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update reference date and examples for changes in REBO

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This commit is contained in:
Axel Kohlmeyer
2019-05-04 20:42:36 -04:00
parent 1214e6ea79
commit fd3eade6d2
19 changed files with 549 additions and 528 deletions
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2
doc/src/pair_airebo.txt
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@ -116,7 +116,7 @@ various dihedral angle preferences in hydrocarbon configurations.
Only a single pair_coeff command is used with the {airebo}, {airebo}
or {rebo} style which specifies an AIREBO, REBO, or AIREBO-M potential
file with parameters for C and H. Note that as of LAMMPS version
15 November 2018 the {rebo} style in LAMMPS uses its own potential
15 May 2019 the {rebo} style in LAMMPS uses its own potential
file (CH.rebo). These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:

1
examples/USER/misc/kolmogorov_crespi_z/CH.airebo
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@ -1 +0,0 @@
../../../../potentials/CH.airebo

1
examples/USER/misc/kolmogorov_crespi_z/CH.rebo Symbolic link
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@ -0,0 +1 @@
../../../../potentials/CH.rebo

2
examples/USER/misc/kolmogorov_crespi_z/in.bilayer-graphene
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@ -22,7 +22,7 @@ group adsorbant type 2
######################## Potential defition ########################
pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0
####################################################################
pair_coeff * * rebo CH.airebo C C # chemical
pair_coeff * * rebo CH.rebo C C # chemical
pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C # long-range
####################################################################

208
examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.1
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@ -1,208 +0,0 @@
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.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
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.airebo C C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
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 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
Loop time of 3.90147 on 1 procs for 1000 steps with 256 atoms
Performance: 2.215 ns/day, 10.837 hours/ns, 256.314 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8786 | 3.8786 | 3.8786 | 0.0 | 99.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.010816 | 0.010816 | 0.010816 | 0.0 | 0.28
Output | 0.002461 | 0.002461 | 0.002461 | 0.0 | 0.06
Modify | 0.0051703 | 0.0051703 | 0.0051703 | 0.0 | 0.13
Other | | 0.004447 | | | 0.11
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: 0:00:03

