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This commit is contained in:
Steven J. Plimpton 2018-05-03 16:55:22 -06:00
parent b0b67ca610 eeee2d3026
commit 2b8576c7c7
3190 changed files with 620824 additions and 58680 deletions
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44
bench/POTENTIALS/CdTe.bop
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elements:
2
48 1.124118e+02 Cd
52 1.276030e+02 Te
global:
1.00e-05 1.00e-05 1.00e-05 1.00e-05 1.00e-05 1.00e-03 1.00e-05
2 9.900000e-01 1.000000e-02
2.0 0.625 1
1.573798e+01 1.137622e+00 2.087779e+00
2.218068e+01 2.689731e+00
2.000000e+00 0.000000e+00
ptrs:
0.000000e+00 1.000000e+00 4.200000e-01
0.000000e+00 1.000000e+00 4.606863e-01
pairs:
3.127600e+00 3.127600e+00 3.730300e+00 4.333000e+00
3.263155e+00 1.553883e+00 2.800000e+00
1.863695e-01 2.383177e-01 9.759853e-02
0.000000e+00 5.611298e-01 0.000000e+00
1.000000e+00 1.000000e+00 0.000000e+00
4.318628e-01 1.500000e+01 1.000000e+06
3.127600e+00 3.127600e+00 4.013800e+00 4.900000e+00
2.587831e+00 1.287478e+00 2.811251e+00
6.314400e-01 8.252896e-01 3.174259e-02
0.000000e+00 1.286955e+00 0.000000e+00
1.000000e+00 1.000000e+00 0.000000e+00
5.000000e-01 0.000000e+00 1.000000e+06
3.162600e+00 3.162600e+00 3.804600e+00 4.446500e+00
2.458846e+00 1.223306e+00 2.799998e+00
8.769118e-01 7.826353e-01 5.312050e-01
0.000000e+00 1.014809e+00 0.000000e+00
1.000000e+00 1.000000e+00 0.000000e+00
3.312269e-01 -2.860190e+00 1.000000e+06
tris:
3.968701e-01 8.810195e-01 -2.778897e-01
-1.007128e-01 10.000000e-01 1.007128e-01
2.007322e-01 6.000000e-01 1.992678e-01
2.095238e-01 6.000000e-01 1.904762e-01
3.928496e-03 9.999272e-01 -3.855665e-03
1.171817e-01 8.348116e-01 4.800670e-02

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18
bench/POTENTIALS/README
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@ -5,7 +5,7 @@ the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
Examples are shown below of how to run these scripts. Log files for
running them on 1 and 4 processors of a Linux box are included in the
directory. This assumes that the executable lmp_linux has been built
directory. This assumes that the executable lmp_mpi has been built
with the appropriate packages installed in order to run with a
particular potential. For the ReaxFF potential invoked by the in.reax
script, you should build the Fortran ReaxFF library in lib/reax, using
@ -15,18 +15,10 @@ the in.reax file.
Any potential parameter file(s) used by the input scripts are also
included in this directory.
Note that some of the input scripts read data files of atomic
coordinates via the "read_data" command. Those data files are NOT
included in this directory, to make the LAMMPS download tarball
smaller. They are available on the Benchmark page of the LAMMPS WWW
site (lammps.sandia.gov/bench), via the tarball link in the table
under the Potentials section. If you download and unpack the tarball
for a particular potential, the data file is included.
------------------------------------------------------------------------
lmp_linux < in.fene
lmp_linux < in.tersoff
lmp_mpi -in in.fene
lmp_mpi -in in.tersoff
mpirun -np 4 lmp_linux < in.fene
mpirun -np 4 lmp_linux < in.protein
mpirun -np 4 lmp_mpi -in in.fene
mpirun -np 4 lmp_mpi -in in.protein

