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move interlayer potentials to their own package

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This commit is contained in:
Axel Kohlmeyer
2021-07-07 15:52:53 -04:00
parent c9ddee5e38
commit 46d5d9724a
81 changed files with 57 additions and 22 deletions
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1
examples/PACKAGES/interlayer/drip/C.drip Symbolic link
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../../../../potentials/C.drip

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examples/PACKAGES/interlayer/drip/CH.rebo Symbolic link
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../../../../potentials/CH.rebo

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examples/PACKAGES/interlayer/drip/README.txt Normal file
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in.C_drip:
Use DRIP and REBO to relax a bilayer graphene.
in.CH_drip:
Use DRIP and REBO to relax a bilayer graphene with additional hydrogen atoms
on top of it.

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examples/PACKAGES/interlayer/drip/data.C Normal file
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LAMMPS data file
400 atoms
1 atom types
0.0 2.465000000000000e+01 xlo xhi
0.0 2.134752620328641e+01 ylo yhi
0.0 3.000000000000000e+01 zlo zhi
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
Masses
1 12.011
Atoms # molecular
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
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376 2 1 2.218500000000000e+01 7.115842067762138e+00 1.841142851923555e+01
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378 2 1 2.465000000000000e+01 7.115842067762138e+00 1.838708488224049e+01
379 2 1 2.588250000000000e+01 7.827426274538350e+00 1.830434555380351e+01
380 2 1 2.711500000000000e+01 7.115842067762138e+00 1.859652575977937e+01
381 2 1 2.834750000000000e+01 7.827426274538350e+00 1.844094595194482e+01
382 2 1 6.162499999999999e+00 9.250594688090777e+00 1.856484810097502e+01
383 2 1 1.109250000000000e+01 7.827426274538350e+00 1.847502232204046e+01
384 2 1 7.395000000000000e+00 9.962178894866991e+00 1.854741705791729e+01
385 2 1 9.859999999999999e+00 9.962178894866991e+00 1.837074522628645e+01
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387 2 1 1.232500000000000e+01 9.962178894866991e+00 1.823251181425658e+01
388 2 1 1.355750000000000e+01 9.250594688090777e+00 1.834993099844037e+01
389 2 1 1.479000000000000e+01 9.962178894866991e+00 1.843248036437880e+01
390 2 1 1.602250000000000e+01 9.250594688090777e+00 1.855142577781635e+01
391 2 1 1.725500000000000e+01 9.962178894866991e+00 1.847587547064991e+01
392 2 1 1.848750000000000e+01 9.250594688090777e+00 1.850249139638135e+01
393 2 1 1.972000000000000e+01 9.962178894866991e+00 1.841266132895000e+01
394 2 1 2.095250000000000e+01 9.250594688090777e+00 1.837466808881276e+01
395 2 1 2.218500000000000e+01 9.962178894866991e+00 1.834587370280250e+01
396 2 1 2.341750000000000e+01 9.250594688090777e+00 1.846590574952954e+01
397 2 1 2.465000000000000e+01 9.962178894866991e+00 1.835650105398410e+01
398 2 1 2.588250000000000e+01 9.250594688090777e+00 1.838143174570202e+01
399 2 1 8.627500000000000e+00 9.250594688090777e+00 1.843904853716322e+01
400 2 1 3.574249999999999e+01 2.063594199651019e+01 1.839864514570517e+01

562
examples/PACKAGES/interlayer/drip/data.CH Normal file
View File

@ -0,0 +1,562 @@
LAMMPS data file
545 atoms
2 atom types
0.0 2.465000000000000e+01 xlo xhi
0.0 2.134752620328641e+01 ylo yhi
0.0 3.000000000000000e+01 zlo zhi
1.232500000000000e+01 0.000000000000000e+00 0.000000000000000e+00 xy xz yz
Masses
1 12.011
2 1.0
Atoms # molecular
1 1 1 0.000000000000000e+00 0.000000000000000e+00 1.498097531971289e+01
2 1 1 9.859999999999999e+00 1.707802096262913e+01 1.489139792549795e+01
3 1 1 2.588250000000000e+01 6.404257860985923e+00 1.495586615731768e+01
4 1 1 2.711500000000000e+01 7.115842067762138e+00 1.501795235919980e+01
5 1 1 4.930000000000000e+00 8.539010481314564e+00 1.492827527515956e+01
6 1 1 6.162499999999999e+00 9.250594688090777e+00 1.500678649580791e+01
7 1 1 3.204499999999999e+01 1.565485254907670e+01 1.511662064028576e+01
8 1 1 3.081250000000000e+01 1.494326834230049e+01 1.505500683988625e+01
9 1 1 7.395000000000000e+00 8.539010481314564e+00 1.504923694256975e+01
10 1 1 8.627500000000000e+00 9.250594688090777e+00 1.503332570633445e+01
11 1 1 9.859999999999999e+00 8.539010481314564e+00 1.508137430939768e+01
12 1 1 1.109250000000000e+01 9.250594688090777e+00 1.510475862694483e+01
13 1 1 1.109250000000000e+01 1.778960516940534e+01 1.494613902888088e+01
14 1 1 2.958000000000000e+01 1.565485254907670e+01 1.516279958068751e+01
15 1 1 1.232500000000000e+01 8.539010481314564e+00 1.511276583208523e+01
16 1 1 1.355750000000000e+01 9.250594688090777e+00 1.495632206546155e+01
17 1 1 1.479000000000000e+01 8.539010481314564e+00 1.498291715828213e+01
18 1 1 1.602250000000000e+01 9.250594688090777e+00 1.509801558902469e+01
19 1 1 2.711499999999999e+01 1.565485254907670e+01 1.500089766276763e+01
20 1 1 2.588250000000000e+01 1.494326834230049e+01 1.505114888970355e+01
21 1 1 1.725500000000000e+01 8.539010481314564e+00 1.504495103103041e+01
22 1 1 1.848750000000000e+01 9.250594688090777e+00 1.513527732850389e+01
23 1 1 1.972000000000000e+01 8.539010481314564e+00 1.502400693288890e+01
24 1 1 2.095250000000000e+01 9.250594688090777e+00 1.490419939433632e+01
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476 2 2 3.697500000000000e+00 7.115842067762137e-01 2.000000000000000e+01
477 2 2 4.929999999999999e+00 1.423168413552427e+00 2.000000000000000e+01
478 2 2 9.859999999999999e+00 1.423168413552427e+00 2.000000000000000e+01
479 2 2 1.109250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
480 2 2 1.232500000000000e+01 1.423168413552427e+00 2.000000000000000e+01
481 2 2 1.355750000000000e+01 7.115842067762137e-01 2.000000000000000e+01
482 2 2 1.479000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
483 2 2 1.602250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
484 2 2 2.095250000000000e+01 7.115842067762137e-01 2.000000000000000e+01
485 2 2 2.218500000000000e+01 1.423168413552427e+00 2.000000000000000e+01
486 2 2 2.341750000000000e+01 7.115842067762137e-01 2.000000000000000e+01
487 2 2 2.465000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
488 2 2 2.465000000000000e+00 2.846336827104855e+00 2.000000000000000e+01
489 2 2 3.697500000000000e+00 3.557921033881068e+00 2.000000000000000e+01
490 2 2 8.627500000000000e+00 3.557921033881068e+00 2.000000000000000e+01
491 2 2 9.859999999999999e+00 2.846336827104855e+00 2.000000000000000e+01
492 2 2 1.109250000000000e+01 3.557921033881068e+00 2.000000000000000e+01
493 2 2 1.232500000000000e+01 2.846336827104855e+00 2.000000000000000e+01
494 2 2 1.355750000000000e+01 3.557921033881068e+00 2.000000000000000e+01
495 2 2 1.972000000000000e+01 1.423168413552427e+00 2.000000000000000e+01
496 2 2 8.627500000000000e+00 1.209693151519563e+01 2.000000000000000e+01
497 2 2 9.859999999999999e+00 1.138534730841942e+01 2.000000000000000e+01
498 2 2 1.109250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
499 2 2 1.232500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
500 2 2 1.355750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
501 2 2 1.479000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
502 2 2 1.602250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
503 2 2 2.095250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
504 2 2 2.218500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
505 2 2 2.341750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
506 2 2 2.465000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
507 2 2 2.588250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
508 2 2 2.711500000000000e+01 1.138534730841942e+01 2.000000000000000e+01
509 2 2 2.834750000000000e+01 1.209693151519563e+01 2.000000000000000e+01
510 2 2 2.958000000000000e+01 1.138534730841942e+01 2.000000000000000e+01
511 2 2 3.081250000000000e+01 1.209693151519563e+01 2.000000000000000e+01
512 2 2 8.627500000000000e+00 1.352009992874806e+01 2.000000000000000e+01
513 2 2 9.859999999999999e+00 1.423168413552428e+01 2.000000000000000e+01
514 2 2 1.109250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
515 2 2 1.602250000000000e+01 1.352009992874806e+01 2.000000000000000e+01
516 2 2 1.725500000000000e+01 1.423168413552428e+01 2.000000000000000e+01
517 2 2 1.848750000000000e+01 1.352009992874806e+01 2.000000000000000e+01
518 2 2 1.972000000000000e+01 1.423168413552428e+01 2.000000000000000e+01
519 2 2 7.395000000000000e+00 1.138534730841942e+01 2.000000000000000e+01
520 2 2 3.451000000000000e+01 1.992435778973398e+01 2.000000000000000e+01
521 2 2 2.834750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
522 2 2 2.711499999999999e+01 9.962178894866991e+00 2.000000000000000e+01
523 2 2 1.355750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
524 2 2 1.479000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
525 2 2 1.972000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
526 2 2 2.095250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
527 2 2 2.218500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
528 2 2 2.341750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
529 2 2 2.465000000000000e+01 7.115842067762138e+00 2.000000000000000e+01
530 2 2 2.588250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
531 2 2 2.711500000000000e+01 7.115842067762138e+00 2.000000000000000e+01
532 2 2 2.834750000000000e+01 7.827426274538350e+00 2.000000000000000e+01
533 2 2 6.162499999999999e+00 9.250594688090777e+00 2.000000000000000e+01
534 2 2 1.109250000000000e+01 7.827426274538350e+00 2.000000000000000e+01
535 2 2 1.232500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
536 2 2 1.355750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
537 2 2 1.479000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
538 2 2 1.602250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
539 2 2 1.725500000000000e+01 9.962178894866991e+00 2.000000000000000e+01
540 2 2 1.848750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
541 2 2 2.341750000000000e+01 9.250594688090777e+00 2.000000000000000e+01
542 2 2 2.465000000000000e+01 9.962178894866991e+00 2.000000000000000e+01
543 2 2 2.588250000000000e+01 9.250594688090777e+00 2.000000000000000e+01
544 2 2 8.627500000000000e+00 9.250594688090777e+00 2.000000000000000e+01
545 2 2 3.574249999999999e+01 2.063594199651019e+01 2.000000000000000e+01

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# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100

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# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
pair_coeff * * rebo CH.rebo C
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
545 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000152826 secs
read_data CPU = 0.000973701 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.92 | 12.92 | 12.92 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.215 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.059 2779.5956
50 0 -3282.4755 0 -3282.4755 -22659.554 2779.5956
57 0 -3282.5011 0 -3282.5011 -23313.198 2779.5956
Loop time of 3.04218 on 1 procs for 57 steps with 545 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2884.37307546 -3282.49993222 -3282.5010627
Force two-norm initial, final = 115.342 0.193154
Force max component initial, final = 12.0934 0.03617
Final line search alpha, max atom move = 1 0.03617
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0291 | 3.0291 | 3.0291 | 0.0 | 99.57
Bond | 1.8835e-05 | 1.8835e-05 | 1.8835e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.05
Output | 0.0079796 | 0.0079796 | 0.0079796 | 0.0 | 0.26
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003517 | | | 0.12
Nlocal: 545 ave 545 max 545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3175 ave 3175 max 3175 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 294122 ave 294122 max 294122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 294122
Ave neighs/atom = 539.673
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.CH
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
545 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000135422 secs
read_data CPU = 0.00368595 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C NULL # only applies to species 1, i.e. C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C H # species 1 is C and species 2 is H
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.03 | 11.1 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2884.3731 0 -2884.3731 366196.9 2779.5956
10 0 -3240.4807 0 -3240.4807 -20237.368 2779.5956
20 0 -3281.0671 0 -3281.0671 -13303.696 2779.5956
30 0 -3282.2176 0 -3282.2176 -19187.216 2779.5956
40 0 -3282.4004 0 -3282.4004 -21740.027 2779.5956
50 0 -3282.4753 0 -3282.4753 -22682.604 2779.5956
57 0 -3282.5023 0 -3282.5023 -23355.081 2779.5956
Loop time of 1.66218 on 4 procs for 57 steps with 545 atoms
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2884.37307546 -3282.50070864 -3282.50227121
Force two-norm initial, final = 115.342 0.228488
Force max component initial, final = 12.0934 0.03365
Final line search alpha, max atom move = 1 0.03365
Iterations, force evaluations = 57 100
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5571 | 1.5945 | 1.6314 | 2.3 | 95.93
Bond | 2.265e-05 | 2.9087e-05 | 3.4571e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.020248 | 0.05608 | 0.092328 | 11.8 | 3.37
Output | 0.0053282 | 0.0054213 | 0.0056982 | 0.2 | 0.33
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006172 | | | 0.37
Nlocal: 136.25 ave 177 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 2874.75 ave 2912 max 2835 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 539.673
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
400 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000912905 secs
read_data CPU = 0.00252986 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair rebo, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 2.93337 on 1 procs for 51 steps with 400 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
Iterations, force evaluations = 51 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 99.68
Bond | 1.2398e-05 | 1.2398e-05 | 1.2398e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010808 | 0.0010808 | 0.0010808 | 0.0 | 0.04
Output | 0.0059283 | 0.0059283 | 0.0059283 | 0.0 | 0.20
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002466 | | | 0.08
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2357 ave 2357 max 2357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 294122 ave 294122 max 294122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 294122
Ave neighs/atom = 735.305
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Define unit set and class of atomic model
units metal
atom_style molecular
# BC
boundary p p s
# read config
read_data data.C
triclinic box = (0 0 0) to (24.65 21.3475 30) with tilt (12.325 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
400 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.0003407 secs
read_data CPU = 0.00411105 secs
# potential
pair_style hybrid/overlay drip rebo
pair_coeff * * drip C.drip C
Reading potential file C.drip with DATE: 2019-04-19
pair_coeff * * rebo CH.rebo C
Reading potential file CH.rebo with DATE: 2018-7-3
compute peratom all pe/atom
# set what thermodynamic information to print to log
thermo 10 # print every 1 timestep
# set what information to write to dump file
dump id all custom 1 lammps.dump id type x y z fx fy fz c_peratom
dump_modify id every 10 format line "%d %d %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e %13.5e"
dump_modify id sort id
# minimize energy
minimize 1.0e-15 1.0e-15 100 100
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17.7
ghost atom cutoff = 17.7
binsize = 8.85, bins = 5 3 1
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair drip, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair rebo, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:934)
Per MPI rank memory allocation (min/avg/max) = 10.7 | 10.77 | 10.83 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -2941.0549 0 -2941.0549 -52204.715 2052.0534
10 0 -2966.9787 0 -2966.9787 -29717.01 2052.0534
20 0 -2967.0695 0 -2967.0695 -29614.636 2052.0534
30 0 -2967.0859 0 -2967.0859 -29867.385 2052.0534
40 0 -2967.0888 0 -2967.0888 -29997.486 2052.0534
50 0 -2967.0896 0 -2967.0896 -30072.387 2052.0534
51 0 -2967.0896 0 -2967.0896 -30076.548 2052.0534
Loop time of 1.47901 on 4 procs for 51 steps with 400 atoms
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2941.05486197 -2967.08958376 -2967.08962073
Force two-norm initial, final = 35.5666 0.0471918
Force max component initial, final = 6.23617 0.0050012
Final line search alpha, max atom move = 1 0.0050012
Iterations, force evaluations = 51 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4314 | 1.4405 | 1.4548 | 0.8 | 97.40
Bond | 1.955e-05 | 2.265e-05 | 2.4796e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.014506 | 0.029363 | 0.038964 | 5.5 | 1.99
Output | 0.00424 | 0.0043345 | 0.0046172 | 0.2 | 0.29
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004772 | | | 0.32
Nlocal: 100 ave 100 max 100 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2132 ave 2132 max 2132 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 73530.5 ave 73544 max 73517 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 294122
Ave neighs/atom = 735.305
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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examples/PACKAGES/interlayer/ilp_graphene_hbn/BNC.tersoff Symbolic link
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../../../../potentials/BNC.tersoff