208
examples/USER/misc/kolmogorov_crespi_z/log.16Mar18.bilayer-graphene.g++.4
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@ -1,208 +0,0 @@
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.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
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.airebo C C # chemical
Reading potential file CH.airebo with DATE: 2011-10-25
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 -1888.67041214 -1898.55881323 300.00000000 0.00000000 3.30000000
10 0.00100000 -1888.67037221 -1898.21029897 289.42778520 -0.00020126 3.30020126
20 0.00200000 -1888.67021541 -1897.22943612 259.67456089 -0.00041357 3.30041357
30 0.00300000 -1888.66999308 -1895.86681311 218.34126559 -0.00063673 3.30063673
40 0.00400000 -1888.66978354 -1894.47163830 176.02000692 -0.00087055 3.30087055
50 0.00500000 -1888.66966068 -1893.37123377 142.63902862 -0.00111486 3.30111486
60 0.00600000 -1888.66966132 -1892.75822749 124.04127205 -0.00136952 3.30136952
70 0.00700000 -1888.66976974 -1892.63445751 120.28297808 -0.00163441 3.30163441
80 0.00800000 -1888.66992867 -1892.83467462 126.35245792 -0.00190946 3.30190946
90 0.00900000 -1888.67006868 -1893.11387069 134.81862145 -0.00219458 3.30219458
100 0.01000000 -1888.67013621 -1893.25481851 139.09272853 -0.00248973 3.30248973
110 0.01100000 -1888.67011201 -1893.15155790 135.96068294 -0.00279489 3.30279489
120 0.01200000 -1888.67001496 -1892.84002960 126.51230266 -0.00311004 3.30311004
130 0.01300000 -1888.66988997 -1892.47004238 115.29120968 -0.00343519 3.30343519
140 0.01400000 -1888.66979230 -1892.23503116 108.16426723 -0.00377038 3.30377038
150 0.01500000 -1888.66976478 -1892.28630583 109.72070257 -0.00411562 3.30411562
160 0.01600000 -1888.66982054 -1892.66640611 121.25071190 -0.00447099 3.30447099
170 0.01700000 -1888.66993790 -1893.28862637 140.12442721 -0.00483654 3.30483654
180 0.01800000 -1888.67007017 -1893.97029258 160.80119589 -0.00521235 3.30521235
190 0.01900000 -1888.67016712 -1894.50458787 177.00801243 -0.00559851 3.30559851
200 0.02000000 -1888.67019459 -1894.73890106 184.11590729 -0.00599512 3.30599512
210 0.02100000 -1888.67014420 -1894.62906014 180.78501932 -0.00640230 3.30640230
220 0.02200000 -1888.67003680 -1894.25249103 169.36370738 -0.00682016 3.30682016
230 0.02300000 -1888.66991386 -1893.77601613 154.91186767 -0.00724883 3.30724883
240 0.02400000 -1888.66982525 -1893.38995084 143.20188490 -0.00768845 3.30768845
250 0.02500000 -1888.66980630 -1893.23138936 138.39193056 -0.00813913 3.30813913
260 0.02600000 -1888.66986130 -1893.32993923 141.38012476 -0.00860097 3.30860097
270 0.02700000 -1888.66996305 -1893.60070606 149.59171763 -0.00907408 3.30907408
280 0.02800000 -1888.67006686 -1893.88587226 158.24010433 -0.00955849 3.30955849
290 0.02900000 -1888.67012981 -1894.02402669 162.42960292 -0.01005424 3.31005424
300 0.03000000 -1888.67012722 -1893.91715234 159.18726627 -0.01056129 3.31056129
310 0.03100000 -1888.67005731 -1893.57037242 148.66857852 -0.01107957 3.31107957
320 0.03200000 -1888.66994573 -1893.09358619 134.20694883 -0.01160898 3.31160898
330 0.03300000 -1888.66983589 -1892.66132663 121.09614207 -0.01214935 3.31214935
340 0.03400000 -1888.66977410 -1892.44446345 114.51869676 -0.01270046 3.31270046
350 0.03500000 -1888.66978826 -1892.53901235 117.38674604 -0.01326207 3.31326207
360 0.03600000 -1888.66987439 -1892.92337288 129.04508371 -0.01383390 3.31383390
370 0.03700000 -1888.66999800 -1893.46445570 145.45701555 -0.01441561 3.31441561
380 0.03800000 -1888.67010960 -1893.97065516 160.81100020 -0.01500688 3.31500688
390 0.03900000 -1888.67016540 -1894.26835818 169.84119247 -0.01560734 3.31560734
400 0.04000000 -1888.67014667 -1894.26967975 169.88185546 -0.01621664 3.31621664
410 0.04100000 -1888.67006166 -1894.00321069 161.80014280 -0.01683442 3.31683442
420 0.04200000 -1888.66994367 -1893.60086324 149.59707418 -0.01746033 3.31746033
430 0.04300000 -1888.66984058 -1893.24559841 138.82197275 -0.01809405 3.31809405
440 0.04400000 -1888.66979399 -1893.09727874 134.32357877 -0.01873527 3.31873527
450 0.04500000 -1888.66982139 -1893.22837442 138.30000378 -0.01938373 3.31938373
460 0.04600000 -1888.66990972 -1893.59670383 149.47191354 -0.02003918 3.32003918
470 0.04700000 -1888.67002173 -1894.06542598 163.68887743 -0.02070143 3.32070143
480 0.04800000 -1888.67011389 -1894.46010842 175.66018439 -0.02137030 3.32137030
490 0.04900000 -1888.67015175 -1894.63688098 181.02206322 -0.02204565 3.32204565
500 0.05000000 -1888.67012158 -1894.53632221 177.97216882 -0.02272740 3.32272740