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bench/POTENTIALS/data.airebo Normal file
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LAMMPS data file from restart file: timestep = 1, procs = 1
60 atoms
2 atom types
-2.1 2.1 xlo xhi
-2.1 2.1 ylo yhi
0 25.5790000000 zlo zhi
Masses
1 12.01
2 1.00794
Atoms
1 1 0.0000000000 0.0000000000 0.0000000000
2 2 0.9010066786 -0.6310205743 0.0000000000
3 2 -0.9010066786 -0.6310205743 0.0000000000
4 1 0.0000000000 0.8470061967 1.2789591482
5 2 0.9010066786 1.4780267710 1.2789591482
6 2 -0.9010066786 1.4780267710 1.2789591482
7 1 0.0000000000 0.0000000000 2.5579182965
8 2 0.9010066786 -0.6310205743 2.5579182965
9 2 -0.9010066786 -0.6310205743 2.5579182965
10 1 0.0000000000 0.8470061967 3.8368774447
11 2 0.9010066786 1.4780267710 3.8368774447
12 2 -0.9010066786 1.4780267710 3.8368774447
13 1 0.0000000000 0.0000000000 5.1158365929
14 2 0.9010066786 -0.6310205743 5.1158365929
15 2 -0.9010066786 -0.6310205743 5.1158365929
16 1 0.0000000000 0.8470061967 6.3947957411
17 2 0.9010066786 1.4780267710 6.3947957411
18 2 -0.9010066786 1.4780267710 6.3947957411
19 1 0.0000000000 0.0000000000 7.6737548894
20 2 0.9010066786 -0.6310205743 7.6737548894
21 2 -0.9010066786 -0.6310205743 7.6737548894
22 1 0.0000000000 0.8470061967 8.9527140376
23 2 0.9010066786 1.4780267710 8.9527140376
24 2 -0.9010066786 1.4780267710 8.9527140376
25 1 0.0000000000 0.0000000000 10.2316731858
26 2 0.9010066786 -0.6310205743 10.2316731858
27 2 -0.9010066786 -0.6310205743 10.2316731858
28 1 0.0000000000 0.8470061967 11.5106323340
29 2 0.9010066786 1.4780267710 11.5106323340
30 2 -0.9010066786 1.4780267710 11.5106323340
31 1 0.0000000000 0.0000000000 12.7895914823
32 2 0.9010066786 -0.6310205743 12.7895914823
33 2 -0.9010066786 -0.6310205743 12.7895914823
34 1 0.0000000000 0.8470061967 14.0685506305
35 2 0.9010066786 1.4780267710 14.0685506305
36 2 -0.9010066786 1.4780267710 14.0685506305
37 1 0.0000000000 0.0000000000 15.3475097787
38 2 0.9010066786 -0.6310205743 15.3475097787
39 2 -0.9010066786 -0.6310205743 15.3475097787
40 1 0.0000000000 0.8470061967 16.6264689269
41 2 0.9010066786 1.4780267710 16.6264689269
42 2 -0.9010066786 1.4780267710 16.6264689269
43 1 0.0000000000 0.0000000000 17.9054280752
44 2 0.9010066786 -0.6310205743 17.9054280752
45 2 -0.9010066786 -0.6310205743 17.9054280752
46 1 0.0000000000 0.8470061967 19.1843872234
47 2 0.9010066786 1.4780267710 19.1843872234
48 2 -0.9010066786 1.4780267710 19.1843872234
49 1 0.0000000000 0.0000000000 20.4633463716
50 2 0.9010066786 -0.6310205743 20.4633463716
51 2 -0.9010066786 -0.6310205743 20.4633463716
52 1 0.0000000000 0.8470061967 21.7423055198
53 2 0.9010066786 1.4780267710 21.7423055198
54 2 -0.9010066786 1.4780267710 21.7423055198
55 1 0.0000000000 0.0000000000 23.0212646681
56 2 0.9010066786 -0.6310205743 23.0212646681
57 2 -0.9010066786 -0.6310205743 23.0212646681
58 1 0.0000000000 0.8470061967 24.3002238163
59 2 0.9010066786 1.4780267710 24.3002238163
60 2 -0.9010066786 1.4780267710 24.3002238163

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bench/POTENTIALS/data.protein Symbolic link
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../data.rhodo