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examples/PACKAGES/interlayer/ilp_graphene_hbn/BNCH-old.ILP Symbolic link
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../../../../potentials/BNCH-old.ILP

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examples/PACKAGES/interlayer/ilp_graphene_hbn/Bi_gr_AB_stack_2L_noH.data Normal file
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examples/PACKAGES/interlayer/ilp_graphene_hbn/gr_hBN_Cstack_2L_noH.data Normal file
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examples/PACKAGES/interlayer/ilp_graphene_hbn/in.bilayer-graphene Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000

56
examples/PACKAGES/interlayer/ilp_graphene_hbn/in.bilayer-hBN Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000

56
examples/PACKAGES/interlayer/ilp_graphene_hbn/in.grhBN Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
group gr molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000

61
examples/PACKAGES/interlayer/ilp_graphene_hbn/in.ilp_graphene_hbn Normal file
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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
group adsorbate type 3 4
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000

127
examples/PACKAGES/interlayer/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.1 Normal file
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000290871 secs
read_data CPU = 0.00159073 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
Loop time of 149.887 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.576 ns/day, 41.635 hours/ns, 6.672 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 149.75 | 149.75 | 149.75 | 0.0 | 99.91
Bond | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.086328 | 0.086328 | 0.086328 | 0.0 | 0.06
Output | 0.00036383 | 0.00036383 | 0.00036383 | 0.0 | 0.00
Modify | 0.028636 | 0.028636 | 0.028636 | 0.0 | 0.02
Other | | 0.01708 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:30

127
examples/PACKAGES/interlayer/ilp_graphene_hbn/log.31Jul19.bilayer-graphene.g++.4 Normal file
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000157118 secs
read_data CPU = 0.00145698 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo ilp/graphene/hbn 16.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * ilp/graphene/hbn BNCH.ILP C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair ilp/graphene/hbn
variable REBO equal c_0 # REBO energy
variable ILP equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_ILP v_Erep v_Evdw temp
thermo_modify lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.879 | 9.879 | 9.879 Mbytes
Step TotEng PotEng KinEng v_REBO v_ILP v_Erep v_Evdw Temp
0 -10037.285 -10089.985 52.699361 -10057.189 -32.795185 43.640104 -76.435288 300
100 -10037.034 -10064.765 27.73131 -10032.181 -32.58421 34.730868 -67.315078 157.86516
200 -10036.963 -10061.144 24.18111 -10028.856 -32.288132 28.179936 -60.468068 137.65505
300 -10037.003 -10063.5 26.496726 -10030.823 -32.677105 34.923849 -67.600954 150.83708
400 -10037.032 -10064.389 27.356526 -10031.853 -32.535415 44.242347 -76.777762 155.73164
500 -10037.023 -10064.114 27.090279 -10031.431 -32.682418 37.229232 -69.91165 154.21598
600 -10037.003 -10063.657 26.653718 -10031.327 -32.329664 28.509073 -60.838737 151.73078
700 -10037.004 -10063.35 26.345697 -10030.801 -32.549231 32.564686 -65.113917 149.97732
800 -10037.025 -10064.219 27.194765 -10031.766 -32.453653 43.381557 -75.83521 154.81078
900 -10037.028 -10064.668 27.639127 -10032.167 -32.500121 39.99345 -72.493571 157.34039
1000 -10037.003 -10063.662 26.658825 -10031.337 -32.325053 29.573578 -61.898631 151.75986
Loop time of 44.6551 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.935 ns/day, 12.404 hours/ns, 22.394 timesteps/s
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 40.304 | 41.221 | 41.998 | 9.5 | 92.31
Bond | 0.00027633 | 0.00029379 | 0.00031424 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.5678 | 3.3334 | 4.2403 | 32.9 | 7.46
Output | 0.0051446 | 0.0054518 | 0.0059683 | 0.4 | 0.01
Modify | 0.0088317 | 0.009002 | 0.0090654 | 0.1 | 0.02
Other | | 0.08586 | | | 0.19
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4628 ave 4628 max 4628 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259250 ave 259250 max 259250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:44

142
examples/PACKAGES/interlayer/ilp_graphene_hbn/log.31Jul19.bilayer-hBN.g++.1 Normal file
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000375509 secs
read_data CPU = 0.00181293 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
Loop time of 211.527 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.408 ns/day, 58.757 hours/ns, 4.728 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 211.4 | 211.4 | 211.4 | 0.0 | 99.94
Bond | 0.00018859 | 0.00018859 | 0.00018859 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.082034 | 0.082034 | 0.082034 | 0.0 | 0.04
Output | 0.00037289 | 0.00037289 | 0.00037289 | 0.0 | 0.00
Modify | 0.027928 | 0.027928 | 0.027928 | 0.0 | 0.01
Other | | 0.0159 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7836 ave 7836 max 7836 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249560 ave 249560 max 249560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.00504e+06 ave 1.00504e+06 max 1.00504e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:31

142
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AA_prime_stack_2L_noH.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000224352 secs
read_data CPU = 0.00160909 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff B N B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0 # Tersoff energy
variable Ecoul equal c_1 # Coulomb energy
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
############# Output ###############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul temp
thermo_modify lost warn
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
4 neighbor lists, perpetual/occasional/extra = 4 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (4)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10193.138 -10245.837 52.699361 -77.557069 -10208.73 -36.776483 40.780586 -77.557069 -0.33075117 300
100 -10192.814 -10215.193 22.37957 -80.997619 -10177.878 -36.967736 44.029884 -80.997619 -0.34809915 127.39947
200 -10192.922 -10221.807 28.884855 -86.370319 -10184.251 -37.168986 49.201334 -86.370319 -0.38644764 164.43191
300 -10192.878 -10219.029 26.151464 -83.063924 -10182.349 -36.30412 46.759804 -83.063924 -0.37660157 148.87162
400 -10192.892 -10218.834 25.942229 -78.394242 -10181.398 -37.110968 41.283274 -78.394242 -0.32494569 147.68051
500 -10192.909 -10221.331 28.422213 -81.768531 -10184.03 -36.946226 44.822304 -81.768531 -0.35489965 161.79824
600 -10192.886 -10219.371 26.48495 -86.278335 -10182.669 -36.29515 49.983185 -86.278335 -0.40636253 150.77004
700 -10192.902 -10220.95 28.048108 -82.28873 -10183.208 -37.39374 44.89499 -82.28873 -0.34777958 159.66859
800 -10192.88 -10218.51 25.630186 -78.011019 -10181.427 -36.754209 41.256811 -78.011019 -0.32904942 145.90415
900 -10192.894 -10220.56 27.665437 -82.474379 -10183.801 -36.381157 46.093222 -82.474379 -0.37703328 157.49017
1000 -10192.897 -10219.01 26.11313 -87.125683 -10181.252 -37.361898 49.763785 -87.125683 -0.39607952 148.65339
Loop time of 68.3631 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.264 ns/day, 18.990 hours/ns, 14.628 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 64.58 | 66.38 | 67.402 | 13.2 | 97.10
Bond | 0.0001719 | 0.00021869 | 0.00024033 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.93767 | 1.9601 | 3.76 | 77.0 | 2.87
Output | 0.00033593 | 0.00061601 | 0.0014501 | 0.0 | 0.00
Modify | 0.0085733 | 0.0089303 | 0.0093236 | 0.4 | 0.01
Other | | 0.01285 | | | 0.02
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4536 ave 4536 max 4536 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 62390 ave 62390 max 62390 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 251260 ave 251260 max 251260 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1005040
Ave neighs/atom = 739
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:08

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000282049 secs
read_data CPU = 0.00159025 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 22.52 | 22.52 | 22.52 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
Loop time of 152.66 on 1 procs for 1000 steps with 1440 atoms
Performance: 0.566 ns/day, 42.406 hours/ns, 6.550 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 152.52 | 152.52 | 152.52 | 0.0 | 99.91
Bond | 0.00023174 | 0.00023174 | 0.00023174 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.087147 | 0.087147 | 0.087147 | 0.0 | 0.06
Output | 0.0004189 | 0.0004189 | 0.0004189 | 0.0 | 0.00
Modify | 0.029972 | 0.029972 | 0.029972 | 0.0 | 0.02
Other | | 0.02057 | | | 0.01
Nlocal: 1440 ave 1440 max 1440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8180 ave 8180 max 8180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 140400 ave 140400 max 140400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 280800 ave 280800 max 280800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:02:32

153
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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer
# so that inter- and intra-layer
# interactions can be specified separately
read_data gr_hBN_Cstack_2L_noH.data
orthogonal box = (0 0 0) to (44.583 42.9 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1440 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.00012207 secs
read_data CPU = 0.00357461 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | membrane
mass 3 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group hBN molecule 1
720 atoms in group hBN
group gr molecule 2
720 atoms in group gr
######################## Potential defition ########################
pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * tersoff BNC.tersoff B N NULL # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C # long range
pair_coeff 1 1 coul/shield 0.70
pair_coeff 1 2 coul/shield 0.69498201415576216335
pair_coeff 2 2 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345 dist gaussian mom yes rot yes
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair tersoff
compute 2 all pair ilp/graphene/hbn
compute 3 all pair coul/shield
variable REBO equal c_0
variable Tersoff equal c_1
variable EILP equal c_2 # total interlayer energy
variable Evdw equal c_2[1] # attractive energy
variable Erep equal c_2[2] # repulsive energy
variable Ecoul equal c_3
############# Output ##############
thermo 100
thermo_style custom step etotal pe ke v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul temp
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
6 neighbor lists, perpetual/occasional/extra = 6 0 0
(1) pair rebo, perpetual, skip from (3)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair tersoff, perpetual, skip from (5)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(3) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(4) pair coul/shield, perpetual, half/full from (2)
attributes: half, newton on
pair build: halffull/newton/skip
stencil: none
bin: none
(5) neighbor class addition, perpetual, copy from (3)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(6) neighbor class addition, perpetual, half/full from (5)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.45 | 12.45 | 12.45 Mbytes
Step TotEng PotEng KinEng v_Evdw v_Tersoff v_REBO v_EILP v_Erep v_Evdw v_Ecoul Temp
0 -10707.284 -10763.085 55.801605 -75.247726 -5401.7348 -5322.2781 -39.072409 36.175318 -75.247726 0 300
100 -10707.074 -10737.127 30.05353 -73.217322 -5389.9568 -5309.2004 -37.970102 35.24722 -73.217322 0 161.57347
200 -10707.016 -10734.932 27.91576 -71.603097 -5389.1294 -5307.7455 -38.056875 33.546222 -71.603097 0 150.08042
300 -10707.013 -10734.987 27.973705 -75.082134 -5388.9196 -5308.1165 -37.950947 37.131186 -75.082134 0 150.39194
400 -10707.012 -10735.498 28.486171 -76.339871 -5389.1657 -5308.153 -38.179442 38.160429 -76.339871 0 153.14706
500 -10707.007 -10734.681 27.674101 -73.312354 -5388.7261 -5307.7384 -38.216944 35.09541 -73.312354 0 148.78121
600 -10707.018 -10735.833 28.815132 -71.927763 -5389.0798 -5308.596 -38.157333 33.77043 -71.927763 0 154.91561
700 -10707.02 -10735.656 28.635377 -74.679371 -5389.2971 -5308.1866 -38.172002 36.507368 -74.679371 0 153.94921
800 -10707.004 -10734.352 27.347425 -76.371288 -5388.5923 -5307.7206 -38.038736 38.332552 -76.371288 0 147.02494
900 -10707.014 -10735.832 28.817405 -73.699332 -5388.9674 -5308.7964 -38.068078 35.631254 -73.699332 0 154.92783
1000 -10706.995 -10733.562 26.56615 -71.439868 -5388.0186 -5307.4414 -38.101452 33.338415 -71.439868 0 142.82466
Loop time of 54.095 on 4 procs for 1000 steps with 1440 atoms
Performance: 1.597 ns/day, 15.026 hours/ns, 18.486 timesteps/s
84.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 42.138 | 45.531 | 49.106 | 42.0 | 84.17
Bond | 0.0003159 | 0.00037384 | 0.000489 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.71 | 8.2803 | 11.682 | 98.3 | 15.31
Output | 0.0021999 | 0.0055975 | 0.013382 | 6.0 | 0.01
Modify | 0.0092845 | 0.010981 | 0.012538 | 1.3 | 0.02
Other | | 0.2673 | | | 0.49
Nlocal: 360 ave 380 max 340 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4716 ave 4736 max 4696 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 35100 ave 37050 max 33150 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 70200 ave 74100 max 66300 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 280800
Ave neighs/atom = 195
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000251532 secs
read_data CPU = 0.00451231 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair tersoff, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, half/full from (4)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 54.59 | 54.59 | 54.59 Mbytes
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
Loop time of 207.028 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.417 ns/day, 57.508 hours/ns, 4.830 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 206.9 | 206.9 | 206.9 | 0.0 | 99.94
Bond | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.081397 | 0.081397 | 0.081397 | 0.0 | 0.04
Output | 0.00036597 | 0.00036597 | 0.00036597 | 0.0 | 0.00
Modify | 0.033408 | 0.033408 | 0.033408 | 0.0 | 0.02
Other | | 0.01615 | | | 0.01
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7840 ave 7840 max 7840 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 249628 ave 249628 max 249628 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 253390 ave 253390 max 253390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 253390
Ave neighs/atom = 186.316
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:27