510 0.05100000 -1888.67003762 -1894.20444731 167.90610436 -0.02341547 3.32341547
520 0.05200000 -1888.66993151 -1893.77231066 154.79891353 -0.02410981 3.32410981
530 0.05300000 -1888.66984505 -1893.40525927 143.66572038 -0.02481040 3.32481040
540 0.05400000 -1888.66981408 -1893.23762083 138.58074854 -0.02551724 3.32551724
550 0.05500000 -1888.66985005 -1893.31793594 141.01630317 -0.02623032 3.32623032
560 0.05600000 -1888.66993737 -1893.59069013 149.28862751 -0.02694963 3.32694963
570 0.05700000 -1888.67003852 -1893.92089571 159.30352588 -0.02767517 3.32767517
580 0.05800000 -1888.67011322 -1894.15124753 166.28980524 -0.02840691 3.32840691
590 0.05900000 -1888.67013192 -1894.16548041 166.72104345 -0.02914478 3.32914478
600 0.06000000 -1888.67008713 -1893.93443318 159.71275856 -0.02988871 3.32988871
610 0.06100000 -1888.66999438 -1893.52841656 147.39760646 -0.03063856 3.33063856
620 0.06200000 -1888.66988809 -1893.09235021 134.17119963 -0.03139416 3.33139416
630 0.06300000 -1888.66980996 -1892.79172016 125.05288240 -0.03215531 3.33215531
640 0.06400000 -1888.66979261 -1892.74755390 123.71346730 -0.03292176 3.33292176
650 0.06500000 -1888.66984332 -1892.98665459 130.96590324 -0.03369323 3.33369323
660 0.06600000 -1888.66994245 -1893.42999868 144.41332389 -0.03446937 3.33446937
670 0.06700000 -1888.67005233 -1893.92310681 159.37018806 -0.03524986 3.33524986
680 0.06800000 -1888.67013309 -1894.29451581 170.63575808 -0.03603430 3.33603430
690 0.06900000 -1888.67015452 -1894.41878117 174.40514192 -0.03682229 3.33682229
700 0.07000000 -1888.67010897 -1894.26288036 169.67671530 -0.03761343 3.33761343
710 0.07100000 -1888.67001367 -1893.89812904 158.61357114 -0.03840729 3.33840729
720 0.07200000 -1888.66990378 -1893.47348746 145.73388454 -0.03920344 3.33920344
730 0.07300000 -1888.66982212 -1893.15984839 136.22099960 -0.04000148 3.34000148
740 0.07400000 -1888.66980109 -1893.08373746 133.91254029 -0.04080098 3.34080098
750 0.07500000 -1888.66984794 -1893.27755511 139.79127024 -0.04160156 3.34160156
760 0.07600000 -1888.66994215 -1893.66837365 151.64528967 -0.04240282 3.34240282
770 0.07700000 -1888.67004554 -1894.10941206 165.02263027 -0.04320441 3.34320441
780 0.07800000 -1888.67011702 -1894.43947545 175.03411436 -0.04400599 3.34400599
790 0.07900000 -1888.67013297 -1894.54590471 178.26254255 -0.04480726 3.34480726
800 0.08000000 -1888.67008751 -1894.40384142 173.95392406 -0.04560792 3.34560792
810 0.08100000 -1888.66999923 -1894.08389003 164.24973321 -0.04640773 3.34640773
820 0.08200000 -1888.66990447 -1893.72313979 153.30795965 -0.04720647 3.34720647
830 0.08300000 -1888.66984367 -1893.46839190 145.58111626 -0.04800393 3.34800393
840 0.08400000 -1888.66984156 -1893.41412536 143.93481093 -0.04879995 3.34879995
850 0.08500000 -1888.66989670 -1893.56426154 148.48805553 -0.04959439 3.34959439
860 0.08600000 -1888.66998222 -1893.83463719 156.68827294 -0.05038713 3.35038713
870 0.08700000 -1888.67006171 -1894.09325045 164.53181920 -0.05117805 3.35117805
880 0.08800000 -1888.67010273 -1894.21712661 168.28880100 -0.05196706 3.35196706
890 0.08900000 -1888.67008993 -1894.14263950 166.02935656 -0.05275408 3.35275408
900 0.09000000 -1888.67002891 -1893.89014571 158.37090587 -0.05353904 3.35353904
910 0.09100000 -1888.66994326 -1893.55535709 148.21649469 -0.05432186 3.35432186
920 0.09200000 -1888.66986526 -1893.27257949 139.63979178 -0.05510247 3.35510247
930 0.09300000 -1888.66982730 -1893.16330891 136.32582949 -0.05588078 3.35588078
940 0.09400000 -1888.66984631 -1893.28643285 140.06065785 -0.05665670 3.35665670
950 0.09500000 -1888.66991503 -1893.61245342 149.94957268 -0.05743015 3.35743015
960 0.09600000 -1888.67000691 -1894.03423922 162.74316516 -0.05820101 3.35820101
970 0.09700000 -1888.67008649 -1894.40848025 174.09469037 -0.05896915 3.35896915
980 0.09800000 -1888.67012436 -1894.61056767 180.22458605 -0.05973444 3.35973444
990 0.09900000 -1888.67010608 -1894.58107659 179.33042338 -0.06049672 3.36049672
1000 0.10000000 -1888.67003981 -1894.34773305 172.25312330 -0.06125581 3.36125581
Loop time of 1.32192 on 4 procs for 1000 steps with 256 atoms
Performance: 6.536 ns/day, 3.672 hours/ns, 756.476 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1157 | 1.172 | 1.2369 | 4.0 | 88.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.071678 | 0.13667 | 0.19304 | 11.8 | 10.34
Output | 0.0029244 | 0.0031272 | 0.0035112 | 0.4 | 0.24
Modify | 0.0016961 | 0.0017477 | 0.0017846 | 0.1 | 0.13
Other | | 0.008334 | | | 0.63
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