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bench/POTENTIALS/data.reax Normal file
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# PETN-I unit cell (space group P4¯21c)
58 atoms
4 atom types
0.0 9.491065 xlo xhi
0.0 9.491065 ylo yhi
0.0 6.99123 zlo zhi
Masses
1 12.0000
2 1.0080
3 15.9990
4 14.0000
Atoms
1 4 0.863455358E-13 1.732320000 4.630010000 0.892350000
2 3 0.863455358E-13 2.969950000 4.192650000 1.864890000
3 3 0.863455358E-13 1.373230000 3.777920000 0.096380000
4 3 0.863455358E-13 1.320990000 5.707670000 1.097690000
5 2 0.863455358E-13 2.884650000 5.896680000 3.317770000
6 2 0.863455358E-13 3.827980000 6.263410000 2.178970000
7 1 0.863455358E-13 5.909570000 4.291490000 2.540550000
8 4 0.863455358E-13 7.726490000 4.862430000 0.940970000
9 3 0.863455358E-13 6.554310000 5.406520000 1.911000000
10 3 0.863455358E-13 8.126280000 5.645810000 0.107790000
11 3 0.863455358E-13 8.070620000 3.697510000 1.039000000
12 2 0.863455358E-13 6.526620000 3.514030000 3.084250000
13 2 0.863455358E-13 5.500710000 3.475690000 1.894580000
14 1 0.863455358E-13 4.305160000 3.663690000 4.373270000
15 4 0.863455358E-13 4.891690000 1.789930000 5.975440000
16 3 0.863455358E-13 5.388500000 3.060710000 5.142620000
17 3 0.863455358E-13 5.709330000 1.320000000 6.723350000
18 3 0.863455358E-13 3.766570000 1.413750000 5.785210000
19 2 0.863455358E-13 3.859620000 2.802480000 3.723820000
20 2 0.863455358E-13 3.303550000 3.975170000 4.811250000
21 1 0.863455358E-13 5.224790000 5.919230000 4.377750000
22 4 0.863455358E-13 4.644030000 7.696520000 6.100900000
23 3 0.863455358E-13 4.146850000 6.645990000 4.999010000
24 3 0.863455358E-13 3.883440000 7.981690000 7.010630000
25 3 0.863455358E-13 5.786660000 8.025100000 5.996670000
26 2 0.863455358E-13 5.906020000 6.611630000 3.756700000
27 2 0.863455358E-13 6.077870000 5.531160000 4.915880000
28 1 0.863455358E-13 3.552720000 5.288480000 2.602930000
29 1 0.863455358E-13 4.757460000 4.786420000 3.446050000
30 1 0.863455358E-13 10.623310000 10.011360000 7.901960000
31 4 0.863455358E-13 12.340670000 9.278570000 9.658210000
32 3 0.863455358E-13 11.173160000 8.908900000 8.591070000
33 3 0.863455358E-13 12.634410000 8.404450000 10.434380000
34 3 0.863455358E-13 12.808850000 10.398130000 9.459970000
35 2 0.863455358E-13 11.336750000 10.607430000 7.235710000
36 2 0.863455358E-13 10.314820000 10.962610000 8.407430000
37 1 0.863455358E-13 8.366600000 8.930150000 7.823850000
38 4 0.863455358E-13 6.680390000 9.584210000 9.655230000
39 3 0.863455358E-13 7.796220000 10.005630000 8.544820000
40 3 0.863455358E-13 6.439700000 10.424020000 10.460020000
41 3 0.863455358E-13 6.239040000 8.465520000 9.442190000
42 2 0.863455358E-13 7.687150000 8.335850000 7.127770000
43 2 0.863455358E-13 8.728770000 7.913540000 8.234250000
44 1 0.863455358E-13 10.045160000 8.333570000 6.100600000
45 4 0.863455358E-13 9.373710000 6.690820000 4.302840000
46 3 0.863455358E-13 8.940460000 7.828420000 5.375480000
47 3 0.863455358E-13 8.526330000 6.420240000 3.522270000
48 3 0.863455358E-13 10.474540000 6.234360000 4.499290000
49 2 0.863455358E-13 10.719930000 7.694230000 6.776840000
50 2 0.863455358E-13 10.913160000 8.873910000 5.574960000
51 1 0.863455358E-13 8.940970000 10.671300000 6.139780000
52 4 0.863455358E-13 9.619090000 12.332990000 4.329510000
53 3 0.863455358E-13 10.055950000 11.263880000 5.506630000
54 3 0.863455358E-13 10.434090000 12.566040000 3.507610000
55 3 0.863455358E-13 8.506740000 12.768990000 4.512780000
56 2 0.863455358E-13 8.359930000 11.424490000 6.758000000
57 2 0.863455358E-13 8.018410000 10.320200000 5.568000000
58 1 0.863455358E-13 9.486900000 9.503450000 6.990810000

