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Merge pull request #540 from lammps/neighrespa 

fix issue with rRESPA inner/middle neighbor lists
This commit is contained in:
sjplimp 2017-06-22 07:54:12 -06:00 committed by GitHub
parent 4fc3f4f7e5 b0ddabbcde
commit 7a4a569859
17 changed files with 834 additions and 779 deletions
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4
doc/src/compute_pair_local.txt
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@ -76,7 +76,9 @@ command for the types of the two atoms is used. For the {radius}
setting, the sum of the radii of the two particles is used as a
cutoff. For example, this is appropriate for granular particles which
only interact when they are overlapping, as computed by "granular pair
styles"_pair_gran.txt.
styles"_pair_gran.txt. Note that if a granular model defines atom
types such that all particles of a specific type are monodisperse
(same diameter), then the two settings are effectively identical.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array

3
doc/src/compute_property_local.txt
View File

@ -79,6 +79,9 @@ the two atoms is used. For the {radius} setting, the sum of the radii
of the two particles is used as a cutoff. For example, this is
appropriate for granular particles which only interact when they are
overlapping, as computed by "granular pair styles"_pair_gran.html.
Note that if a granular model defines atom types such that all
particles of a specific type are monodisperse (same diameter), then
the two settings are effectively identical.
If the inputs are bond, angle, etc attributes, the local data is
generated by looping over all the atoms owned on a processor and

10
doc/src/dihedral_charmm.txt
View File

@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively.
[Restrictions:]
This dihedral style can only be used if LAMMPS was built with the
When using run_style "respa"_run_style.html, these dihedral styles
must be assigned to the same r-RESPA level as {pair} or {outer}.
When used in combination with CHARMM pair styles, the 1-4
"special_bonds"_special_bonds.html scaling factors must be set to 0.0.
Otherwise non-bonded contributions for these 1-4 pairs will be
computed multiple times.
These dihedral styles can only be used if LAMMPS was built with the
MOLECULE package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info on packages.

4
doc/src/run_style.txt
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@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
{verlet/split} args = none
{respa} args = N n1 n2 ... keyword values ...
N = # of levels of rRESPA
n1, n2, ... = loop factor between rRESPA levels (N-1 values)
n1, n2, ... = loop factors between rRESPA levels (N-1 values)
zero or more keyword/value pairings may be appended to the loop factors
keyword = {bond} or {angle} or {dihedral} or {improper} or
{pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace}
@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l
run_style verlet
run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre
run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre
[Description:]

2
examples/USER/misc/filter_corotate/in.bpti
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@ -28,7 +28,7 @@ thermo 100
thermo_style multi
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
#dump dump1 all atom 100 4pti.dump

2
examples/USER/misc/filter_corotate/in.peptide
View File

@ -20,7 +20,7 @@ thermo 50
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 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

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

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

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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

147
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 Normal file
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@ -0,0 +1,147 @@
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
examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4 Normal file
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@ -0,0 +1,147 @@
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

18
src/MOLECULE/dihedral_charmm.cpp
View File

@ -18,6 +18,7 @@
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "dihedral_charmm.h"
#include "atom.h"
#include "comm.h"
@ -26,6 +27,7 @@
#include "force.h"
#include "pair.h"
#include "update.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@ -368,10 +370,26 @@ void DihedralCharmm::coeff(int narg, char **arg)
void DihedralCharmm::init_style()
{
if (strstr(update->integrate_style,"respa")) {
Respa *r = (Respa *) update->integrate;
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
error->all(FLERR,"Dihedral style charmm must be set to same"
" r-RESPA level as 'pair'");
if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
error->all(FLERR,"Dihedral style charmm must be set to same"
" r-RESPA level as 'outer'");
}
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
// also verify that the correct 1-4 scaling is set
if (weightflag) {
if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
error->all(FLERR,"Must use 'special_bonds charmm' with"
" dihedral style charmm for use with CHARMM pair styles");
int itmp;
if (force->pair == NULL)
error->all(FLERR,"Dihedral charmm is incompatible with Pair style");

18
src/MOLECULE/dihedral_charmmfsw.cpp
View File

@ -21,6 +21,7 @@
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "dihedral_charmmfsw.h"
#include "atom.h"
#include "comm.h"
@ -29,6 +30,7 @@
#include "force.h"
#include "pair.h"
#include "update.h"
#include "respa.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
@ -386,10 +388,26 @@ void DihedralCharmmfsw::coeff(int narg, char **arg)
void DihedralCharmmfsw::init_style()
{
if (strstr(update->integrate_style,"respa")) {
Respa *r = (Respa *) update->integrate;
if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
error->all(FLERR,"Dihedral style charmmfsw must be set to same"
" r-RESPA level as 'pair'");
if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
error->all(FLERR,"Dihedral style charmmfsw must be set to same"
" r-RESPA level as 'outer'");
}
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
// also verify that the correct 1-4 scaling is set
if (weightflag) {
if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
error->all(FLERR,"Must use 'special_bonds charmm' with"
" dihedral style charmm for use with CHARMM pair styles");
int itmp;
if (force->pair == NULL)
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");

4
src/neighbor.cpp
View File

@ -1268,9 +1268,11 @@ void Neighbor::morph_copy()
if (irq->ghost && !jrq->ghost) continue;
// do not copy from a history list
// do not copy from a history list or a respa middle/inner list
if (jrq->history) continue;
if (jrq->respamiddle) continue;
if (jrq->respainner) continue;
// these flags must be same,
// else 2 lists do not store same pairs