210
examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.1 Normal file
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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
examples/USER/misc/kolmogorov_crespi_z/log.30Apr19.bilayer-graphene.g++.4 Normal file
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@ -0,0 +1,210 @@
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

1
examples/airebo/CH.rebo Symbolic link
View File

@ -0,0 +1 @@
../../potentials/CH.rebo

2
examples/airebo/in.airebo-0-0
View File

@ -11,7 +11,7 @@ neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341

4
examples/airebo/in.rebo2
View File

@ -1,4 +1,4 @@
# AIREBO polyethelene benchmark
# REBO polyethelene benchmark
units metal
atom_style atomic
@ -11,7 +11,7 @@ neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
pair_coeff * * CH.rebo C H
velocity all create 300.0 761341

30
examples/airebo/log.12Dec18.airebo-0-0.g++.1 → examples/airebo/log.30Apr2019.airebo-0-0.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,19 +11,20 @@ read_data data.airebo
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000232458 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00132823 secs
replicate CPU = 0.00206327 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
pair_coeff * * CH.airebo C H
Reading potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 202.34667 -138029.28 0 -137175.59 -7623.6634
90 194.92367 -137997.12 0 -137174.75 -32277.173
100 185.2078 -137954.64 0 -137173.26 -6888.5104
Loop time of 4.96876 on 1 procs for 100 steps with 32640 atoms
Loop time of 9.70367 on 1 procs for 100 steps with 32640 atoms
Performance: 0.869 ns/day, 27.604 hours/ns, 20.126 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.445 ns/day, 53.909 hours/ns, 10.305 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 | 3.4535 | 3.4535 | 3.4535 | 0.0 | 69.50
Neigh | 1.4688 | 1.4688 | 1.4688 | 0.0 | 29.56
Comm | 0.015106 | 0.015106 | 0.015106 | 0.0 | 0.30
Output | 0.00098944 | 0.00098944 | 0.00098944 | 0.0 | 0.02
Modify | 0.021631 | 0.021631 | 0.021631 | 0.0 | 0.44
Other | | 0.008734 | | | 0.18
Pair | 7.2508 | 7.2508 | 7.2508 | 0.0 | 74.72
Neigh | 2.3573 | 2.3573 | 2.3573 | 0.0 | 24.29
Comm | 0.03116 | 0.03116 | 0.03116 | 0.0 | 0.32
Output | 0.0014739 | 0.0014739 | 0.0014739 | 0.0 | 0.02
Modify | 0.0447 | 0.0447 | 0.0447 | 0.0 | 0.46
Other | | 0.01819 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -84,4 +86,4 @@ Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:10