1
bench/POTENTIALS/data.rebo Symbolic link
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data.airebo

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bench/POTENTIALS/in.bop
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@ -13,11 +13,11 @@ create_box 2 box
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
pair_style bop
pair_coeff * * CdTe.bop Cd Te
pair_coeff * * CdTe.bop.table Cd Te
mass 1 112.4
mass 2 127.6
communicate single cutoff 14.7
comm_modify cutoff 14.7
velocity all create 1000.0 376847 loop geom

2
bench/POTENTIALS/in.eff
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@ -10,7 +10,7 @@ pair_coeff * *
neigh_modify one 6000 page 60000
communicate single vel yes
comm_modify vel yes
compute effTemp all temp/eff

2
bench/POTENTIALS/in.granular
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@ -4,7 +4,7 @@ units lj
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
comm_modify vel yes
read_data data.granular

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bench/POTENTIALS/in.meamc Normal file
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# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
region box block 0 20 0 20 0 20
create_box 1 box
create_atoms 1 box
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100

2
bench/POTENTIALS/in.reaxc
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@ -10,7 +10,7 @@ replicate 7 8 10
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax 1 2 3 4
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve

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bench/POTENTIALS/log.16Mar18.adp.1 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184107 secs
pair_style adp
pair_coeff * * Ni.adp Ni
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.168
ghost atom cutoff = 6.168
binsize = 3.084, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair adp, 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) = 27.56 | 27.56 | 27.56 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 11.9854 on 1 procs for 100 steps with 32000 atoms
Performance: 3.604 ns/day, 6.659 hours/ns, 8.344 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 | 11.447 | 11.447 | 11.447 | 0.0 | 95.51
Neigh | 0.48465 | 0.48465 | 0.48465 | 0.0 | 4.04
Comm | 0.019317 | 0.019317 | 0.019317 | 0.0 | 0.16
Output | 0.00011063 | 0.00011063 | 0.00011063 | 0.0 | 0.00
Modify | 0.025319 | 0.025319 | 0.025319 | 0.0 | 0.21
Other | | 0.009125 | | | 0.08
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:12

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bench/POTENTIALS/log.16Mar18.adp.4 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in ADP
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000586033 secs
pair_style adp
pair_coeff * * Ni.adp Ni
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.168
ghost atom cutoff = 6.168
binsize = 3.084, bins = 23 23 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair adp, 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) = 12.45 | 12.45 | 12.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 3.49752 on 4 procs for 100 steps with 32000 atoms
Performance: 12.352 ns/day, 1.943 hours/ns, 28.592 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3203 | 3.3261 | 3.3317 | 0.3 | 95.10
Neigh | 0.12544 | 0.12594 | 0.12634 | 0.1 | 3.60
Comm | 0.024059 | 0.03001 | 0.035574 | 2.9 | 0.86
Output | 4.8161e-05 | 6.8128e-05 | 0.00011802 | 0.0 | 0.00
Modify | 0.010666 | 0.010841 | 0.011109 | 0.2 | 0.31
Other | | 0.00457 | | | 0.13
Nlocal: 8000 ave 8044 max 7960 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 9131 ave 9171 max 9087 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 334259 ave 336108 max 332347 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
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 = 0.00154901 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 106.4 | 106.4 | 106.4 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 60.9424 on 1 procs for 100 steps with 32640 atoms
Performance: 0.071 ns/day, 338.569 hours/ns, 1.641 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 | 55.299 | 55.299 | 55.299 | 0.0 | 90.74
Neigh | 5.5777 | 5.5777 | 5.5777 | 0.0 | 9.15
Comm | 0.027658 | 0.027658 | 0.027658 | 0.0 | 0.05
Output | 0.0011463 | 0.0011463 | 0.0011463 | 0.0 | 0.00
Modify | 0.024684 | 0.024684 | 0.024684 | 0.0 | 0.04
Other | | 0.012 | | | 0.02
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48190 ave 48190 max 48190 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: 2.22179e+07 ave 2.22179e+07 max 2.22179e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:01:02

