_coeff 4 6 lj/charmm/coul/long 0.001202 2.975602 0.000669 2.886512 #HGA3 CG311
pair_coeff 4 7 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CG321
pair_coeff 4 8 lj/charmm/coul/long 0.001875 3.020147 0.000669 2.886512 #HGA3 CG331
pair_coeff 4 9 lj/charmm/coul/long 0.001644 2.993420 0.000669 2.886512 #HGA3 CG3C52
pair_coeff 4 10 lj/charmm/coul/long 0.003003 2.841967 0.003003 2.841967 #HGA3 NG2R53
pair_coeff 4 11 lj/charmm/coul/long 0.002326 2.708333 0.002326 2.441063 #HGA3 OG2D1
pair_coeff 4 12 lj/charmm/coul/long 0.001257 2.387609 0.001257 2.387609 #HGA3 HCA2
pair_coeff 4 13 lj/charmm/coul/long 0.001439 1.393811 0.001439 1.393811 #HGA3 HCP1
pair_coeff 4 14 lj/charmm/coul/long 0.001590 2.984511 0.000669 2.886512 #HGA3 CC32A
pair_coeff 4 15 lj/charmm/coul/long 0.002943 2.766240 0.002943 2.766240 #HGA3 OC311
pair_coeff 5 5 lj/charmm/coul/long 0.000870 3.919954 0.000870 3.919954 #CG2R53CG2R53
pair_coeff 5 6 lj/charmm/coul/long 0.001100 3.741775 0.000612 3.652685 #CG2R53CG311
pair_coeff 5 7 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CG321
pair_coeff 5 8 lj/charmm/coul/long 0.001715 3.786320 0.000612 3.652685 #CG2R53CG331
pair_coeff 5 9 lj/charmm/coul/long 0.001504 3.759593 0.000612 3.652685 #CG2R53CG3C52
pair_coeff 5 10 lj/charmm/coul/long 0.002746 3.608140 0.002746 3.608140 #CG2R53NG2R53
pair_coeff 5 11 lj/charmm/coul/long 0.002127 3.474505 0.002127 3.207235 #CG2R53OG2D1
pair_coeff 5 12 lj/charmm/coul/long 0.001150 3.153782 0.001150 3.153782 #CG2R53HCA2
pair_coeff 5 13 lj/charmm/coul/long 0.001316 2.159984 0.001316 2.159984 #CG2R53HCP1
pair_coeff 5 14 lj/charmm/coul/long 0.001454 3.750684 0.000612 3.652685 #CG2R53CC32A
pair_coeff 5 15 lj/charmm/coul/long 0.002692 3.532413 0.002692 3.532413 #CG2R53OC311
pair_coeff 6 6 lj/charmm/coul/long 0.001390 3.563595 0.000430 3.385415 #CG311 CG311
pair_coeff 6 7 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CG321
pair_coeff 6 8 lj/charmm/coul/long 0.002168 3.608140 0.000430 3.385415 #CG311 CG331
pair_coeff 6 9 lj/charmm/coul/long 0.001901 3.581413 0.000430 3.385415 #CG311 CG3C52
pair_coeff 6 10 lj/charmm/coul/long 0.003471 3.429960 0.001931 3.340870 #CG311 NG2R53
pair_coeff 6 11 lj/charmm/coul/long 0.002688 3.296326 0.001495 2.939966 #CG311 OG2D1
pair_coeff 6 12 lj/charmm/coul/long 0.001454 2.975602 0.000808 2.886512 #CG311 HCA2
pair_coeff 6 13 lj/charmm/coul/long 0.001663 1.981804 0.000925 1.892714 #CG311 HCP1
pair_coeff 6 14 lj/charmm/coul/long 0.001838 3.572504 0.000430 3.385415 #CG311 CC32A
pair_coeff 6 15 lj/charmm/coul/long 0.003403 3.354233 0.001893 3.265143 #CG311 OC311
pair_coeff 7 7 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CG321
pair_coeff 7 8 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG321 CG331
pair_coeff 7 9 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG321 CG3C52
pair_coeff 7 10 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #CG321 NG2R53
pair_coeff 7 11 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #CG321 OG2D1
pair_coeff 7 12 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #CG321 HCA2
pair_coeff 7 13 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #CG321 HCP1
pair_coeff 7 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CG321 CC32A
pair_coeff 7 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CG321 OC311
pair_coeff 8 8 lj/charmm/coul/long 0.003380 3.652685 0.000430 3.385415 #CG331 CG331
pair_coeff 8 9 lj/charmm/coul/long 0.002964 3.625958 0.000430 3.385415 #CG331 CG3C52
pair_coeff 8 10 lj/charmm/coul/long 0.005413 3.474505 0.001931 3.340870 #CG331 NG2R53
pair_coeff 8 11 lj/charmm/coul/long 0.004192 3.340871 0.001495 2.939966 #CG331 OG2D1
pair_coeff 8 12 lj/charmm/coul/long 0.002267 3.020147 0.000808 2.886512 #CG331 HCA2
pair_coeff 8 13 lj/charmm/coul/long 0.002593 2.026349 0.000925 1.892714 #CG331 HCP1