30
examples/airebo/log.12Dec18.airebo-0-0.g++.4 → examples/airebo/log.30Apr2019.airebo-0-0.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,19 +11,20 @@ read_data data.airebo
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000363827 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000664234 secs
replicate CPU = 0.00244427 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 0 0
pair_coeff * * ../../potentials/CH.airebo C H
Reading potential file ../../potentials/CH.airebo with DATE: 2011-10-25
pair_coeff * * CH.airebo C H
Reading potential file CH.airebo with DATE: 2011-10-25
velocity all create 300.0 761341
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 202.34667 -138029.28 0 -137175.59 -7623.6634
90 194.92367 -137997.12 0 -137174.75 -32277.173
100 185.2078 -137954.64 0 -137173.26 -6888.5104
Loop time of 1.44469 on 4 procs for 100 steps with 32640 atoms
Loop time of 6.71962 on 4 procs for 100 steps with 32640 atoms
Performance: 2.990 ns/day, 8.026 hours/ns, 69.219 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.643 ns/day, 37.331 hours/ns, 14.882 timesteps/s
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.92215 | 0.93812 | 0.95363 | 1.6 | 64.94
Neigh | 0.45592 | 0.45842 | 0.46002 | 0.2 | 31.73
Comm | 0.016539 | 0.03352 | 0.050276 | 8.6 | 2.32
Output | 0.00043154 | 0.00059217 | 0.001025 | 0.0 | 0.04
Modify | 0.0087888 | 0.0090455 | 0.0095809 | 0.3 | 0.63
Other | | 0.004989 | | | 0.35
Pair | 4.4598 | 4.6375 | 4.7708 | 5.5 | 69.01
Neigh | 1.5903 | 1.6452 | 1.7207 | 3.8 | 24.48
Comm | 0.16708 | 0.37041 | 0.56709 | 25.1 | 5.51
Output | 0.001061 | 0.0059808 | 0.0090635 | 4.3 | 0.09
Modify | 0.030086 | 0.03154 | 0.032522 | 0.5 | 0.47
Other | | 0.02897 | | | 0.43
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@ -84,4 +86,4 @@ Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01
Total wall time: 0:00:07

26
examples/airebo/log.12Dec18.airebo-m.g++.1 → examples/airebo/log.30Apr2019.airebo-m.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,12 +11,13 @@ read_data data.airebo
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000225067 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.00136471 secs
replicate CPU = 0.00226521 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5517
Loop time of 64.5779 on 1 procs for 100 steps with 32640 atoms
Loop time of 111.537 on 1 procs for 100 steps with 32640 atoms
Performance: 0.067 ns/day, 358.766 hours/ns, 1.549 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.039 ns/day, 619.650 hours/ns, 0.897 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 | 59.905 | 59.905 | 59.905 | 0.0 | 92.76
Neigh | 4.615 | 4.615 | 4.615 | 0.0 | 7.15
Comm | 0.024453 | 0.024453 | 0.024453 | 0.0 | 0.04
Output | 0.00099945 | 0.00099945 | 0.00099945 | 0.0 | 0.00
Modify | 0.021971 | 0.021971 | 0.021971 | 0.0 | 0.03
Other | | 0.01029 | | | 0.02
Pair | 103.58 | 103.58 | 103.58 | 0.0 | 92.87
Neigh | 7.8371 | 7.8371 | 7.8371 | 0.0 | 7.03
Comm | 0.046259 | 0.046259 | 0.046259 | 0.0 | 0.04
Output | 0.001497 | 0.001497 | 0.001497 | 0.0 | 0.00
Modify | 0.047151 | 0.047151 | 0.047151 | 0.0 | 0.04
Other | | 0.02204 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -84,4 +86,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:05
Total wall time: 0:01:53

26
examples/airebo/log.12Dec18.airebo-m.g++.4 → examples/airebo/log.30Apr2019.airebo-m.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,12 +11,13 @@ read_data data.airebo
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000880957 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000692129 secs
replicate CPU = 0.00271702 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 164.28396 -138709.5 0 -138016.4 -1524.7353
90 180.26403 -138776.42 0 -138015.9 -27143.467
100 164.05694 -138706.58 0 -138014.44 5157.5517
Loop time of 17.8093 on 4 procs for 100 steps with 32640 atoms
Loop time of 68.9923 on 4 procs for 100 steps with 32640 atoms
Performance: 0.243 ns/day, 98.940 hours/ns, 5.615 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.063 ns/day, 383.290 hours/ns, 1.449 timesteps/s
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.932 | 16.012 | 16.082 | 1.5 | 89.91
Neigh | 1.5933 | 1.6063 | 1.6173 | 0.7 | 9.02
Comm | 0.098741 | 0.17402 | 0.2676 | 16.8 | 0.98
Output | 0.00044513 | 0.00074279 | 0.0016048 | 0.0 | 0.00
Modify | 0.0088906 | 0.0089375 | 0.008992 | 0.0 | 0.05
Other | | 0.007106 | | | 0.04
Pair | 60.09 | 60.276 | 60.515 | 2.1 | 87.37
Neigh | 6.7521 | 6.8996 | 7.0678 | 4.3 | 10.00
Comm | 1.5441 | 1.7514 | 2.0838 | 16.9 | 2.54
Output | 0.0010803 | 0.001972 | 0.0043106 | 3.0 | 0.00
Modify | 0.031365 | 0.032539 | 0.034404 | 0.7 | 0.05
Other | | 0.03104 | | | 0.04
Nlocal: 8160 ave 8167 max 8153 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -84,4 +86,4 @@ Total # of neighbors = 22210922
Ave neighs/atom = 680.482
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:18
Total wall time: 0:01:10