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
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 = 0.00070262 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.7
ghost atom cutoff = 10.7
binsize = 5.35, bins = 14 13 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair airebo, 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) = 29.37 | 29.75 | 30.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 7998.7287
10 161.33916 -138711.85 0 -138031.17 33242.273
20 208.59505 -138911.77 0 -138031.73 -3199.2371
30 139.73485 -138617.76 0 -138028.23 10890.529
40 142.15332 -138628.03 0 -138028.3 14614.022
50 114.21945 -138509.87 0 -138027.98 24700.885
60 164.9432 -138725.08 0 -138029.19 35135.722
70 162.14928 -138714.86 0 -138030.77 5666.4609
80 157.17575 -138694.81 0 -138031.7 19838.161
90 196.16354 -138859.65 0 -138032.05 -7942.9718
100 178.30378 -138783.8 0 -138031.55 31012.15
Loop time of 16.768 on 4 procs for 100 steps with 32640 atoms
Performance: 0.258 ns/day, 93.156 hours/ns, 5.964 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.538 | 14.589 | 14.654 | 1.3 | 87.00
Neigh | 1.8853 | 1.8992 | 1.9159 | 0.8 | 11.33
Comm | 0.18073 | 0.25896 | 0.31361 | 10.6 | 1.54
Output | 0.00050807 | 0.0040419 | 0.0077746 | 5.6 | 0.02
Modify | 0.0094635 | 0.0096973 | 0.0099616 | 0.2 | 0.06
Other | | 0.007481 | | | 0.04
Nlocal: 8160 ave 8174 max 8146 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 22614.5 ave 22629 max 22601 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55447e+06 ave 5.56557e+06 max 5.54193e+06 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 22217870
Ave neighs/atom = 680.695
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:17

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.00191426 secs
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
comm_modify cutoff 14.7
velocity all create 1000.0 376847 loop geom
neighbor 0.1 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 14.7
binsize = 2.5, bins = 55 55 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair bop, 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) = 19.39 | 19.39 | 19.39 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 24.1696 on 1 procs for 100 steps with 32000 atoms
Performance: 0.357 ns/day, 67.138 hours/ns, 4.137 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 | 23.355 | 23.355 | 23.355 | 0.0 | 96.63
Neigh | 0.7545 | 0.7545 | 0.7545 | 0.0 | 3.12
Comm | 0.026978 | 0.026978 | 0.026978 | 0.0 | 0.11
Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.00
Modify | 0.024145 | 0.024145 | 0.024145 | 0.0 | 0.10
Other | | 0.009326 | | | 0.04
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35071 ave 35071 max 35071 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: 141288 ave 141288 max 141288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:24