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LAMMPS (31 Jul 2019)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data hBN_AB_stack_2L_noH_equi_300K.data
orthogonal box = (0 0 0) to (43.38 42.5773 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000332117 secs
read_data CPU = 0.00270581 secs
mass 1 10.8110 # boron mass (g/mole) | membrane
mass 2 14.0067 # nitrogen mass (g/mole) | adsorbate
mass 3 10.8110 # boron mass (g/mole) | membrane
mass 4 14.0067 # nitrogen mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1 2
680 atoms in group membrane
group adsorbate type 3 4
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 1
####################################################################
pair_coeff * * tersoff BNC.tersoff NULL NULL B N # chemical
Reading potential file BNC.tersoff with DATE: 2013-03-21
pair_coeff * * ilp/graphene/hbn BNCH-old.ILP B N B N # long range
pair_coeff 1 3 coul/shield 0.70
pair_coeff 1 4 coul/shield 0.69498201415576216335
pair_coeff 2 3 coul/shield 0.69498201415576216335
pair_coeff 2 4 coul/shield 0.69
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
#velocity adsorbate create 300.0 12345
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair tersoff
compute 1 all pair coul/shield ecoul
compute 2 all pair ilp/graphene/hbn
variable Tersoff equal c_0
variable Ecoul equal c_1
variable ILP equal c_2
variable Evdw equal c_2[1]
variable Erep equal c_2[2]
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw temp
thermo_modify lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
5 neighbor lists, perpetual/occasional/extra = 5 0 0
(1) pair tersoff, perpetual, skip from (4)
attributes: full, newton on
pair build: skip
stencil: none
bin: none
(2) pair ilp/graphene/hbn, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(3) pair coul/shield, perpetual, skip from (5)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(4) neighbor class addition, perpetual, copy from (2)
attributes: full, newton on
pair build: copy
stencil: none
bin: none
(5) neighbor class addition, perpetual, half/full from (4)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 28.9 | 28.9 | 28.9 Mbytes
Step TotEng PotEng KinEng v_Tersoff v_ILP v_Ecoul v_Erep v_Evdw Temp
0 -5114.6628 -5127.8586 13.195828 -5091.4121 -36.083114 -0.36343598 38.918674 -75.001787 75.119474
100 -5114.6621 -5127.6958 13.033777 -5091.2408 -36.09276 -0.36228286 38.769906 -74.862666 74.196973
200 -5114.6631 -5127.5945 12.93145 -5091.1508 -36.086669 -0.35708801 38.20076 -74.287429 73.614462
300 -5114.6694 -5128.3286 13.65924 -5091.8646 -36.110786 -0.35328159 37.758284 -73.86907 77.757528
400 -5114.6614 -5127.6424 12.980975 -5091.2348 -36.049634 -0.35794328 38.247252 -74.296886 73.896389
500 -5114.66 -5127.4098 12.749794 -5090.9285 -36.119571 -0.36174976 38.745548 -74.865119 72.580351
600 -5114.6673 -5128.0913 13.424021 -5091.6339 -36.09384 -0.36356991 38.927401 -75.021241 76.418503
700 -5114.661 -5127.7467 13.085707 -5091.2811 -36.106639 -0.35892399 38.332616 -74.439255 74.492596
800 -5114.6623 -5128.013 13.350778 -5091.5694 -36.089718 -0.35392503 37.851602 -73.94132 76.001554
900 -5114.6675 -5128.1497 13.482146 -5091.6704 -36.124679 -0.35462869 37.885183 -74.009861 76.749392
1000 -5114.6683 -5128.3365 13.668146 -5091.937 -36.037596 -0.36184347 38.709718 -74.747314 77.808228
Loop time of 65.9005 on 4 procs for 1000 steps with 1360 atoms
Performance: 1.311 ns/day, 18.306 hours/ns, 15.174 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 63.244 | 64.208 | 65.281 | 10.1 | 97.43
Bond | 0.00013971 | 0.00017679 | 0.00022101 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.58237 | 1.6612 | 2.6292 | 63.1 | 2.52
Output | 0.0003171 | 0.00062358 | 0.0015192 | 0.0 | 0.00
Modify | 0.010251 | 0.010509 | 0.01075 | 0.2 | 0.02
Other | | 0.02025 | | | 0.03
Nlocal: 340 ave 346 max 336 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 4537.5 ave 4540 max 4534 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 62407 ave 62413 max 62402 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs: 63347.5 ave 65585 max 61866 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 253926
Ave neighs/atom = 186.71
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:06

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examples/PACKAGES/interlayer/kolmogorov_crespi_full/CH_taper.KC Symbolic link
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../../../../potentials/CH_taper.KC

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# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
group layer2 molecule 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000

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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000353813 secs
read_data CPU = 0.0043292 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0
variable KC equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair kolmogorov/crespi/full, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.96 | 16.96 | 16.96 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393292 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
900 -5025.3984547937 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 103.724 on 1 procs for 1000 steps with 1360 atoms
Performance: 0.833 ns/day, 28.812 hours/ns, 9.641 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 103.59 | 103.59 | 103.59 | 0.0 | 99.87
Bond | 0.00022388 | 0.00022388 | 0.00022388 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.082476 | 0.082476 | 0.082476 | 0.0 | 0.08
Output | 0.0010884 | 0.0010884 | 0.0010884 | 0.0 | 0.00
Modify | 0.032938 | 0.032938 | 0.032938 | 0.0 | 0.03
Other | | 0.01749 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 265206 ave 265206 max 265206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:43

139
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
# read lammps data file
read_data Bi_gr_AB_stack_2L_noH_300K.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
reading velocities ...
1360 velocities
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000187874 secs
read_data CPU = 0.00234103 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group membrane type 1
680 atoms in group membrane
group adsorbate type 2
680 atoms in group adsorbate
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
####################################################################
pair_coeff * * rebo CH.rebo NULL C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CC.KC-full C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# calculate the COM
variable adsxcom equal xcm(adsorbate,x)
variable adsycom equal xcm(adsorbate,y)
variable adszcom equal xcm(adsorbate,z)
variable adsvxcom equal vcm(adsorbate,x)
variable adsvycom equal vcm(adsorbate,y)
variable adsvzcom equal vcm(adsorbate,z)
#### Simulation settings ####
timestep 0.001
fix subf membrane setforce 0.0 0.0 0.0
fix thermostat all nve
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0
variable KC equal c_1
############################
# Output
thermo 100
thermo_style custom step etotal pe ke v_REBO v_KC temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
thermo_modify line one format float %.10f
thermo_modify flush yes norm no lost warn #ignore
#dump 1 all custom 1000 traj.lammpstrj id mol type xu yu zu
#dump_modify 1 format line "%7d %3d %3d %15.10g %15.10g %15.10g" flush yes
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual, skip from (2)
attributes: full, newton on, ghost
pair build: skip/ghost
stencil: none
bin: none
(2) pair kolmogorov/crespi/full, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.13 | 11.13 | 11.13 Mbytes
Step TotEng PotEng KinEng v_REBO v_KC Temp v_adsxcom v_adsycom v_adszcom v_adsvxcom v_adsvycom v_adsvzcom
0 -5025.3867727863 -5040.0767396377 14.6899668514 -5011.2636302897 -28.8131093480 83.6251135127 22.0155657205 20.2812150219 3.4623630945 0.0282287195 0.0535565745 0.2193320108
100 -5025.3962438431 -5041.3829780735 15.9867342304 -5012.5109382383 -28.8720398352 91.0071804956 22.0181858078 20.2867731676 3.4456714402 0.0241525932 0.0573807336 -0.5235069015
200 -5025.3942574000 -5041.9638225847 16.5695651847 -5012.7804304371 -29.1833921476 94.3250439874 22.0203529515 20.2926376511 3.3740502908 0.0186420748 0.0595018114 -0.7867265578
300 -5025.3919468212 -5040.9705424499 15.5785956286 -5012.0510300232 -28.9195124266 88.6837826792 22.0218424095 20.2984380400 3.3199036613 0.0106250874 0.0544668352 -0.1513745907
400 -5025.3965382086 -5041.6929969192 16.2964587107 -5012.6418095739 -29.0511873454 92.7703393291 22.0224243957 20.3034636122 3.3515794172 0.0006844935 0.0458598502 0.6967704497
500 -5025.4050178038 -5042.1712315208 16.7662137170 -5013.1850223792 -28.9862091417 95.4444989189 22.0220673443 20.3074634962 3.4286173278 -0.0078273439 0.0340764532 0.6845095066
600 -5025.3985720873 -5041.2158953052 15.8173232179 -5012.4875324499 -28.7283628553 90.0427797386 22.0209262700 20.3103065099 3.4653840648 -0.0141442608 0.0229602847 0.0009001092
700 -5025.3997566711 -5041.6276726420 16.2279159709 -5012.7093586298 -28.9183140122 92.3801482242 22.0191651506 20.3120184840 3.4291788224 -0.0208485646 0.0104216414 -0.6668311565
800 -5025.3967608874 -5042.3401691104 16.9434082230 -5013.3044882226 -29.0356808878 96.4532085250 22.0167259920 20.3122737443 3.3535033285 -0.0279747378 -0.0060833621 -0.7003492926
900 -5025.3984547938 -5042.2820672614 16.8836124676 -5013.4066846579 -28.8753826035 96.1128111040 22.0136711877 20.3107854823 3.3206430872 -0.0331979094 -0.0237440547 0.1335648640
1000 -5025.3988190757 -5041.9160827657 16.5172636900 -5012.8147743212 -29.1013084444 94.0273089090 22.0102627032 20.3075977018 3.3736867454 -0.0340065996 -0.0390649991 0.7872380119
Loop time of 33.7338 on 4 procs for 1000 steps with 1360 atoms
Performance: 2.561 ns/day, 9.370 hours/ns, 29.644 timesteps/s
94.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 30.833 | 31.356 | 32.18 | 9.1 | 92.95
Bond | 0.00026059 | 0.00029182 | 0.00031185 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.443 | 2.2722 | 2.8091 | 34.3 | 6.74
Output | 0.00068855 | 0.00095087 | 0.0017185 | 0.0 | 0.00
Modify | 0.010187 | 0.011709 | 0.015284 | 1.9 | 0.03
Other | | 0.09241 | | | 0.27
Nlocal: 340 ave 344 max 334 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4628 ave 4634 max 4624 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 66301.5 ave 67860 max 63963 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 265206
Ave neighs/atom = 195.004
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:33

129
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
1 by 1 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000143357 secs
read_data CPU = 0.00128686 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 17.21 | 17.21 | 17.21 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.7640583248121402 -10090.4634194413119985 52.6993611164999436 -10057.1894932863488066 -33.2739261549639664 35.9559834316876348 -69.2299095866357561 299.9999999999996589
100 5.3877589240437374 -10037.5122858156355505 -10065.4637593850693520 27.9514735694345475 -10032.2132655062632693 -33.2504938788055995 25.2100699045900747 -58.4605637833913789 159.1184768311149185
200 10.7755050340201706 -10037.4414086674350983 -10061.6271012692632212 24.1856926018286202 -10028.9093252939674130 -32.7177759752951403 18.5366534598604176 -51.2544294351563394 137.6811336385792970
300 16.1665089030284435 -10037.4824653300311184 -10064.2845326005663082 26.8020672705344225 -10030.9195389405322203 -33.3649936600345924 26.3639208740001152 -59.7289145340284122 152.5752876469470891
400 21.5454839280573651 -10037.5105626329259394 -10064.8769084956420556 27.3663458627154164 -10031.8478821022799821 -33.0290263933626349 36.6142885774199272 -69.6433149707719963 155.7875386888538571
500 26.9370588400634006 -10037.5010433785082569 -10064.8363209936451312 27.3352776151367571 -10031.4417172103931080 -33.3946037832518243 26.2980262321670750 -59.6926300154142595 155.6106774503846850
600 32.4204196080099791 -10037.4817772372425679 -10064.1925798287738871 26.7108025915316247 -10031.4376178099264507 -32.7549620188478201 18.5745873777024606 -51.3295493965519327 152.0557480714992380
700 37.8001567909959704 -10037.4834430268438155 -10064.1291975032218033 26.6457544763788299 -10030.8722888097800023 -33.2569086934421492 25.2322818106646771 -58.4891905041015008 151.6854507067418467
800 43.1622281169984490 -10037.5047888097760733 -10064.8671187128948077 27.3623299031188978 -10031.9815058608437539 -32.8856128520517217 36.5236695083771536 -69.4092823604148350 155.7646771616279011
900 48.5261204120470211 -10037.5068323940176924 -10065.3998155271074211 27.8929831330889542 -10032.1734374829957233 -33.2263780441125931 27.7314849391008309 -60.9578629832065317 158.7855101588076820
1000 53.8888844919856638 -10037.4811494880468672 -10064.0099109142265661 26.5287614261789670 -10031.3325267421259923 -32.6773841721003464 18.9005970229871600 -51.5779811950879434 151.0194480396057202
Loop time of 53.8889 on 1 procs for 1000 steps with 1360 atoms
Performance: 1.603 ns/day, 14.969 hours/ns, 18.557 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 53.836 | 53.836 | 53.836 | 0.0 | 99.90
Bond | 0.00043479 | 0.00043479 | 0.00043479 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.032452 | 0.032452 | 0.032452 | 0.0 | 0.06
Output | 0.00058326 | 0.00058326 | 0.00058326 | 0.0 | 0.00
Modify | 0.0094135 | 0.0094135 | 0.0094135 | 0.0 | 0.02
Other | | 0.009815 | | | 0.02
Nlocal: 1360 ave 1360 max 1360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7964 ave 7964 max 7964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.037e+06 ave 1.037e+06 max 1.037e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:54