26
examples/airebo/log.12Dec18.airebo.g++.1 → examples/airebo/log.30Apr2019.airebo.g++.1
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,12 +11,13 @@ read_data data.airebo
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000217438 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.0013268 secs
replicate CPU = 0.00204968 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 57.482 on 1 procs for 100 steps with 32640 atoms
Loop time of 98.1502 on 1 procs for 100 steps with 32640 atoms
Performance: 0.075 ns/day, 319.344 hours/ns, 1.740 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.044 ns/day, 545.279 hours/ns, 1.019 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 | 52.796 | 52.796 | 52.796 | 0.0 | 91.85
Neigh | 4.6286 | 4.6286 | 4.6286 | 0.0 | 8.05
Comm | 0.024035 | 0.024035 | 0.024035 | 0.0 | 0.04
Output | 0.00098443 | 0.00098443 | 0.00098443 | 0.0 | 0.00
Modify | 0.021958 | 0.021958 | 0.021958 | 0.0 | 0.04
Other | | 0.01014 | | | 0.02
Pair | 90.237 | 90.237 | 90.237 | 0.0 | 91.94
Neigh | 7.796 | 7.796 | 7.796 | 0.0 | 7.94
Comm | 0.048884 | 0.048884 | 0.048884 | 0.0 | 0.05
Output | 0.0016053 | 0.0016053 | 0.0016053 | 0.0 | 0.00
Modify | 0.045511 | 0.045511 | 0.045511 | 0.0 | 0.05
Other | | 0.0217 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -84,4 +86,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:58
Total wall time: 0:01:39

26
examples/airebo/log.12Dec18.airebo.g++.4 → examples/airebo/log.30Apr2019.airebo.g++.4
View File

@ -1,4 +1,5 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
@ -10,12 +11,13 @@ read_data data.airebo
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000266314 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000614405 secs
replicate CPU = 0.00146151 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 157.16184 -138695.77 0 -138032.72 19824.698
90 196.15907 -138860.65 0 -138033.07 -7950.8463
100 178.31875 -138784.89 0 -138032.57 30997.671
Loop time of 15.9743 on 4 procs for 100 steps with 32640 atoms
Loop time of 60.4943 on 4 procs for 100 steps with 32640 atoms
Performance: 0.270 ns/day, 88.746 hours/ns, 6.260 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.071 ns/day, 336.080 hours/ns, 1.653 timesteps/s
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.13 | 14.185 | 14.258 | 1.3 | 88.80
Neigh | 1.5945 | 1.6093 | 1.6237 | 0.9 | 10.07
Comm | 0.075436 | 0.16329 | 0.23273 | 14.3 | 1.02
Output | 0.00041533 | 0.00069332 | 0.0014405 | 0.0 | 0.00
Modify | 0.0089853 | 0.0090484 | 0.0091338 | 0.1 | 0.06
Other | | 0.007319 | | | 0.05
Pair | 51.737 | 52.46 | 52.86 | 6.2 | 86.72
Neigh | 6.5823 | 6.6605 | 6.726 | 2.0 | 11.01
Comm | 0.92426 | 1.3125 | 2.0111 | 37.0 | 2.17
Output | 0.0010669 | 0.0019811 | 0.0043974 | 3.1 | 0.00
Modify | 0.030364 | 0.031523 | 0.032495 | 0.5 | 0.05
Other | | 0.028 | | | 0.05
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
@ -84,4 +86,4 @@ Total # of neighbors = 22217840
Ave neighs/atom = 680.694
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:16
Total wall time: 0:01:01

32
examples/airebo/log.12Dec18.rebo2.g++.1 → examples/airebo/log.30Apr2019.rebo2.g++.1
View File