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk CdTe via BOP
units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
2 by 2 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
Time spent = 0.000597477 secs
pair_style bop
pair_coeff * * CdTe.bop.table Cd Te
Reading potential file CdTe.bop.table with DATE: 2012-06-25
Reading potential file CdTe.bop.table with DATE: 2012-06-25
mass 1 112.4
mass 2 127.6
comm_modify cutoff 14.7
velocity all create 1000.0 376847 loop geom
neighbor 0.1 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 14.7
binsize = 2.5, bins = 55 55 28
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair bop, 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) = 8.497 | 8.497 | 8.497 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.487 0 -65403.292 3473.2595
100 572.16481 -67769.936 0 -65403.35 1838.6993
Loop time of 6.50033 on 4 procs for 100 steps with 32000 atoms
Performance: 1.329 ns/day, 18.056 hours/ns, 15.384 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.7879 | 5.975 | 6.1607 | 5.4 | 91.92
Neigh | 0.27603 | 0.27621 | 0.27647 | 0.0 | 4.25
Comm | 0.049869 | 0.23531 | 0.42241 | 27.2 | 3.62
Output | 4.9829e-05 | 5.9724e-05 | 8.5592e-05 | 0.0 | 0.00
Modify | 0.0089927 | 0.0090921 | 0.0092406 | 0.1 | 0.14
Other | | 0.004665 | | | 0.07
Nlocal: 8000 ave 8006 max 7994 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 15171 ave 15177 max 15165 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: 35322 ave 35412 max 35267 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 141288
Ave neighs/atom = 4.41525
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
32400 atoms
mass 1 28.0855
group type1 type 1
10800 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
21600 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Si O
neighbor 0.5 bin
neigh_modify every 10 delay 0 check yes
timestep 0.0002
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
thermo_modify norm yes
velocity all create 300.0 3482028
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 10 0.001 file fq.out
thermo 10
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 12 12 14
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair comb, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 106.2 | 106.2 | 106.2 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
0 300 -6.8032038 -6.8419806 4.6274455 -11.469426 2.8875895 -1.4437947 13386.415 462016.62
10 273.21913 -6.8032489 -6.8385642 4.6221303 -11.460695 2.8872353 -1.4436176 13076.442 462016.62
20 242.0051 -6.803367 -6.8346477 4.6208311 -11.455479 2.8870176 -1.4435087 12080.423 462016.62
30 214.5618 -6.8034588 -6.8311922 4.620067 -11.451259 2.8870575 -1.4435287 10307.876 462016.62
40 198.14521 -6.8035174 -6.8291289 4.6202931 -11.449422 2.8874526 -1.4437263 7765.732 462016.62
50 197.15561 -6.8035468 -6.8290303 4.6219602 -11.450991 2.8883366 -1.4441683 4432.7134 462016.62
60 212.04532 -6.8035584 -6.8309666 4.6260476 -11.457014 2.8896425 -1.4448212 324.71226 462016.62
70 239.37999 -6.8035665 -6.8345078 4.6322984 -11.466806 2.8912723 -1.4456361 -4497.0492 462016.62
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 517.206 on 1 procs for 100 steps with 32400 atoms
Performance: 0.003 ns/day, 7183.417 hours/ns, 0.193 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 | 114.18 | 114.18 | 114.18 | 0.0 | 22.08
Neigh | 0.47558 | 0.47558 | 0.47558 | 0.0 | 0.09
Comm | 0.030611 | 0.030611 | 0.030611 | 0.0 | 0.01
Output | 0.0024922 | 0.0024922 | 0.0024922 | 0.0 | 0.00
Modify | 402.51 | 402.51 | 402.51 | 0.0 | 77.82
Other | | 0.006137 | | | 0.00
Nlocal: 32400 ave 32400 max 32400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 42518 ave 42518 max 42518 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: 1.85317e+07 ave 1.85317e+07 max 1.85317e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:09:18