129
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LAMMPS (5 Jun 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use different molecule ids for each layer of hBN
# so that inter- and intra-layer
# interactions can be specified separately
read_data Bi_gr_AB_stack_2L_noH.data
orthogonal box = (0 0 0) to (42.6 41.8117 100)
2 by 2 by 1 MPI processor grid
reading atoms ...
1360 atoms
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000245051 secs
read_data CPU = 0.00257704 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Separate atom groups
group layer1 molecule 1
680 atoms in group layer1
group layer2 molecule 2
680 atoms in group layer2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff * * kolmogorov/crespi/full CH_taper.KC C C # long range
####################################################################
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
#### Simulation settings ####
timestep 0.001
velocity all create 300.0 12345
compute 0 all pair rebo
compute 1 all pair kolmogorov/crespi/full
variable REBO equal c_0 # REBO energy
variable KC equal c_1 # total interlayer energy
variable Evdw equal c_1[1] # attractive energy
variable Erep equal c_1[2] # repulsive energy
############################
# Output
thermo 100
thermo_style custom step cpu etotal pe ke v_REBO v_KC v_Erep v_Evdw temp
thermo_modify line one format float %.16f
thermo_modify flush yes norm no lost warn
###### Run molecular dynamics ######
fix thermostat all nve
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 5 5 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/full, perpetual, copy from (1)
attributes: full, newton on, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 9.878 | 9.878 | 9.878 Mbytes
Step CPU TotEng PotEng KinEng v_REBO v_KC v_Erep v_Evdw Temp
0 0.0000000000000000 -10037.7640583250176860 -10090.4634194415175443 52.6993611164999933 -10057.1894932866325689 -33.2739261548851388 35.9559834317043467 -69.2299095866038954 299.9999999999999432
100 1.5180600649910048 -10037.5122858156355505 -10065.4637593850711710 27.9514735694348637 -10032.2132655062741833 -33.2504938787968172 25.2100699046001573 -58.4605637833912795 159.1184768311167090
200 3.0089348420733586 -10037.4414086674296414 -10061.6271012692577642 24.1856926018279914 -10028.9093252939601371 -32.7177759752976272 18.5366534598677504 -51.2544294351567515 137.6811336385757158
300 4.5315427089808509 -10037.4824653300020145 -10064.2845326005372044 26.8020672705348311 -10030.9195389405158494 -33.3649936600211205 26.3639208740115549 -59.7289145340278722 152.5752876469494197
400 6.0353655620710924 -10037.5105626329095685 -10064.8769084956238657 27.3663458627148124 -10031.8478821022818011 -33.0290263933414394 36.6142885774347562 -69.6433149707726074 155.7875386888504181
500 7.5396006110822782 -10037.5010433784900670 -10064.8363209936269413 27.3352776151361780 -10031.4417172103858320 -33.3946037832416351 26.2980262321774489 -59.6926300154146787 155.6106774503813881
600 9.2617433650884777 -10037.4817772372534819 -10064.1925798287848011 26.7108025915320830 -10031.4376178099319077 -32.7549620188514226 18.5745873777100208 -51.3295493965524017 152.0557480715018528
700 10.7484918619738892 -10037.4834430268347205 -10064.1291975032127084 26.6457544763787268 -10030.8722888097836403 -33.2569086934306739 25.2322818106757047 -58.4891905041008613 151.6854507067412499
800 12.2509897360578179 -10037.5047888097869873 -10064.8671187129039026 27.3623299031166667 -10031.9815058608728577 -32.8856128520297801 36.5236695083899718 -69.4092823604150908 155.7646771616151966
900 13.7584852169966325 -10037.5068323939758557 -10065.3998155270637653 27.8929831330881477 -10032.1734374829648004 -33.2263780440982259 27.7314849391120788 -60.9578629832060841 158.7855101588031062
1000 15.2755981830414385 -10037.4811494880432292 -10064.0099109142211091 26.5287614261777058 -10031.3325267421205353 -32.6773841721017888 18.9005970229946634 -51.5779811950868776 151.0194480395985295
Loop time of 15.2757 on 4 procs for 1000 steps with 1360 atoms
Performance: 5.656 ns/day, 4.243 hours/ns, 65.464 timesteps/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.985 | 14.446 | 14.823 | 7.9 | 94.57
Bond | 0.00040979 | 0.00042456 | 0.00046059 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.43692 | 0.81428 | 1.2749 | 33.2 | 5.33
Output | 0.00028016 | 0.00037143 | 0.00063561 | 0.0 | 0.00
Modify | 0.0045586 | 0.0046468 | 0.0047903 | 0.1 | 0.03
Other | | 0.01041 | | | 0.07
Nlocal: 340 ave 340 max 340 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4628 ave 4628 max 4628 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259250 ave 259250 max 259250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037000
Ave neighs/atom = 762.5
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

1
examples/PACKAGES/interlayer/kolmogorov_crespi_z/CC.KC Symbolic link
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../../../../potentials/CC.KC

1
examples/PACKAGES/interlayer/kolmogorov_crespi_z/CH.rebo Symbolic link
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../../../../potentials/CH.rebo

266
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info: xyz2data 18:31, Mon 27-02-2017
256 atoms
2 atom types
0.00000000 17.04000000 xlo xhi
0.00000000 19.67609717 ylo yhi
-20.00000000 40.00000000 zlo zhi
Atoms
1 1 0.00000000 0.00000000 0.00000000
2 1 1.42000000 0.00000000 0.00000000
3 2 1.42000000 0.00000000 3.30000000
4 2 2.84000000 0.00000000 3.30000000
5 1 2.13000000 1.22975607 0.00000000
6 1 3.55000000 1.22975607 0.00000000
7 2 3.55000000 1.22975607 3.30000000
8 2 4.97000000 1.22975607 3.30000000
9 1 0.00000000 2.45951215 0.00000000
10 1 1.42000000 2.45951215 0.00000000
11 2 1.42000000 2.45951215 3.30000000
12 2 2.84000000 2.45951215 3.30000000
13 1 2.13000000 3.68926822 0.00000000
14 1 3.55000000 3.68926822 0.00000000
15 2 3.55000000 3.68926822 3.30000000
16 2 4.97000000 3.68926822 3.30000000
17 1 0.00000000 4.91902429 0.00000000
18 1 1.42000000 4.91902429 0.00000000
19 2 1.42000000 4.91902429 3.30000000
20 2 2.84000000 4.91902429 3.30000000
21 1 2.13000000 6.14878037 0.00000000
22 1 3.55000000 6.14878037 0.00000000
23 2 3.55000000 6.14878037 3.30000000
24 2 4.97000000 6.14878037 3.30000000
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196 2 15.62000000 0.00000000 3.30000000
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212 2 15.62000000 4.91902429 3.30000000
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216 2 17.75000000 6.14878037 3.30000000
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220 2 15.62000000 7.37853644 3.30000000
221 1 14.91000000 8.60829251 0.00000000
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228 2 15.62000000 9.83804859 3.30000000
229 1 14.91000000 11.06780466 0.00000000
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232 2 17.75000000 11.06780466 3.30000000
233 1 12.78000000 12.29756073 0.00000000
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236 2 15.62000000 12.29756073 3.30000000
237 1 14.91000000 13.52731681 0.00000000
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240 2 17.75000000 13.52731681 3.30000000
241 1 12.78000000 14.75707288 0.00000000
242 1 14.20000000 14.75707288 0.00000000
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244 2 15.62000000 14.75707288 3.30000000
245 1 14.91000000 15.98682895 0.00000000
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248 2 17.75000000 15.98682895 3.30000000
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252 2 15.62000000 17.21658503 3.30000000
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256 2 17.75000000 18.44634110 3.30000000

139
examples/PACKAGES/interlayer/kolmogorov_crespi_z/data.graphene-adsorbant Normal file
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@ -0,0 +1,139 @@
info: xyz2data 11:52, Tue 28-02-2017
129 atoms
2 atom types
0.00000000 17.04000000 xlo xhi
0.00000000 19.67609717 ylo yhi
-10.00000000 40.00000000 zlo zhi
Atoms
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2 1 1.42000000 0.00000000 0.00000000
3 1 2.13000000 1.22975607 0.00000000
4 1 3.55000000 1.22975607 0.00000000
5 1 0.00000000 2.45951215 0.00000000
6 1 1.42000000 2.45951215 0.00000000
7 1 2.13000000 3.68926822 0.00000000
8 1 3.55000000 3.68926822 0.00000000
9 1 0.00000000 4.91902429 0.00000000
10 1 1.42000000 4.91902429 0.00000000
11 1 2.13000000 6.14878037 0.00000000
12 1 3.55000000 6.14878037 0.00000000
13 1 0.00000000 7.37853644 0.00000000
14 1 1.42000000 7.37853644 0.00000000
15 1 2.13000000 8.60829251 0.00000000
16 1 3.55000000 8.60829251 0.00000000
17 1 0.00000000 9.83804859 0.00000000
18 1 1.42000000 9.83804859 0.00000000
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20 1 3.55000000 11.06780466 0.00000000
21 1 0.00000000 12.29756073 0.00000000
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24 1 3.55000000 13.52731681 0.00000000
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26 1 1.42000000 14.75707288 0.00000000
27 1 2.13000000 15.98682895 0.00000000
28 1 3.55000000 15.98682895 0.00000000
29 1 0.00000000 17.21658503 0.00000000
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33 1 4.26000000 0.00000000 0.00000000
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84 1 12.07000000 11.06780466 0.00000000
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86 1 9.94000000 12.29756073 0.00000000
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108 1 16.33000000 6.14878037 0.00000000
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110 1 14.20000000 7.37853644 0.00000000
111 1 14.91000000 8.60829251 0.00000000
112 1 16.33000000 8.60829251 0.00000000
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116 1 16.33000000 11.06780466 0.00000000
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119 1 14.91000000 13.52731681 0.00000000
120 1 16.33000000 13.52731681 0.00000000
121 1 12.78000000 14.75707288 0.00000000
122 1 14.20000000 14.75707288 0.00000000
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124 1 16.33000000 15.98682895 0.00000000
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45
examples/PACKAGES/interlayer/kolmogorov_crespi_z/in.atom-diffusion Normal file
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@ -0,0 +1,45 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000

45
examples/PACKAGES/interlayer/kolmogorov_crespi_z/in.bilayer-graphene Normal file
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@ -0,0 +1,45 @@
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000

200
examples/PACKAGES/interlayer/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.1 Normal file
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@ -0,0 +1,200 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
1 by 1 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
1 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 3 3 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.206 | 3.206 | 3.206 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.34689 on 1 procs for 10000 steps with 129 atoms
Performance: 249.070 ns/day, 0.096 hours/ns, 28827.585 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2028 | 0.2028 | 0.2028 | 0.0 | 58.46
Neigh | 0.00021529 | 0.00021529 | 0.00021529 | 0.0 | 0.06
Comm | 0.10656 | 0.10656 | 0.10656 | 0.0 | 30.72
Output | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.44
Modify | 0.011605 | 0.011605 | 0.011605 | 0.0 | 3.35
Other | | 0.0242 | | | 6.98
Nlocal: 129 ave 129 max 129 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1867 ave 1867 max 1867 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 290 ave 290 max 290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 290
Ave neighs/atom = 2.24806
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

200
examples/PACKAGES/interlayer/kolmogorov_crespi_z/log.16Mar18.atom-diffusion.g++.4 Normal file
View File