pair_coeff 8 14 lj/charmm/coul/long 0.002866 3.617049 0.000430 3.385415 #CG331 CC32A
pair_coeff 8 15 lj/charmm/coul/long 0.005306 3.398778 0.001893 3.265143 #CG331 OC311
pair_coeff 9 9 lj/charmm/coul/long 0.002600 3.599231 0.000430 3.385415 #CG3C52CG3C52
pair_coeff 9 10 lj/charmm/coul/long 0.004748 3.447778 0.001931 3.340870 #CG3C52NG2R53
pair_coeff 9 11 lj/charmm/coul/long 0.003677 3.314144 0.001495 2.939966 #CG3C52OG2D1
pair_coeff 9 12 lj/charmm/coul/long 0.001988 2.993420 0.000808 2.886512 #CG3C52HCA2
pair_coeff 9 13 lj/charmm/coul/long 0.002275 1.999622 0.000925 1.892714 #CG3C52HCP1
pair_coeff 9 14 lj/charmm/coul/long 0.002514 3.590322 0.000430 3.385415 #CG3C52CC32A
pair_coeff 9 15 lj/charmm/coul/long 0.004654 3.372051 0.001893 3.265143 #CG3C52OC311
pair_coeff 10 10 lj/charmm/coul/long 0.008670 3.296325 0.008670 3.296325 #NG2R53NG2R53
pair_coeff 10 11 lj/charmm/coul/long 0.006714 3.162691 0.006714 2.895421 #NG2R53OG2D1
pair_coeff 10 12 lj/charmm/coul/long 0.003630 2.841967 0.003630 2.841967 #NG2R53HCA2
pair_coeff 10 13 lj/charmm/coul/long 0.004154 1.848169 0.004154 1.848169 #NG2R53HCP1
pair_coeff 10 14 lj/charmm/coul/long 0.004590 3.438869 0.001931 3.340870 #NG2R53CC32A
pair_coeff 10 15 lj/charmm/coul/long 0.008498 3.220598 0.008498 3.220598 #NG2R53OC311
pair_coeff 11 11 lj/charmm/coul/long 0.005200 3.029056 0.005200 2.494516 #OG2D1 OG2D1
pair_coeff 11 12 lj/charmm/coul/long 0.002811 2.708333 0.002811 2.441063 #OG2D1 HCA2
pair_coeff 11 13 lj/charmm/coul/long 0.003217 1.714535 0.003217 1.447265 #OG2D1 HCP1
pair_coeff 11 14 lj/charmm/coul/long 0.003555 3.305235 0.001495 2.939966 #OG2D1 CC32A
pair_coeff 11 15 lj/charmm/coul/long 0.006581 3.086964 0.006581 2.819694 #OG2D1 OC311
pair_coeff 12 12 lj/charmm/coul/long 0.001520 2.387609 0.001520 2.387609 #HCA2 HCA2
pair_coeff 12 13 lj/charmm/coul/long 0.001739 1.393811 0.001739 1.393811 #HCA2 HCP1
pair_coeff 12 14 lj/charmm/coul/long 0.001922 2.984511 0.000808 2.886512 #HCA2 CC32A
pair_coeff 12 15 lj/charmm/coul/long 0.003558 2.766240 0.003558 2.766240 #HCA2 OC311
pair_coeff 13 13 lj/charmm/coul/long 0.001990 0.400014 0.001990 0.400014 #HCP1 HCP1
pair_coeff 13 14 lj/charmm/coul/long 0.002199 1.990713 0.000925 1.892714 #HCP1 CC32A
pair_coeff 13 15 lj/charmm/coul/long 0.004071 1.772443 0.004071 1.772443 #HCP1 OC311
pair_coeff 14 14 lj/charmm/coul/long 0.002430 3.581413 0.000430 3.385415 #CC32A CC32A
pair_coeff 14 15 lj/charmm/coul/long 0.004499 3.363142 0.001893 3.265143 #CC32A OC311
pair_coeff 15 15 lj/charmm/coul/long 0.008330 3.144872 0.008330 3.144872 #OC311 OC311
special_bonds charmm
# ----------------- Run Section -----------------
timestep 0.001
minimize 1.0e-3 1.0e-5 1000 10000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 24276 11664
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 8 23
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair eam/fs, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/charmm/coul/long, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) pair momb, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) pair morse, perpetual, copy from (3)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, 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) = 21.64 | 38.62 | 61.37 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10035.476 218.18376 -9817.2917 -1066.914
9 0 -10244.892 211.35072 -10033.541 -3283.8636
Loop time of 1.52429 on 4 procs for 9 steps with 18146 atoms
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-9817.29174185 -10023.887559 -10033.5413886
Force two-norm initial, final = 76.9233 27.3547
Force max component initial, final = 11.8658 7.37882
Final line search alpha, max atom move = 0.0472944 0.348977
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13871 | 0.61412 | 1.3512 | 63.6 | 40.29
Bond | 0.0010097 | 0.021249 | 0.047945 | 13.0 | 1.39