@ -1,6 +1,7 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
# REBO polyethelene benchmark
units metal
atom_style atomic
@ -10,19 +11,20 @@ read_data data.airebo
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000190735 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
1 by 1 by 1 MPI processor grid
32640 atoms
Time spent = 0.0013907 secs
replicate CPU = 0.00197148 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3
pair_coeff * * CH.rebo C H
Reading potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 4.96341 on 1 procs for 100 steps with 32640 atoms
Loop time of 9.44819 on 1 procs for 100 steps with 32640 atoms
Performance: 0.870 ns/day, 27.574 hours/ns, 20.147 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.457 ns/day, 52.490 hours/ns, 10.584 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 | 3.4476 | 3.4476 | 3.4476 | 0.0 | 69.46
Neigh | 1.4692 | 1.4692 | 1.4692 | 0.0 | 29.60
Comm | 0.015226 | 0.015226 | 0.015226 | 0.0 | 0.31
Output | 0.00098777 | 0.00098777 | 0.00098777 | 0.0 | 0.02
Modify | 0.021646 | 0.021646 | 0.021646 | 0.0 | 0.44
Other | | 0.008718 | | | 0.18
Pair | 7.037 | 7.037 | 7.037 | 0.0 | 74.48
Neigh | 2.3182 | 2.3182 | 2.3182 | 0.0 | 24.54
Comm | 0.029898 | 0.029898 | 0.029898 | 0.0 | 0.32
Output | 0.0014331 | 0.0014331 | 0.0014331 | 0.0 | 0.02
Modify | 0.043851 | 0.043851 | 0.043851 | 0.0 | 0.46
Other | | 0.01774 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -84,4 +86,4 @@ Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05
Total wall time: 0:00:09

32
examples/airebo/log.12Dec18.rebo2.g++.4 → examples/airebo/log.30Apr2019.rebo2.g++.4
View File

@ -1,6 +1,7 @@
LAMMPS (12 Dec 2018)
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
# AIREBO polyethelene benchmark
# REBO polyethelene benchmark
units metal
atom_style atomic
@ -10,19 +11,20 @@ read_data data.airebo
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
read_data CPU = 0.000682831 secs
replicate 17 16 2
orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158)
2 by 2 by 1 MPI processor grid
32640 atoms
Time spent = 0.000644684 secs
replicate CPU = 0.00221777 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * ../../potentials/CH.rebo C H
Reading potential file ../../potentials/CH.rebo with DATE: 2018-7-3
pair_coeff * * CH.rebo C H
Reading potential file CH.rebo with DATE: 2018-7-3
velocity all create 300.0 761341
@ -56,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press
80 202.37482 -138029.39 0 -137175.59 -7622.7319
90 194.90628 -137997.05 0 -137174.75 -32267.471
100 185.17818 -137954.51 0 -137173.26 -6901.7499
Loop time of 1.4517 on 4 procs for 100 steps with 32640 atoms
Loop time of 6.35645 on 4 procs for 100 steps with 32640 atoms
Performance: 2.976 ns/day, 8.065 hours/ns, 68.885 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.680 ns/day, 35.314 hours/ns, 15.732 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.92079 | 0.93883 | 0.95524 | 1.6 | 64.67
Neigh | 0.45826 | 0.46013 | 0.46316 | 0.3 | 31.70
Comm | 0.02183 | 0.038046 | 0.052974 | 7.5 | 2.62
Output | 0.00044131 | 0.00057179 | 0.00093198 | 0.0 | 0.04
Modify | 0.0088243 | 0.0089917 | 0.0092998 | 0.2 | 0.62
Other | | 0.005127 | | | 0.35
Pair | 4.4335 | 4.5041 | 4.56 | 2.1 | 70.86
Neigh | 1.5332 | 1.5919 | 1.6466 | 3.6 | 25.04
Comm | 0.098299 | 0.20854 | 0.26277 | 14.2 | 3.28
Output | 0.0011072 | 0.0018047 | 0.0037503 | 2.6 | 0.03
Modify | 0.028811 | 0.030358 | 0.031516 | 0.6 | 0.48
Other | | 0.01977 | | | 0.31
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
@ -84,4 +86,4 @@ Total # of neighbors = 4902134
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01
Total wall time: 0:00:06