@ -0,0 +1,200 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.graphene-adsorbant # read lammps data file
orthogonal box = (0 0 -10) to (17.04 19.6761 40)
2 by 2 by 1 MPI processor grid
reading atoms ...
129 atoms
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
1 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * none
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
fix thermostat adsorbant nve
fix rigid_membrane membrane setforce 0 0 0
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 100
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 3 3 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair kolmogorov/crespi/z, perpetual, skip from (2)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.167 | 3.167 | 3.168 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -0.02562011 -0.02562011 0.00000000 0.00000000 3.30000000
100 0.01000000 -0.02562011 -0.02584808 0.01377831 0.00000000 3.30302413
200 0.02000000 -0.02562011 -0.02650010 0.05318658 0.00000000 3.31198892
300 0.03000000 -0.02562011 -0.02748822 0.11290898 0.00000000 3.32658305
400 0.04000000 -0.02562011 -0.02868854 0.18545625 0.00000000 3.34632324
500 0.05000000 -0.02562011 -0.02996656 0.26269978 0.00000000 3.37059992
600 0.06000000 -0.02562011 -0.03120006 0.33725276 0.00000000 3.39872815
700 0.07000000 -0.02562011 -0.03229421 0.40338328 0.00000000 3.42999603
800 0.08000000 -0.02562011 -0.03318758 0.45737874 0.00000000 3.46370507
900 0.09000000 -0.02562011 -0.03385069 0.49745690 0.00000000 3.49919977
1000 0.10000000 -0.02562011 -0.03428002 0.52340564 0.00000000 3.53588638
1100 0.11000000 -0.02562011 -0.03449041 0.53612164 0.00000000 3.57324216
1200 0.12000000 -0.02562011 -0.03450775 0.53717016 0.00000000 3.61081749
1300 0.13000000 -0.02562011 -0.03436312 0.52842859 0.00000000 3.64823296
1400 0.14000000 -0.02562011 -0.03408851 0.51183115 0.00000000 3.68517357
1500 0.15000000 -0.02562011 -0.03371417 0.48920613 0.00000000 3.72138134
1600 0.16000000 -0.02562011 -0.03326714 0.46218758 0.00000000 3.75664759
1700 0.17000000 -0.02562011 -0.03277063 0.43217815 0.00000000 3.79080541
1800 0.18000000 -0.02562011 -0.03224395 0.40034589 0.00000000 3.82372274
1900 0.19000000 -0.02562011 -0.03170282 0.36763982 0.00000000 3.85529629
2000 0.20000000 -0.02562011 -0.03115972 0.33481494 0.00000000 3.88544626
2100 0.21000000 -0.02562011 -0.03062440 0.30246010 0.00000000 3.91411185
2200 0.22000000 -0.02562011 -0.03010433 0.27102702 0.00000000 3.94124749
2300 0.23000000 -0.02562011 -0.02960514 0.24085558 0.00000000 3.96681976
2400 0.24000000 -0.02562011 -0.02913096 0.21219623 0.00000000 3.99080483
2500 0.25000000 -0.02562011 -0.02868478 0.18522907 0.00000000 4.01318637
2600 0.26000000 -0.02562011 -0.02826867 0.16007955 0.00000000 4.03395384
2700 0.27000000 -0.02562011 -0.02788403 0.13683143 0.00000000 4.05310113
2800 0.28000000 -0.02562011 -0.02753171 0.11553708 0.00000000 4.07062542
2900 0.29000000 -0.02562011 -0.02721220 0.09622581 0.00000000 4.08652629
3000 0.30000000 -0.02562011 -0.02692571 0.07891041 0.00000000 4.10080498
3100 0.31000000 -0.02562011 -0.02667226 0.06359229 0.00000000 4.11346382
3200 0.32000000 -0.02562011 -0.02645177 0.05026555 0.00000000 4.12450573
3300 0.33000000 -0.02562011 -0.02626406 0.03892009 0.00000000 4.13393390
3400 0.34000000 -0.02562011 -0.02610893 0.02954399 0.00000000 4.14175142
3500 0.35000000 -0.02562011 -0.02598618 0.02212545 0.00000000 4.14796110
3600 0.36000000 -0.02562011 -0.02589566 0.01665409 0.00000000 4.15256529
3700 0.37000000 -0.02562011 -0.02583722 0.01312208 0.00000000 4.15556569
3800 0.38000000 -0.02562011 -0.02581079 0.01152492 0.00000000 4.15696329
3900 0.39000000 -0.02562011 -0.02581636 0.01186148 0.00000000 4.15675830
4000 0.40000000 -0.02562011 -0.02585398 0.01413478 0.00000000 4.15495012
4100 0.41000000 -0.02562011 -0.02592375 0.01835185 0.00000000 4.15153731
4200 0.42000000 -0.02562011 -0.02602587 0.02452390 0.00000000 4.14651764
4300 0.43000000 -0.02562011 -0.02616057 0.03266513 0.00000000 4.13988811
4400 0.44000000 -0.02562011 -0.02632813 0.04279292 0.00000000 4.13164506
4500 0.45000000 -0.02562011 -0.02652889 0.05492664 0.00000000 4.12178432
4600 0.46000000 -0.02562011 -0.02676317 0.06908643 0.00000000 4.11030130
4700 0.47000000 -0.02562011 -0.02703129 0.08529164 0.00000000 4.09719124
4800 0.48000000 -0.02562011 -0.02733352 0.10355859 0.00000000 4.08244950
4900 0.49000000 -0.02562011 -0.02767004 0.12389788 0.00000000 4.06607186
5000 0.50000000 -0.02562011 -0.02804086 0.14631034 0.00000000 4.04805502
5100 0.51000000 -0.02562011 -0.02844575 0.17078211 0.00000000 4.02839708
5200 0.52000000 -0.02562011 -0.02888415 0.19727899 0.00000000 4.00709829
5300 0.53000000 -0.02562011 -0.02935502 0.22573844 0.00000000 3.98416189
5400 0.54000000 -0.02562011 -0.02985670 0.25605986 0.00000000 3.95959511
5500 0.55000000 -0.02562011 -0.03038669 0.28809268 0.00000000 3.93341053
5600 0.56000000 -0.02562011 -0.03094143 0.32162137 0.00000000 3.90562766
5700 0.57000000 -0.02562011 -0.03151597 0.35634628 0.00000000 3.87627492
5800 0.58000000 -0.02562011 -0.03210361 0.39186361 0.00000000 3.84539210
5900 0.59000000 -0.02562011 -0.03269556 0.42764084 0.00000000 3.81303330
6000 0.60000000 -0.02562011 -0.03328042 0.46299030 0.00000000 3.77927044
6100 0.61000000 -0.02562011 -0.03384380 0.49704060 0.00000000 3.74419758
6200 0.62000000 -0.02562011 -0.03436783 0.52871353 0.00000000 3.70793588
6300 0.63000000 -0.02562011 -0.03483104 0.55670974 0.00000000 3.67063945
6400 0.64000000 -0.02562011 -0.03520832 0.57951248 0.00000000 3.63250187
6500 0.65000000 -0.02562011 -0.03547159 0.59542438 0.00000000 3.59376331
6600 0.66000000 -0.02562011 -0.03559125 0.60265655 0.00000000 3.55471782
6700 0.67000000 -0.02562011 -0.03553879 0.59948637 0.00000000 3.51572023
6800 0.68000000 -0.02562011 -0.03529110 0.58451568 0.00000000 3.47719153
6900 0.69000000 -0.02562011 -0.03483635 0.55703035 0.00000000 3.43962129
7000 0.70000000 -0.02562011 -0.03418150 0.51745146 0.00000000 3.40356509
7100 0.71000000 -0.02562011 -0.03336032 0.46781889 0.00000000 3.36963482
7200 0.72000000 -0.02562011 -0.03243997 0.41219328 0.00000000 3.33847933
7300 0.73000000 -0.02562011 -0.03152342 0.35679665 0.00000000 3.31075400
7400 0.74000000 -0.02562011 -0.03074422 0.30970201 0.00000000 3.28707906
7500 0.75000000 -0.02562011 -0.03025182 0.27994115 0.00000000 3.26798907
7600 0.76000000 -0.02562011 -0.03018799 0.27608346 0.00000000 3.25387900
7700 0.77000000 -0.02562011 -0.03065928 0.30456818 0.00000000 3.24495492
7800 0.78000000 -0.02562011 -0.03171321 0.36826788 0.00000000 3.24119821
7900 0.79000000 -0.02562011 -0.03332635 0.46576624 0.00000000 3.24235091
8000 0.80000000 -0.02562011 -0.03540847 0.59160963 0.00000000 3.24792582
8100 0.81000000 -0.02562011 -0.03782107 0.73742737 0.00000000 3.25723999
8200 0.82000000 -0.02562011 -0.04040358 0.89351498 0.00000000 3.26946524
8300 0.83000000 -0.02562011 -0.04299943 1.05040805 0.00000000 3.28368734
8400 0.84000000 -0.02562011 -0.04547588 1.20008497 0.00000000 3.29896495
8500 0.85000000 -0.02562011 -0.04773539 1.33664998 0.00000000 3.31438148
8600 0.86000000 -0.02562011 -0.04971913 1.45654768 0.00000000 3.32908572
8700 0.87000000 -0.02562011 -0.05140498 1.55844058 0.00000000 3.34231951
8800 0.88000000 -0.02562011 -0.05280154 1.64284923 0.00000000 3.35343297
8900 0.89000000 -0.02562011 -0.05394019 1.71166905 0.00000000 3.36188901
9000 0.90000000 -0.02562011 -0.05486563 1.76760281 0.00000000 3.36725955
9100 0.91000000 -0.02562011 -0.05562624 1.81357448 0.00000000 3.36921674
9200 0.92000000 -0.02562011 -0.05626439 1.85214388 0.00000000 3.36752214
9300 0.93000000 -0.02562011 -0.05680723 1.88495335 0.00000000 3.36201704
9400 0.94000000 -0.02562011 -0.05725852 1.91222952 0.00000000 3.35261669
9500 0.95000000 -0.02562011 -0.05759110 1.93233038 0.00000000 3.33931122
9600 0.96000000 -0.02562011 -0.05774152 1.94142215 0.00000000 3.32217490
9700 0.97000000 -0.02562011 -0.05760814 1.93336063 0.00000000 3.30138553
9800 0.98000000 -0.02562012 -0.05705439 1.89989139 0.00000000 3.27725394
9900 0.99000000 -0.02562012 -0.05592079 1.83137685 0.00000000 3.25026233
10000 1.00000000 -0.02562012 -0.05404919 1.71825669 0.00000000 3.22110695
Loop time of 0.524797 on 4 procs for 10000 steps with 129 atoms
Performance: 164.635 ns/day, 0.146 hours/ns, 19054.971 timesteps/s
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.043099 | 0.060851 | 0.10153 | 9.7 | 11.60
Neigh | 6.2704e-05 | 6.628e-05 | 6.8188e-05 | 0.0 | 0.01
Comm | 0.35059 | 0.39384 | 0.41232 | 4.0 | 75.05
Output | 0.0028515 | 0.0031345 | 0.0037408 | 0.6 | 0.60
Modify | 0.0063083 | 0.0065277 | 0.0066838 | 0.2 | 1.24
Other | | 0.06038 | | | 11.50
Nlocal: 32.25 ave 33 max 32 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 1305.75 ave 1306 max 1305 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 72.5 ave 144 max 43 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 290
Ave neighs/atom = 2.24806
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

210
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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
1 by 1 by 1 MPI processor grid
reading atoms ...
256 atoms
read_data CPU = 0.000291348 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
128 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 3 3 8
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.998 | 4.998 | 4.998 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126
20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357
30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673
40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055
50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486
60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952
70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441
80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946
90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458
100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973
110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489
120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004
130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519
140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038
150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562
160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099
170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654
180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235
190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851
200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512
210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230
220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016
230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883
240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845
250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913
260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097
270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408
280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849
290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424
300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129
310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957
320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898
330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935
340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046
350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207
360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390
370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561
380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688
390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734
400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664
410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442
420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033
430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405
440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527
450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373
460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918
470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143
480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030
490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565
500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740
510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547
520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981
530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040
540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724
550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032
560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963
570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517
580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691
590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478
600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871
610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856
620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416
630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531
640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176
650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323
660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937
670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986
680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430
690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229
700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343
710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729
720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344
730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148
740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098
750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156
760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282
770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441
780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599
790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726
800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792
810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773
820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647
830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393
840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995
850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439
860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713
870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805
880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706
890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408
900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904
910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186
920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247
930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078
940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670
950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015
960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101
970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915
980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672
1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581
Loop time of 2.60456 on 1 procs for 1000 steps with 256 atoms
Performance: 3.317 ns/day, 7.235 hours/ns, 383.942 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 | 2.5864 | 2.5864 | 2.5864 | 0.0 | 99.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0079134 | 0.0079134 | 0.0079134 | 0.0 | 0.30
Output | 0.0027175 | 0.0027175 | 0.0027175 | 0.0 | 0.10
Modify | 0.00419 | 0.00419 | 0.00419 | 0.0 | 0.16
Other | | 0.00331 | | | 0.13
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1721 ave 1721 max 1721 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37312 ave 37312 max 37312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 94592 ave 94592 max 94592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

210
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LAMMPS (30 Apr 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style atomic
processors * * 1 # domain decomposition over x and y
# System and atom definition
# we use 2 atom types so that inter- and intra-layer
# interactions can be specified separately
read_data data.bilayer-graphene # read lammps data file
orthogonal box = (0 0 -20) to (17.04 19.6761 40)
2 by 2 by 1 MPI processor grid
reading atoms ...
256 atoms
read_data CPU = 0.0488505 secs
mass 1 12.0107 # carbon mass (g/mole) | membrane
mass 2 12.0107 # carbon mass (g/mole) | adsorbate
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1
neigh_modify delay 0
neigh_modify check yes
# Separate atom groups
group membrane type 1
128 atoms in group membrane
group adsorbant type 2
128 atoms in group adsorbant
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.rebo C C # chemical
Reading potential file CH.rebo with DATE: 2018-7-3
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################
#### Simulation settings ####
timestep 0.0001
velocity all create 300.0 12345
fix thermostat all nve
compute COM1 membrane com
compute COM2 adsorbant com
############################
# Output
#dump 1 all xyz 100 trajec.xyz
#dump_modify 1 format line "%s %12.6f %12.6f %12.6f" element "C" "C"
thermo 10
thermo_style custom step time etotal pe temp c_COM1[3] c_COM2[3] # spcpu
thermo_modify line one format float %14.8f
###### Run molecular dynamics ######
run 1000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
binsize = 8, bins = 3 3 8
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair rebo, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair kolmogorov/crespi/z, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes
Step Time TotEng PotEng Temp c_COM1[3] c_COM2[3]
0 0.00000000 -1888.67041233 -1898.55881343 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037240 -1898.21029916 289.42778520 -0.00020126 3.30020126
20 0.00200000 -1888.67021561 -1897.22943631 259.67456089 -0.00041357 3.30041357
30 0.00300000 -1888.66999327 -1895.86681330 218.34126559 -0.00063673 3.30063673
40 0.00400000 -1888.66978373 -1894.47163849 176.02000692 -0.00087055 3.30087055
50 0.00500000 -1888.66966087 -1893.37123396 142.63902861 -0.00111486 3.30111486
60 0.00600000 -1888.66966151 -1892.75822768 124.04127204 -0.00136952 3.30136952
70 0.00700000 -1888.66976993 -1892.63445770 120.28297806 -0.00163441 3.30163441
80 0.00800000 -1888.66992887 -1892.83467481 126.35245790 -0.00190946 3.30190946
90 0.00900000 -1888.67006887 -1893.11387088 134.81862143 -0.00219458 3.30219458
100 0.01000000 -1888.67013641 -1893.25481870 139.09272852 -0.00248973 3.30248973
110 0.01100000 -1888.67011221 -1893.15155809 135.96068294 -0.00279489 3.30279489
120 0.01200000 -1888.67001516 -1892.84002980 126.51230266 -0.00311004 3.30311004
130 0.01300000 -1888.66989017 -1892.47004258 115.29120969 -0.00343519 3.30343519
140 0.01400000 -1888.66979250 -1892.23503136 108.16426724 -0.00377038 3.30377038
150 0.01500000 -1888.66976498 -1892.28630603 109.72070258 -0.00411562 3.30411562
160 0.01600000 -1888.66982073 -1892.66640631 121.25071190 -0.00447099 3.30447099
170 0.01700000 -1888.66993810 -1893.28862656 140.12442720 -0.00483654 3.30483654
180 0.01800000 -1888.67007037 -1893.97029277 160.80119589 -0.00521235 3.30521235
190 0.01900000 -1888.67016732 -1894.50458806 177.00801243 -0.00559851 3.30559851
200 0.02000000 -1888.67019479 -1894.73890125 184.11590729 -0.00599512 3.30599512
210 0.02100000 -1888.67014440 -1894.62906034 180.78501933 -0.00640230 3.30640230
220 0.02200000 -1888.67003699 -1894.25249122 169.36370739 -0.00682016 3.30682016
230 0.02300000 -1888.66991405 -1893.77601632 154.91186768 -0.00724883 3.30724883
240 0.02400000 -1888.66982545 -1893.38995103 143.20188490 -0.00768845 3.30768845
250 0.02500000 -1888.66980650 -1893.23138955 138.39193054 -0.00813913 3.30813913
260 0.02600000 -1888.66986149 -1893.32993943 141.38012473 -0.00860097 3.30860097
270 0.02700000 -1888.66996324 -1893.60070625 149.59171759 -0.00907408 3.30907408
280 0.02800000 -1888.67006705 -1893.88587245 158.24010430 -0.00955849 3.30955849
290 0.02900000 -1888.67013001 -1894.02402688 162.42960290 -0.01005424 3.31005424
300 0.03000000 -1888.67012741 -1893.91715254 159.18726627 -0.01056129 3.31056129
310 0.03100000 -1888.67005750 -1893.57037262 148.66857854 -0.01107957 3.31107957
320 0.03200000 -1888.66994592 -1893.09358639 134.20694885 -0.01160898 3.31160898
330 0.03300000 -1888.66983608 -1892.66132683 121.09614209 -0.01214935 3.31214935
340 0.03400000 -1888.66977429 -1892.44446364 114.51869677 -0.01270046 3.31270046
350 0.03500000 -1888.66978845 -1892.53901254 117.38674604 -0.01326207 3.31326207
360 0.03600000 -1888.66987459 -1892.92337308 129.04508370 -0.01383390 3.31383390
370 0.03700000 -1888.66999819 -1893.46445589 145.45701553 -0.01441561 3.31441561
380 0.03800000 -1888.67010979 -1893.97065536 160.81100019 -0.01500688 3.31500688
390 0.03900000 -1888.67016559 -1894.26835837 169.84119248 -0.01560734 3.31560734
400 0.04000000 -1888.67014686 -1894.26967995 169.88185548 -0.01621664 3.31621664
410 0.04100000 -1888.67006186 -1894.00321089 161.80014284 -0.01683442 3.31683442
420 0.04200000 -1888.66994386 -1893.60086344 149.59707422 -0.01746033 3.31746033
430 0.04300000 -1888.66984078 -1893.24559860 138.82197278 -0.01809405 3.31809405
440 0.04400000 -1888.66979419 -1893.09727893 134.32357877 -0.01873527 3.31873527
450 0.04500000 -1888.66982159 -1893.22837461 138.30000376 -0.01938373 3.31938373
460 0.04600000 -1888.66990991 -1893.59670402 149.47191350 -0.02003918 3.32003918
470 0.04700000 -1888.67002193 -1894.06542618 163.68887740 -0.02070143 3.32070143
480 0.04800000 -1888.67011408 -1894.46010861 175.66018436 -0.02137030 3.32137030
490 0.04900000 -1888.67015195 -1894.63688117 181.02206322 -0.02204565 3.32204565
500 0.05000000 -1888.67012178 -1894.53632241 177.97216884 -0.02272740 3.32272740
510 0.05100000 -1888.67003782 -1894.20444750 167.90610440 -0.02341547 3.32341547
520 0.05200000 -1888.66993171 -1893.77231086 154.79891357 -0.02410981 3.32410981
530 0.05300000 -1888.66984524 -1893.40525947 143.66572040 -0.02481040 3.32481040
540 0.05400000 -1888.66981428 -1893.23762103 138.58074854 -0.02551724 3.32551724
550 0.05500000 -1888.66985024 -1893.31793613 141.01630314 -0.02623032 3.32623032
560 0.05600000 -1888.66993756 -1893.59069032 149.28862746 -0.02694963 3.32694963
570 0.05700000 -1888.67003871 -1893.92089591 159.30352583 -0.02767517 3.32767517
580 0.05800000 -1888.67011342 -1894.15124772 166.28980520 -0.02840691 3.32840691
590 0.05900000 -1888.67013211 -1894.16548061 166.72104344 -0.02914478 3.32914478
600 0.06000000 -1888.67008732 -1893.93443338 159.71275857 -0.02988871 3.32988871
610 0.06100000 -1888.66999458 -1893.52841675 147.39760649 -0.03063856 3.33063856
620 0.06200000 -1888.66988829 -1893.09235041 134.17119966 -0.03139416 3.33139416
630 0.06300000 -1888.66981016 -1892.79172036 125.05288241 -0.03215531 3.33215531
640 0.06400000 -1888.66979281 -1892.74755409 123.71346729 -0.03292176 3.33292176
650 0.06500000 -1888.66984352 -1892.98665478 130.96590321 -0.03369323 3.33369323
660 0.06600000 -1888.66994264 -1893.42999887 144.41332385 -0.03446937 3.33446937
670 0.06700000 -1888.67005253 -1893.92310700 159.37018803 -0.03524986 3.33524986
680 0.06800000 -1888.67013328 -1894.29451600 170.63575807 -0.03603430 3.33603430
690 0.06900000 -1888.67015472 -1894.41878137 174.40514195 -0.03682229 3.33682229
700 0.07000000 -1888.67010916 -1894.26288055 169.67671536 -0.03761343 3.33761343
710 0.07100000 -1888.67001386 -1893.89812923 158.61357122 -0.03840729 3.33840729
720 0.07200000 -1888.66990397 -1893.47348765 145.73388461 -0.03920344 3.33920344
730 0.07300000 -1888.66982231 -1893.15984859 136.22099965 -0.04000148 3.34000148
740 0.07400000 -1888.66980129 -1893.08373765 133.91254030 -0.04080098 3.34080098
750 0.07500000 -1888.66984814 -1893.27755530 139.79127022 -0.04160156 3.34160156
760 0.07600000 -1888.66994235 -1893.66837384 151.64528962 -0.04240282 3.34240282
770 0.07700000 -1888.67004573 -1894.10941225 165.02263022 -0.04320441 3.34320441
780 0.07800000 -1888.67011722 -1894.43947564 175.03411433 -0.04400599 3.34400599
790 0.07900000 -1888.67013317 -1894.54590490 178.26254255 -0.04480726 3.34480726
800 0.08000000 -1888.67008771 -1894.40384162 173.95392409 -0.04560792 3.34560792
810 0.08100000 -1888.66999942 -1894.08389023 164.24973325 -0.04640773 3.34640773
820 0.08200000 -1888.66990467 -1893.72313999 153.30795968 -0.04720647 3.34720647
830 0.08300000 -1888.66984387 -1893.46839210 145.58111627 -0.04800393 3.34800393
840 0.08400000 -1888.66984175 -1893.41412556 143.93481091 -0.04879995 3.34879995
850 0.08500000 -1888.66989690 -1893.56426173 148.48805548 -0.04959439 3.34959439
860 0.08600000 -1888.66998242 -1893.83463738 156.68827289 -0.05038713 3.35038713
870 0.08700000 -1888.67006191 -1894.09325064 164.53181916 -0.05117805 3.35117805
880 0.08800000 -1888.67010292 -1894.21712680 168.28880099 -0.05196706 3.35196706
890 0.08900000 -1888.67009013 -1894.14263970 166.02935659 -0.05275408 3.35275408
900 0.09000000 -1888.67002911 -1893.89014590 158.37090593 -0.05353904 3.35353904
910 0.09100000 -1888.66994346 -1893.55535729 148.21649476 -0.05432186 3.35432186
920 0.09200000 -1888.66986545 -1893.27257968 139.63979183 -0.05510247 3.35510247
930 0.09300000 -1888.66982750 -1893.16330910 136.32582951 -0.05588078 3.35588078
940 0.09400000 -1888.66984650 -1893.28643304 140.06065783 -0.05665670 3.35665670
950 0.09500000 -1888.66991522 -1893.61245361 149.94957262 -0.05743015 3.35743015
960 0.09600000 -1888.67000710 -1894.03423941 162.74316510 -0.05820101 3.35820101
970 0.09700000 -1888.67008668 -1894.40848044 174.09469033 -0.05896915 3.35896915
980 0.09800000 -1888.67012456 -1894.61056787 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010627 -1894.58107679 179.33042341 -0.06049672 3.36049672
1000 0.10000000 -1888.67004000 -1894.34773324 172.25312335 -0.06125581 3.36125581
Loop time of 1.55992 on 4 procs for 1000 steps with 256 atoms
Performance: 5.539 ns/day, 4.333 hours/ns, 641.059 timesteps/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3161 | 1.3724 | 1.4128 | 3.0 | 87.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11734 | 0.16017 | 0.21617 | 8.9 | 10.27
Output | 0.0032182 | 0.0051764 | 0.010916 | 4.6 | 0.33
Modify | 0.0020187 | 0.0022321 | 0.0026002 | 0.5 | 0.14
Other | | 0.0199 | | | 1.28
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 1265 ave 1265 max 1265 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 9328 ave 9328 max 9328 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 23648 ave 23648 max 23648 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 94592
Ave neighs/atom = 369.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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examples/PACKAGES/interlayer/lebedeva/2particles.dat Normal file
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Ideal graphene structure in YZ plane created with create_graphen.pl
2 atoms
2 atom types
0.0 20 xlo xhi
0.0 20 ylo yhi
0.0 5 zlo zhi
Atoms
1 1 10 10 0.0
2 2 0 0 3.35