Kspace | 0.11351 | 0.87771 | 1.3739 | 55.2 | 57.58
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0040638 | 0.0056078 | 0.0067704 | 1.6 | 0.37
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005606 | | | 0.37
Nlocal: 4536.5 ave 8000 max 700 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 11329.2 ave 16795 max 5072 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 109797 ave 237808 max 8314 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 439189
Ave neighs/atom = 24.2031
Ave special neighs/atom = 5.92362
Neighbor list builds = 0
Dangerous builds = 0
reset_timestep 0
velocity all create 413.0 12378 dist gaussian
thermo 10
thermo_style custom step pe ke etotal temp press pxx pyy pzz
variable STEP equal step
variable PE equal pe
variable KE equal ke
variable ETOTAL equal etotal
variable TEMP equal temp
variable VOL equal vol
variable PRESS equal press
variable LX equal lx
variable LZ equal lz
variable PXX equal pxx
variable PYY equal pyy
variable PZZ equal pzz
fix 1 all nvt temp 413.0 413.0 0.1 fixedpoint 0.0 0.0 0.0
#fix thermo_output all print 2000 "${STEP} ${PE} ${KE} ${ETOTAL} ${TEMP} ${VOL} ${PRESS} ${LX} ${LZ} ${PXX} ${PYY} ${PZZ}" file thermo.lammps title "# Step PotEng KinEng TotEng Temp Volume Press Lx Lz Pxx Pyy Pzz"
#dump 1 all custom 10 traj_npt.lammpstrj id mol type x y z ix iy iz
run 100
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.224856
grid = 27 27 64
stencil order = 5
estimated absolute RMS force accuracy = 0.00015081
estimated relative force accuracy = 1.04732e-05
using double precision FFTs
3d grid and FFT values/proc = 24276 11664
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:218)
Per MPI rank memory allocation (min/avg/max) = 20.51 | 36.93 | 59.12 Mbytes
Step PotEng KinEng TotEng Temp Press Pxx Pyy Pzz
0 -10033.541 968.66066 -9064.8807 413 -1034.7033 5221.7757 -4827.0742 -3498.8115
10 -9717.5642 663.69058 -9053.8736 282.97238 -392.07182 5076.3825 -3643.5902 -2609.0078
20 -9592.3732 550.97993 -9041.3932 234.91685 -737.21307 4729.9669 -4234.1008 -2707.5053
30 -9689.9997 645.41353 -9044.5862 275.17974 -1095.6905 5368.8361 -5243.8524 -3412.0551
40 -9721.5122 675.86683 -9045.6453 288.16387 -138.73949 6292.4674 -3623.6807 -3085.0052
50 -9576.7583 544.96028 -9031.798 232.3503 -552.64225 4683.2668 -3286.1479 -3055.0457
60 -9542.5531 522.39339 -9020.1597 222.72864 -1044.0254 3675.027 -3821.1015 -2986.0017
70 -9572.4447 551.73535 -9020.7093 235.23893 132.77197 4550.5092 -2208.7446 -1943.4487
80 -9684.4674 666.4064 -9018.061 284.1303 999.60397 3345.5104 -202.16376 -144.53477
90 -9553.3377 550.82743 -9002.5103 234.85183 -1291.4189 1264.3148 -2496.9658 -2641.6058
100 -9551.9716 560.31802 -8991.6536 238.89826 -1189.4791 1842.8208 -3025.5224 -2385.7357
Loop time of 10.6085 on 4 procs for 100 steps with 18146 atoms
Performance: 0.814 ns/day, 29.468 hours/ns, 9.426 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1362 | 3.9541 | 8.4741 | 152.5 | 37.27
Bond | 0.0070739 | 0.16051 | 0.36228 | 36.1 | 1.51
Kspace | 0.96032 | 5.5204 | 8.3734 | 130.4 | 52.04
Neigh | 0.70817 | 0.7087 | 0.70915 | 0.0 | 6.68
Comm | 0.061705 | 0.2165 | 0.40455 | 26.6 | 2.04
Output | 0.0013981 | 0.001441 | 0.0015171 | 0.1 | 0.01
Modify | 0.024801 | 0.030292 | 0.039353 | 3.1 | 0.29
Other | | 0.01646 | | | 0.16
Nlocal: 4536.5 ave 8016 max 572 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 11368.2 ave 16706 max 5173 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 110474 ave 236783 max 9217 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 441898
Ave neighs/atom = 24.3524
Ave special neighs/atom = 5.92362
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:12

80476
examples/USER/misc/momb/system.data Normal file
View File

File diff suppressed because it is too large Load Diff