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examples/PACKAGES/interlayer/lebedeva/2particles.in Normal file
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# After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# ---------- Start simulation ---------------------
clear
units metal
dimension 3
boundary f f f
atom_style atomic
# ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10
create_box 2 whole
read_data 2particles.dat add append
region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2
group graphene1 type 1
group graphene2 type 2
pair_style hybrid/overlay lebedeva/z 20
pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
mass 1 12.01 # Carbon
mass 2 12.01 # Carbon
neighbor 0.3 bin
neigh_modify delay 1 check yes
compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3
thermo 10
thermo_style custom step pe press temp
thermo_modify lost ignore
label STEP_LOOP
variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
run 1
next MYSTEP
jump SELF STEP_LOOP
print "all done"

14
examples/PACKAGES/interlayer/lebedeva/CC.Lebedeva Normal file
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# Lebedeva Potential. Original values from Lebedeva. May be played with ;)
#
# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin,
# Modeling of graphene-based NEMS
# Physica E 44 (6), 949 (2012)
# https://doi.org/10.1016/j.physe.2011.07.018
#
# Parameters must be in this order as here, otherwise their values may be changed.
# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C
# A B C z0 alpha D1 D2 lambda1 lambda2 S
# These are values according to Levedeva et al
#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0
# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162
C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0

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dump_lebedeva_000.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
dump_lebedeva_001.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07
dump_lebedeva_002.cfg:2 0.1 0.1 3.35 -7.5313e-07 5.01468e-07 5.01468e-07 -1.69689e-07
dump_lebedeva_003.cfg:2 0.15 0.15 3.35 -7.78625e-07 5.18417e-07 5.18417e-07 -1.76314e-07
dump_lebedeva_004.cfg:2 0.2 0.2 3.35 -8.04983e-07 5.36017e-07 5.36017e-07 -1.8323e-07
dump_lebedeva_005.cfg:2 0.25 0.25 3.35 -8.32238e-07 5.54298e-07 5.54298e-07 -1.90451e-07
dump_lebedeva_006.cfg:2 0.3 0.3 3.35 -8.60425e-07 5.73288e-07 5.73288e-07 -1.97991e-07
dump_lebedeva_007.cfg:2 0.35 0.35 3.35 -8.89579e-07 5.93019e-07 5.93019e-07 -2.05867e-07
dump_lebedeva_008.cfg:2 0.4 0.4 3.35 -9.19739e-07 6.13522e-07 6.13522e-07 -2.14094e-07
dump_lebedeva_009.cfg:2 0.45 0.45 3.35 -9.50945e-07 6.34832e-07 6.34832e-07 -2.2269e-07
dump_lebedeva_010.cfg:2 0.5 0.5 3.35 -9.83237e-07 6.56984e-07 6.56984e-07 -2.31673e-07
dump_lebedeva_011.cfg:2 0.55 0.55 3.35 -1.01666e-06 6.80016e-07 6.80016e-07 -2.41064e-07
dump_lebedeva_012.cfg:2 0.6 0.6 3.35 -1.05125e-06 7.03966e-07 7.03966e-07 -2.50881e-07
dump_lebedeva_013.cfg:2 0.65 0.65 3.35 -1.08707e-06 7.28875e-07 7.28875e-07 -2.61148e-07
dump_lebedeva_014.cfg:2 0.7 0.7 3.35 -1.12416e-06 7.54787e-07 7.54787e-07 -2.71886e-07
dump_lebedeva_015.cfg:2 0.75 0.75 3.35 -1.16257e-06 7.81747e-07 7.81747e-07 -2.83119e-07
dump_lebedeva_016.cfg:2 0.8 0.8 3.35 -1.20235e-06 8.09802e-07 8.09802e-07 -2.94873e-07
dump_lebedeva_017.cfg:2 0.85 0.85 3.35 -1.24357e-06 8.39001e-07 8.39001e-07 -3.07175e-07
dump_lebedeva_018.cfg:2 0.9 0.9 3.35 -1.28627e-06 8.69398e-07 8.69398e-07 -3.20053e-07
dump_lebedeva_019.cfg:2 0.95 0.95 3.35 -1.33053e-06 9.01046e-07 9.01046e-07 -3.33537e-07
dump_lebedeva_020.cfg:2 1 1 3.35 -1.3764e-06 9.34005e-07 9.34005e-07 -3.47657e-07
dump_lebedeva_021.cfg:2 1.05 1.05 3.35 -1.42395e-06 9.68333e-07 9.68333e-07 -3.62449e-07
dump_lebedeva_022.cfg:2 1.1 1.1 3.35 -1.47325e-06 1.0041e-06 1.0041e-06 -3.77946e-07
dump_lebedeva_023.cfg:2 1.15 1.15 3.35 -1.52438e-06 1.04136e-06 1.04136e-06 -3.94187e-07
dump_lebedeva_024.cfg:2 1.2 1.2 3.35 -1.57742e-06 1.08019e-06 1.08019e-06 -4.1121e-07
dump_lebedeva_025.cfg:2 1.25 1.25 3.35 -1.63243e-06 1.12067e-06 1.12067e-06 -4.29058e-07
dump_lebedeva_026.cfg:2 1.3 1.3 3.35 -1.68951e-06 1.16288e-06 1.16288e-06 -4.47775e-07
dump_lebedeva_027.cfg:2 1.35 1.35 3.35 -1.74875e-06 1.20689e-06 1.20689e-06 -4.67407e-07
dump_lebedeva_028.cfg:2 1.4 1.4 3.35 -1.81023e-06 1.25279e-06 1.25279e-06 -4.88004e-07
dump_lebedeva_029.cfg:2 1.45 1.45 3.35 -1.87406e-06 1.30067e-06 1.30067e-06 -5.0962e-07
dump_lebedeva_030.cfg:2 1.5 1.5 3.35 -1.94033e-06 1.35063e-06 1.35063e-06 -5.32308e-07
dump_lebedeva_031.cfg:2 1.55 1.55 3.35 -2.00916e-06 1.40277e-06 1.40277e-06 -5.56129e-07
dump_lebedeva_032.cfg:2 1.6 1.6 3.35 -2.08065e-06 1.4572e-06 1.4572e-06 -5.81145e-07
dump_lebedeva_033.cfg:2 1.65 1.65 3.35 -2.15492e-06 1.51402e-06 1.51402e-06 -6.07422e-07
dump_lebedeva_034.cfg:2 1.7 1.7 3.35 -2.23209e-06 1.57336e-06 1.57336e-06 -6.3503e-07
dump_lebedeva_035.cfg:2 1.75 1.75 3.35 -2.3123e-06 1.63533e-06 1.63533e-06 -6.64045e-07
dump_lebedeva_036.cfg:2 1.8 1.8 3.35 -2.39567e-06 1.70008e-06 1.70008e-06 -6.94545e-07
dump_lebedeva_037.cfg:2 1.85 1.85 3.35 -2.48236e-06 1.76774e-06 1.76774e-06 -7.26615e-07
dump_lebedeva_038.cfg:2 1.9 1.9 3.35 -2.5725e-06 1.83844e-06 1.83844e-06 -7.60344e-07
dump_lebedeva_039.cfg:2 1.95 1.95 3.35 -2.66625e-06 1.91236e-06 1.91236e-06 -7.95827e-07
dump_lebedeva_040.cfg:2 2 2 3.35 -2.76379e-06 1.98965e-06 1.98965e-06 -8.33165e-07
dump_lebedeva_041.cfg:2 2.05 2.05 3.35 -2.86528e-06 2.07047e-06 2.07047e-06 -8.72464e-07
dump_lebedeva_042.cfg:2 2.1 2.1 3.35 -2.9709e-06 2.15503e-06 2.15503e-06 -9.1384e-07
dump_lebedeva_043.cfg:2 2.15 2.15 3.35 -3.08085e-06 2.24349e-06 2.24349e-06 -9.57413e-07
dump_lebedeva_044.cfg:2 2.2 2.2 3.35 -3.19532e-06 2.33607e-06 2.33607e-06 -1.00331e-06
dump_lebedeva_045.cfg:2 2.25 2.25 3.35 -3.31452e-06 2.43298e-06 2.43298e-06 -1.05167e-06
dump_lebedeva_046.cfg:2 2.3 2.3 3.35 -3.43869e-06 2.53444e-06 2.53444e-06 -1.10265e-06
dump_lebedeva_047.cfg:2 2.35 2.35 3.35 -3.56805e-06 2.6407e-06 2.6407e-06 -1.15638e-06
dump_lebedeva_048.cfg:2 2.4 2.4 3.35 -3.70284e-06 2.752e-06 2.752e-06 -1.21305e-06
dump_lebedeva_049.cfg:2 2.45 2.45 3.35 -3.84334e-06 2.86861e-06 2.86861e-06 -1.27283e-06
dump_lebedeva_050.cfg:2 2.5 2.5 3.35 -3.9898e-06 2.99082e-06 2.99082e-06 -1.3359e-06
dump_lebedeva_051.cfg:2 2.55 2.55 3.35 -4.14252e-06 3.11892e-06 3.11892e-06 -1.40247e-06
dump_lebedeva_052.cfg:2 2.6 2.6 3.35 -4.30179e-06 3.25323e-06 3.25323e-06 -1.47275e-06
dump_lebedeva_053.cfg:2 2.65 2.65 3.35 -4.46795e-06 3.39408e-06 3.39408e-06 -1.54696e-06
dump_lebedeva_054.cfg:2 2.7 2.7 3.35 -4.64132e-06 3.54184e-06 3.54184e-06 -1.62536e-06
dump_lebedeva_055.cfg:2 2.75 2.75 3.35 -4.82225e-06 3.69686e-06 3.69686e-06 -1.70821e-06
dump_lebedeva_056.cfg:2 2.8 2.8 3.35 -5.01113e-06 3.85956e-06 3.85956e-06 -1.79577e-06
dump_lebedeva_057.cfg:2 2.85 2.85 3.35 -5.20835e-06 4.03036e-06 4.03036e-06 -1.88835e-06
dump_lebedeva_058.cfg:2 2.9 2.9 3.35 -5.41431e-06 4.2097e-06 4.2097e-06 -1.98627e-06
dump_lebedeva_059.cfg:2 2.95 2.95 3.35 -5.62947e-06 4.39805e-06 4.39805e-06 -2.08985e-06
dump_lebedeva_060.cfg:2 3 3 3.35 -5.85427e-06 4.59593e-06 4.59593e-06 -2.19948e-06
dump_lebedeva_061.cfg:2 3.05 3.05 3.35 -6.08923e-06 4.80386e-06 4.80386e-06 -2.31553e-06
dump_lebedeva_062.cfg:2 3.1 3.1 3.35 -6.33484e-06 5.02241e-06 5.02241e-06 -2.43842e-06
dump_lebedeva_063.cfg:2 3.15 3.15 3.35 -6.59165e-06 5.25219e-06 5.25219e-06 -2.56859e-06
dump_lebedeva_064.cfg:2 3.2 3.2 3.35 -6.86025e-06 5.49384e-06 5.49384e-06 -2.70652e-06
dump_lebedeva_065.cfg:2 3.25 3.25 3.35 -7.14125e-06 5.74802e-06 5.74802e-06 -2.85272e-06
dump_lebedeva_066.cfg:2 3.3 3.3 3.35 -7.43528e-06 6.01548e-06 6.01548e-06 -3.00774e-06
dump_lebedeva_067.cfg:2 3.35 3.35 3.35 -7.74303e-06 6.29696e-06 6.29696e-06 -3.17215e-06
dump_lebedeva_068.cfg:2 3.4 3.4 3.35 -8.06522e-06 6.5933e-06 6.5933e-06 -3.3466e-06
dump_lebedeva_069.cfg:2 3.45 3.45 3.35 -8.40262e-06 6.90535e-06 6.90535e-06 -3.53174e-06
dump_lebedeva_070.cfg:2 3.5 3.5 3.35 -8.75603e-06 7.23404e-06 7.23404e-06 -3.72831e-06
dump_lebedeva_071.cfg:2 3.55 3.55 3.35 -9.12632e-06 7.58035e-06 7.58035e-06 -3.93708e-06
dump_lebedeva_072.cfg:2 3.6 3.6 3.35 -9.51438e-06 7.94533e-06 7.94533e-06 -4.15889e-06
dump_lebedeva_073.cfg:2 3.65 3.65 3.35 -9.92118e-06 8.33009e-06 8.33009e-06 -4.39462e-06
dump_lebedeva_074.cfg:2 3.7 3.7 3.35 -1.03477e-05 8.73582e-06 8.73582e-06 -4.64524e-06
dump_lebedeva_075.cfg:2 3.75 3.75 3.35 -1.07951e-05 9.16377e-06 9.16377e-06 -4.91178e-06
dump_lebedeva_076.cfg:2 3.8 3.8 3.35 -1.12645e-05 9.61529e-06 9.61529e-06 -5.19536e-06
dump_lebedeva_077.cfg:2 3.85 3.85 3.35 -1.17571e-05 1.00918e-05 1.00918e-05 -5.49717e-06
dump_lebedeva_078.cfg:2 3.9 3.9 3.35 -1.22741e-05 1.05949e-05 1.05949e-05 -5.8185e-06
dump_lebedeva_079.cfg:2 3.95 3.95 3.35 -1.2817e-05 1.11261e-05 1.11261e-05 -6.16074e-06
dump_lebedeva_080.cfg:2 4 4 3.35 -1.33872e-05 1.16872e-05 1.16872e-05 -6.52537e-06
dump_lebedeva_081.cfg:2 4.05 4.05 3.35 -1.39863e-05 1.22801e-05 1.22801e-05 -6.91402e-06
dump_lebedeva_082.cfg:2 4.1 4.1 3.35 -1.46158e-05 1.29067e-05 1.29067e-05 -7.32841e-06
dump_lebedeva_083.cfg:2 4.15 4.15 3.35 -1.52776e-05 1.35692e-05 1.35692e-05 -7.77041e-06
dump_lebedeva_084.cfg:2 4.2 4.2 3.35 -1.59734e-05 1.42698e-05 1.42698e-05 -8.24204e-06
dump_lebedeva_085.cfg:2 4.25 4.25 3.35 -1.67052e-05 1.50109e-05 1.50109e-05 -8.74547e-06
dump_lebedeva_086.cfg:2 4.3 4.3 3.35 -1.74752e-05 1.57951e-05 1.57951e-05 -9.28307e-06
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dump_lebedeva_260.cfg:2 13 13 3.35 -0.000310593 -0.000378175 -0.000378175 -0.000422436
dump_lebedeva_261.cfg:2 13.05 13.05 3.35 -0.000292267 -0.000355095 -0.000355095 -0.000390146
dump_lebedeva_262.cfg:2 13.1 13.1 3.35 -0.000275062 -0.000333333 -0.000333333 -0.000360319
dump_lebedeva_263.cfg:2 13.15 13.15 3.35 -0.000258913 -0.000312838 -0.000312838 -0.000332786
dump_lebedeva_264.cfg:2 13.2 13.2 3.35 -0.000243758 -0.000293556 -0.000293556 -0.000307385
dump_lebedeva_265.cfg:2 13.25 13.25 3.35 -0.000229538 -0.000275433 -0.000275433 -0.000283962
dump_lebedeva_266.cfg:2 13.3 13.3 3.35 -0.000216196 -0.000258414 -0.000258414 -0.000262372
dump_lebedeva_267.cfg:2 13.35 13.35 3.35 -0.000203679 -0.000242442 -0.000242442 -0.000242475
dump_lebedeva_268.cfg:2 13.4 13.4 3.35 -0.000191936 -0.000227463 -0.000227463 -0.000224142
dump_lebedeva_269.cfg:2 13.45 13.45 3.35 -0.000180917 -0.000213422 -0.000213422 -0.000207254
dump_lebedeva_270.cfg:2 13.5 13.5 3.35 -0.000170579 -0.000200265 -0.000200265 -0.000191696
dump_lebedeva_271.cfg:2 13.55 13.55 3.35 -0.000160877 -0.000187942 -0.000187942 -0.000177363
dump_lebedeva_272.cfg:2 13.6 13.6 3.35 -0.000151771 -0.000176402 -0.000176402 -0.000164159
dump_lebedeva_273.cfg:2 13.65 13.65 3.35 -0.000143224 -0.000165599 -0.000165599 -0.000151993
dump_lebedeva_274.cfg:2 13.7 13.7 3.35 -0.0001352 -0.000155486 -0.000155486 -0.000140781
dump_lebedeva_275.cfg:2 13.75 13.75 3.35 -0.000127665 -0.00014602 -0.00014602 -0.000130447
dump_lebedeva_276.cfg:2 13.8 13.8 3.35 -0.000120588 -0.000137161 -0.000137161 -0.00012092
dump_lebedeva_277.cfg:2 13.85 13.85 3.35 -0.000113939 -0.000128869 -0.000128869 -0.000112134
dump_lebedeva_278.cfg:2 13.9 13.9 3.35 -0.000107692 -0.000121109 -0.000121109 -0.00010403
dump_lebedeva_279.cfg:2 13.95 13.95 3.35 -0.00010182 -0.000113845 -0.000113845 -9.65522e-05
dump_lebedeva_280.cfg:2 14 14 3.35 -9.62998e-05 -0.000107044 -0.000107044 -8.96501e-05
dump_lebedeva_281.cfg:2 14.05 14.05 3.35 -9.11085e-05 -0.000100678 -0.000100678 -8.32771e-05
dump_lebedeva_282.cfg:2 14.1 14.1 3.35 -8.62253e-05 -9.47167e-05 -9.47167e-05 -7.73906e-05
dump_lebedeva_283.cfg:2 14.15 14.15 3.35 -8.16306e-05 -8.91338e-05 -8.91338e-05 -7.19515e-05
dump_lebedeva_284.cfg:2 14.2 14.2 3.35 -7.7306e-05 -8.39045e-05 -8.39045e-05 -6.69239e-05
dump_lebedeva_285.cfg:2 14.25 14.25 3.35 -7.32346e-05 -7.90054e-05 -7.90054e-05 -6.22749e-05
dump_lebedeva_286.cfg:2 14.3 14.3 3.35 -6.94003e-05 -7.44146e-05 -7.44146e-05 -5.79742e-05
dump_lebedeva_287.cfg:2 14.35 14.35 3.35 -6.57883e-05 -7.01119e-05 -7.01119e-05 -5.39942e-05
dump_lebedeva_288.cfg:2 14.4 14.4 3.35 -6.23847e-05 -6.60782e-05 -6.60782e-05 -5.03095e-05
dump_lebedeva_289.cfg:2 14.45 14.45 3.35 -5.91763e-05 -6.22957e-05 -6.22957e-05 -4.68968e-05
dump_lebedeva_290.cfg:2 14.5 14.5 3.35 -5.61512e-05 -5.8748e-05 -5.8748e-05 -4.37346e-05
dump_lebedeva_291.cfg:2 14.55 14.55 3.35 -5.32979e-05 -5.54196e-05 -5.54196e-05 -4.08035e-05
dump_lebedeva_292.cfg:2 14.6 14.6 3.35 -5.06058e-05 -5.22962e-05 -5.22962e-05 -3.80853e-05
dump_lebedeva_293.cfg:2 14.65 14.65 3.35 -4.80651e-05 -4.93643e-05 -4.93643e-05 -3.55636e-05
dump_lebedeva_294.cfg:2 14.7 14.7 3.35 -4.56664e-05 -4.66115e-05 -4.66115e-05 -3.32231e-05
dump_lebedeva_295.cfg:2 14.75 14.75 3.35 -4.34011e-05 -4.4026e-05 -4.4026e-05 -3.10499e-05
dump_lebedeva_296.cfg:2 14.8 14.8 3.35 -4.12612e-05 -4.15971e-05 -4.15971e-05 -2.90313e-05
dump_lebedeva_297.cfg:2 14.85 14.85 3.35 -3.9239e-05 -3.93146e-05 -3.93146e-05 -2.71554e-05
dump_lebedeva_298.cfg:2 14.9 14.9 3.35 -3.73274e-05 -3.7169e-05 -3.7169e-05 -2.54115e-05
dump_lebedeva_299.cfg:2 14.95 14.95 3.35 -3.55199e-05 -3.51516e-05 -3.51516e-05 -2.37895e-05
dump_lebedeva_300.cfg:2 15 15 3.35 -3.38103e-05 -3.32542e-05 -3.32542e-05 -2.22803e-05
dump_lebedeva_301.cfg:2 15.05 15.05 3.35 -3.21926e-05 -3.1469e-05 -3.1469e-05 -2.08755e-05
dump_lebedeva_302.cfg:2 15.1 15.1 3.35 -3.06616e-05 -2.9789e-05 -2.9789e-05 -1.95673e-05
dump_lebedeva_303.cfg:2 15.15 15.15 3.35 -2.92121e-05 -2.82074e-05 -2.82074e-05 -1.83485e-05
dump_lebedeva_304.cfg:2 15.2 15.2 3.35 -2.78393e-05 -2.67182e-05 -2.67182e-05 -1.72127e-05
dump_lebedeva_305.cfg:2 15.25 15.25 3.35 -2.65389e-05 -2.53153e-05 -2.53153e-05 -1.61536e-05
dump_lebedeva_306.cfg:2 15.3 15.3 3.35 -2.53065e-05 -2.39936e-05 -2.39936e-05 -1.51657e-05
dump_lebedeva_307.cfg:2 15.35 15.35 3.35 -2.41382e-05 -2.27478e-05 -2.27478e-05 -1.42439e-05
dump_lebedeva_308.cfg:2 15.4 15.4 3.35 -2.30305e-05 -2.15733e-05 -2.15733e-05 -1.33834e-05
dump_lebedeva_309.cfg:2 15.45 15.45 3.35 -2.19798e-05 -2.04656e-05 -2.04656e-05 -1.25798e-05
dump_lebedeva_310.cfg:2 15.5 15.5 3.35 -2.09829e-05 -1.94207e-05 -1.94207e-05 -1.1829e-05
dump_lebedeva_311.cfg:2 15.55 15.55 3.35 -2.00367e-05 -1.84346e-05 -1.84346e-05 -1.11272e-05
dump_lebedeva_312.cfg:2 15.6 15.6 3.35 -1.91385e-05 -1.75039e-05 -1.75039e-05 -1.04711e-05
dump_lebedeva_313.cfg:2 15.65 15.65 3.35 -1.82855e-05 -1.66251e-05 -1.66251e-05 -9.85736e-06
dump_lebedeva_314.cfg:2 15.7 15.7 3.35 -1.74752e-05 -1.57951e-05 -1.57951e-05 -9.28307e-06
dump_lebedeva_315.cfg:2 15.75 15.75 3.35 -1.67052e-05 -1.50109e-05 -1.50109e-05 -8.74547e-06
dump_lebedeva_316.cfg:2 15.8 15.8 3.35 -1.59734e-05 -1.42698e-05 -1.42698e-05 -8.24204e-06
dump_lebedeva_317.cfg:2 15.85 15.85 3.35 -1.52776e-05 -1.35692e-05 -1.35692e-05 -7.77041e-06
dump_lebedeva_318.cfg:2 15.9 15.9 3.35 -1.46158e-05 -1.29067e-05 -1.29067e-05 -7.32841e-06
dump_lebedeva_319.cfg:2 15.95 15.95 3.35 -1.39863e-05 -1.22801e-05 -1.22801e-05 -6.91402e-06
dump_lebedeva_320.cfg:2 16 16 3.35 -1.33872e-05 -1.16872e-05 -1.16872e-05 -6.52537e-06
dump_lebedeva_321.cfg:2 16.05 16.05 3.35 -1.2817e-05 -1.11261e-05 -1.11261e-05 -6.16074e-06
dump_lebedeva_322.cfg:2 16.1 16.1 3.35 -1.22741e-05 -1.05949e-05 -1.05949e-05 -5.8185e-06
dump_lebedeva_323.cfg:2 16.15 16.15 3.35 -1.17571e-05 -1.00918e-05 -1.00918e-05 -5.49717e-06
dump_lebedeva_324.cfg:2 16.2 16.2 3.35 -1.12645e-05 -9.61529e-06 -9.61529e-06 -5.19536e-06
dump_lebedeva_325.cfg:2 16.25 16.25 3.35 -1.07951e-05 -9.16377e-06 -9.16377e-06 -4.91178e-06
dump_lebedeva_326.cfg:2 16.3 16.3 3.35 -1.03477e-05 -8.73582e-06 -8.73582e-06 -4.64524e-06
dump_lebedeva_327.cfg:2 16.35 16.35 3.35 -9.92118e-06 -8.33009e-06 -8.33009e-06 -4.39462e-06
dump_lebedeva_328.cfg:2 16.4 16.4 3.35 -9.51438e-06 -7.94533e-06 -7.94533e-06 -4.15889e-06
dump_lebedeva_329.cfg:2 16.45 16.45 3.35 -9.12632e-06 -7.58035e-06 -7.58035e-06 -3.93708e-06
dump_lebedeva_330.cfg:2 16.5 16.5 3.35 -8.75603e-06 -7.23404e-06 -7.23404e-06 -3.72831e-06
dump_lebedeva_331.cfg:2 16.55 16.55 3.35 -8.40262e-06 -6.90535e-06 -6.90535e-06 -3.53174e-06
dump_lebedeva_332.cfg:2 16.6 16.6 3.35 -8.06522e-06 -6.5933e-06 -6.5933e-06 -3.3466e-06
dump_lebedeva_333.cfg:2 16.65 16.65 3.35 -7.74303e-06 -6.29696e-06 -6.29696e-06 -3.17215e-06
dump_lebedeva_334.cfg:2 16.7 16.7 3.35 -7.43528e-06 -6.01548e-06 -6.01548e-06 -3.00774e-06
dump_lebedeva_335.cfg:2 16.75 16.75 3.35 -7.14125e-06 -5.74802e-06 -5.74802e-06 -2.85272e-06
dump_lebedeva_336.cfg:2 16.8 16.8 3.35 -6.86025e-06 -5.49384e-06 -5.49384e-06 -2.70652e-06
dump_lebedeva_337.cfg:2 16.85 16.85 3.35 -6.59165e-06 -5.25219e-06 -5.25219e-06 -2.56859e-06
dump_lebedeva_338.cfg:2 16.9 16.9 3.35 -6.33484e-06 -5.02241e-06 -5.02241e-06 -2.43842e-06
dump_lebedeva_339.cfg:2 16.95 16.95 3.35 -6.08923e-06 -4.80386e-06 -4.80386e-06 -2.31553e-06
dump_lebedeva_340.cfg:2 17 17 3.35 -5.85427e-06 -4.59593e-06 -4.59593e-06 -2.19948e-06
dump_lebedeva_341.cfg:2 17.05 17.05 3.35 -5.62947e-06 -4.39805e-06 -4.39805e-06 -2.08985e-06
dump_lebedeva_342.cfg:2 17.1 17.1 3.35 -5.41431e-06 -4.2097e-06 -4.2097e-06 -1.98627e-06
dump_lebedeva_343.cfg:2 17.15 17.15 3.35 -5.20835e-06 -4.03036e-06 -4.03036e-06 -1.88835e-06
dump_lebedeva_344.cfg:2 17.2 17.2 3.35 -5.01113e-06 -3.85956e-06 -3.85956e-06 -1.79577e-06
dump_lebedeva_345.cfg:2 17.25 17.25 3.35 -4.82225e-06 -3.69686e-06 -3.69686e-06 -1.70821e-06
dump_lebedeva_346.cfg:2 17.3 17.3 3.35 -4.64132e-06 -3.54184e-06 -3.54184e-06 -1.62536e-06
dump_lebedeva_347.cfg:2 17.35 17.35 3.35 -4.46795e-06 -3.39408e-06 -3.39408e-06 -1.54696e-06
dump_lebedeva_348.cfg:2 17.4 17.4 3.35 -4.30179e-06 -3.25323e-06 -3.25323e-06 -1.47275e-06
dump_lebedeva_349.cfg:2 17.45 17.45 3.35 -4.14252e-06 -3.11892e-06 -3.11892e-06 -1.40247e-06
dump_lebedeva_350.cfg:2 17.5 17.5 3.35 -3.9898e-06 -2.99082e-06 -2.99082e-06 -1.3359e-06
dump_lebedeva_351.cfg:2 17.55 17.55 3.35 -3.84334e-06 -2.86861e-06 -2.86861e-06 -1.27283e-06
dump_lebedeva_352.cfg:2 17.6 17.6 3.35 -3.70284e-06 -2.752e-06 -2.752e-06 -1.21305e-06
dump_lebedeva_353.cfg:2 17.65 17.65 3.35 -3.56805e-06 -2.6407e-06 -2.6407e-06 -1.15638e-06
dump_lebedeva_354.cfg:2 17.7 17.7 3.35 -3.43869e-06 -2.53444e-06 -2.53444e-06 -1.10265e-06
dump_lebedeva_355.cfg:2 17.75 17.75 3.35 -3.31452e-06 -2.43298e-06 -2.43298e-06 -1.05167e-06
dump_lebedeva_356.cfg:2 17.8 17.8 3.35 -3.19532e-06 -2.33607e-06 -2.33607e-06 -1.00331e-06
dump_lebedeva_357.cfg:2 17.85 17.85 3.35 -3.08085e-06 -2.24349e-06 -2.24349e-06 -9.57413e-07
dump_lebedeva_358.cfg:2 17.9 17.9 3.35 -2.9709e-06 -2.15503e-06 -2.15503e-06 -9.1384e-07
dump_lebedeva_359.cfg:2 17.95 17.95 3.35 -2.86528e-06 -2.07047e-06 -2.07047e-06 -8.72464e-07
dump_lebedeva_360.cfg:2 18 18 3.35 -2.76379e-06 -1.98965e-06 -1.98965e-06 -8.33165e-07
dump_lebedeva_361.cfg:2 18.05 18.05 3.35 -2.66625e-06 -1.91236e-06 -1.91236e-06 -7.95827e-07
dump_lebedeva_362.cfg:2 18.1 18.1 3.35 -2.5725e-06 -1.83844e-06 -1.83844e-06 -7.60344e-07
dump_lebedeva_363.cfg:2 18.15 18.15 3.35 -2.48236e-06 -1.76774e-06 -1.76774e-06 -7.26615e-07
dump_lebedeva_364.cfg:2 18.2 18.2 3.35 -2.39567e-06 -1.70008e-06 -1.70008e-06 -6.94545e-07
dump_lebedeva_365.cfg:2 18.25 18.25 3.35 -2.3123e-06 -1.63533e-06 -1.63533e-06 -6.64045e-07
dump_lebedeva_366.cfg:2 18.3 18.3 3.35 -2.23209e-06 -1.57336e-06 -1.57336e-06 -6.3503e-07
dump_lebedeva_367.cfg:2 18.35 18.35 3.35 -2.15492e-06 -1.51402e-06 -1.51402e-06 -6.07422e-07
dump_lebedeva_368.cfg:2 18.4 18.4 3.35 -2.08065e-06 -1.4572e-06 -1.4572e-06 -5.81145e-07
dump_lebedeva_369.cfg:2 18.45 18.45 3.35 -2.00916e-06 -1.40277e-06 -1.40277e-06 -5.56129e-07
dump_lebedeva_370.cfg:2 18.5 18.5 3.35 -1.94033e-06 -1.35063e-06 -1.35063e-06 -5.32308e-07
dump_lebedeva_371.cfg:2 18.55 18.55 3.35 -1.87406e-06 -1.30067e-06 -1.30067e-06 -5.0962e-07
dump_lebedeva_372.cfg:2 18.6 18.6 3.35 -1.81023e-06 -1.25279e-06 -1.25279e-06 -4.88004e-07
dump_lebedeva_373.cfg:2 18.65 18.65 3.35 -1.74875e-06 -1.20689e-06 -1.20689e-06 -4.67407e-07
dump_lebedeva_374.cfg:2 18.7 18.7 3.35 -1.68951e-06 -1.16288e-06 -1.16288e-06 -4.47775e-07
dump_lebedeva_375.cfg:2 18.75 18.75 3.35 -1.63243e-06 -1.12067e-06 -1.12067e-06 -4.29058e-07
dump_lebedeva_376.cfg:2 18.8 18.8 3.35 -1.57742e-06 -1.08019e-06 -1.08019e-06 -4.1121e-07
dump_lebedeva_377.cfg:2 18.85 18.85 3.35 -1.52438e-06 -1.04136e-06 -1.04136e-06 -3.94187e-07
dump_lebedeva_378.cfg:2 18.9 18.9 3.35 -1.47325e-06 -1.0041e-06 -1.0041e-06 -3.77946e-07
dump_lebedeva_379.cfg:2 18.95 18.95 3.35 -1.42395e-06 -9.68333e-07 -9.68333e-07 -3.62449e-07
dump_lebedeva_380.cfg:2 19 19 3.35 -1.3764e-06 -9.34005e-07 -9.34005e-07 -3.47657e-07
dump_lebedeva_381.cfg:2 19.05 19.05 3.35 -1.33053e-06 -9.01046e-07 -9.01046e-07 -3.33537e-07
dump_lebedeva_382.cfg:2 19.1 19.1 3.35 -1.28627e-06 -8.69398e-07 -8.69398e-07 -3.20053e-07
dump_lebedeva_383.cfg:2 19.15 19.15 3.35 -1.24357e-06 -8.39001e-07 -8.39001e-07 -3.07175e-07
dump_lebedeva_384.cfg:2 19.2 19.2 3.35 -1.20235e-06 -8.09802e-07 -8.09802e-07 -2.94873e-07
dump_lebedeva_385.cfg:2 19.25 19.25 3.35 -1.16257e-06 -7.81747e-07 -7.81747e-07 -2.83119e-07
dump_lebedeva_386.cfg:2 19.3 19.3 3.35 -1.12416e-06 -7.54787e-07 -7.54787e-07 -2.71886e-07
dump_lebedeva_387.cfg:2 19.35 19.35 3.35 -1.08707e-06 -7.28875e-07 -7.28875e-07 -2.61148e-07
dump_lebedeva_388.cfg:2 19.4 19.4 3.35 -1.05125e-06 -7.03966e-07 -7.03966e-07 -2.50881e-07
dump_lebedeva_389.cfg:2 19.45 19.45 3.35 -1.01666e-06 -6.80016e-07 -6.80016e-07 -2.41064e-07
dump_lebedeva_390.cfg:2 19.5 19.5 3.35 -9.83237e-07 -6.56984e-07 -6.56984e-07 -2.31673e-07
dump_lebedeva_391.cfg:2 19.55 19.55 3.35 -9.50945e-07 -6.34832e-07 -6.34832e-07 -2.2269e-07
dump_lebedeva_392.cfg:2 19.6 19.6 3.35 -9.19739e-07 -6.13522e-07 -6.13522e-07 -2.14094e-07
dump_lebedeva_393.cfg:2 19.65 19.65 3.35 -8.89579e-07 -5.93019e-07 -5.93019e-07 -2.05867e-07
dump_lebedeva_394.cfg:2 19.7 19.7 3.35 -8.60425e-07 -5.73288e-07 -5.73288e-07 -1.97991e-07
dump_lebedeva_395.cfg:2 19.75 19.75 3.35 -8.32238e-07 -5.54298e-07 -5.54298e-07 -1.90451e-07
dump_lebedeva_396.cfg:2 19.8 19.8 3.35 -8.04983e-07 -5.36017e-07 -5.36017e-07 -1.8323e-07
dump_lebedeva_397.cfg:2 19.85 19.85 3.35 -7.78625e-07 -5.18417e-07 -5.18417e-07 -1.76314e-07
dump_lebedeva_398.cfg:2 19.9 19.9 3.35 -7.5313e-07 -5.01468e-07 -5.01468e-07 -1.69689e-07
dump_lebedeva_399.cfg:2 19.95 19.95 3.35 -7.28468e-07 -4.85145e-07 -4.85145e-07 -1.6334e-07

90
examples/PACKAGES/interlayer/lebedeva/LebDer.pl Executable file
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#!/usr/bin/perl
# Computes potential energy of atom as a function of distance from another atom
# and computes numerical derivates of potential.
# The script was used to check if results from LAMMPS (using 2particles.in)
# are the same as these computed b this script.
# Prints results to STDOUT.
# Hence, use it like this:
# ./LebDer.pl > PerlResult.dat
# After that use lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# Parameters used by ZJK for Lebedeva
my $LEB_A = -14.558;
my $LEB_B = 21.204;
my $LEB_alpha = 4.16;
my $LEB_C = 1.8;
my $LEB_D1 = -0.862;
my $LEB_D2 = 0.10049; # has very strong influence on position of minimum
my $LEB_lambda1 = 0.6; # has influance on splitting of AB-AA.
my $LEB_lambda2 = 0.4; # has strong influence on position of minimum
my $LEB_z0 = 3.198;
my $LEBSCALE =1.0;
$Z0=3.35;
$CX0 = 10;
$CY0 = 10;
for (my $t=0; $t<400; $t++) {
my $X0 = 0.001 + 0.05*$t;
my $Y0 = 0.001 + 0.05*$t;
my $Z = $Z0;
print $X0, "\t", $Y0, "\t", $Z, "\t",&LEB($X0, $Y0, $Z), "\t", &DLEBX($X0, $Y0, $Z),"\t",&DLEBY($X0, $Y0, $Z), "\t", &DLEBZ($X0, $Y0, $Z),"\n";
}
###############################################################################################
sub LEB {
my $x = shift;
my $y = shift;
my $z = shift;
my $rho2 = ($x-$CX0)*($x-$CX0) + ($y-$CY0)*($y-$CY0);
my $r = sqrt($rho2 + ($Z0)*($Z0));
my $zr = ($LEB_z0/$r)*($LEB_z0/$r);
my $zr6 = $zr*$zr*$zr;
my $ONE = $LEB_C*(1+$LEB_D1*$rho2+$LEB_D2*$rho2*$rho2);
my $TWO = exp(-$LEB_lambda1*$rho2)*exp(-$LEB_lambda2*($z*$z-$LEB_z0*$LEB_z0));
my $U = $LEB_A*$zr6 +$LEB_B*exp(-$LEB_alpha*($r-$LEB_z0)) + $ONE*$TWO;
return $U;
}
sub DLEBX { # finding derivative at $x
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x+$h, $y, $z)-&LEB($x-$h, $y, $z))/(2*$h);
return $D;
}
sub DLEBY { # finding derivative at $y
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x, $y+$h, $z)-&LEB($x, $y-$h, $z))/(2*$h);
return $D;
}
sub DLEBZ { # finding derivative at $z
my $x = shift;
my $y = shift;
my $z = shift;
my $h = 0.0001;
my $D = (&LEB($x, $y, $z+$h)-&LEB($x, $y, $z-$h))/(2*$h);
return $D;
}

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examples/PACKAGES/interlayer/lebedeva/lebedeva00.plot Normal file
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# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
set term x11;
unset log
unset title
set size 1.0,1.0
set encoding iso_8859_1
#set term postscript eps enhanced color "Helvetica" 18;
#set output "lebedeva00.eps"
set zero 1e-018;
set xlabel "x,y [{\305}]" font "Helvetica,18";
set ylabel "U [eV/atom]" font "Helvetica,18";
set key font ",18"
set key right
set key top
set pointsize 1.2
set xrange [0:20]
set yrange [-0.002:0.001]
#set yrange [-0.01:0.01]
#set yrange [*:*]
plot \
"LamppsResult.dat" u 2:5 t "Leb LAMMPS",\
"PerlResult.dat" u 1:($4*0.001/2.) w l t "Leb Perl"
exit