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SiO2 for COMB potential
units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
32400 atoms
mass 1 28.0855
group type1 type 1
10800 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
21600 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Si O
neighbor 0.5 bin
neigh_modify every 10 delay 0 check yes
timestep 0.0002
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
thermo_modify norm yes
velocity all create 300.0 3482028
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 10 0.001 file fq.out
thermo 10
run 100
Neighbor list info ...
update every 10 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 12 12 14
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair comb, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 32.11 | 32.11 | 32.11 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Press Volume
0 300 -6.8032038 -6.8419806 4.6274455 -11.469426 2.8875895 -1.4437947 13386.415 462016.62
10 273.21913 -6.8032489 -6.8385642 4.6221303 -11.460695 2.8872353 -1.4436176 13076.442 462016.62
20 242.0051 -6.803367 -6.8346477 4.6208311 -11.455479 2.8870176 -1.4435087 12080.423 462016.62
30 214.5618 -6.8034588 -6.8311922 4.620067 -11.451259 2.8870575 -1.4435287 10307.876 462016.62
40 198.14521 -6.8035174 -6.8291289 4.6202931 -11.449422 2.8874526 -1.4437263 7765.732 462016.62
50 197.15561 -6.8035468 -6.8290303 4.6219602 -11.450991 2.8883366 -1.4441683 4432.7134 462016.62
60 212.04532 -6.8035584 -6.8309666 4.6260476 -11.457014 2.8896425 -1.4448212 324.71226 462016.62
70 239.37999 -6.8035665 -6.8345078 4.6322984 -11.466806 2.8912723 -1.4456361 -4497.0492 462016.62
80 272.98301 -6.803583 -6.8388677 4.6404093 -11.479277 2.8932784 -1.4466392 -9896.1704 462016.62
90 305.77651 -6.8036184 -6.8431419 4.6512736 -11.494415 2.8953109 -1.4476554 -15675.983 462016.62
100 331.58255 -6.8036753 -6.8465344 4.662727 -11.509261 2.897273 -1.4486365 -21675.515 462016.62
Loop time of 131.437 on 4 procs for 100 steps with 32400 atoms
Performance: 0.013 ns/day, 1825.518 hours/ns, 0.761 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 28.847 | 28.874 | 28.913 | 0.5 | 21.97
Neigh | 0.10981 | 0.11084 | 0.11145 | 0.2 | 0.08
Comm | 0.28924 | 0.32866 | 0.3556 | 4.5 | 0.25
Output | 0.0010426 | 0.0011656 | 0.0015302 | 0.6 | 0.00
Modify | 102.12 | 102.12 | 102.12 | 0.0 | 77.69
Other | | 0.003455 | | | 0.00
Nlocal: 8100 ave 8110 max 8090 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 20725.2 ave 20772 max 20694 min
Histogram: 1 1 0 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: 4.63294e+06 ave 4.63866e+06 max 4.62736e+06 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 18531740
Ave neighs/atom = 571.967
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:02:21

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
units lj
atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0018332 secs
mass 1 1.0
velocity all create 1.0 87287 loop geom
pair_style dpd 1.0 1.0 928948
pair_coeff 1 1 25.0 4.5
neighbor 0.5 bin
neigh_modify delay 0 every 1
fix 1 all nve
timestep 0.04
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75, bins = 30 30 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd, 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) = 11.32 | 11.32 | 11.32 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.880274
100 1.0246036 4.5727353 0 6.1095927 23.859969
Loop time of 3.09286 on 1 procs for 100 steps with 32000 atoms
Performance: 111741.340 tau/day, 32.333 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 | 1.5326 | 1.5326 | 1.5326 | 0.0 | 49.55
Neigh | 1.4771 | 1.4771 | 1.4771 | 0.0 | 47.76
Comm | 0.044292 | 0.044292 | 0.044292 | 0.0 | 1.43
Output | 0.00011039 | 0.00011039 | 0.00011039 | 0.0 | 0.00
Modify | 0.022322 | 0.022322 | 0.022322 | 0.0 | 0.72
Other | | 0.01648 | | | 0.53
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14981 ave 14981 max 14981 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 660587 ave 660587 max 660587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660587
Ave neighs/atom = 20.6433
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:03

75
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# DPD benchmark
units lj
atom_style atomic
comm_modify mode single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000589132 secs
mass 1 1.0
velocity all create 1.0 87287 loop geom
pair_style dpd 1.0 1.0 928948
pair_coeff 1 1 25.0 4.5
neighbor 0.5 bin
neigh_modify delay 0 every 1
fix 1 all nve
timestep 0.04
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.5
ghost atom cutoff = 1.5
binsize = 0.75, bins = 30 30 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd, 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) = 3.874 | 3.874 | 3.874 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.911346
100 1.0219182 4.5817845 0 6.1146139 23.803115
Loop time of 0.83904 on 4 procs for 100 steps with 32000 atoms
Performance: 411899.440 tau/day, 119.184 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.39605 | 0.40101 | 0.40702 | 0.6 | 47.79
Neigh | 0.38186 | 0.38494 | 0.38738 | 0.4 | 45.88
Comm | 0.032073 | 0.039688 | 0.045953 | 2.9 | 4.73
Output | 4.4823e-05 | 5.4002e-05 | 7.844e-05 | 0.0 | 0.01
Modify | 0.0056572 | 0.0056887 | 0.0057547 | 0.1 | 0.68
Other | | 0.007655 | | | 0.91
Nlocal: 8000 ave 8014 max 7986 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6744 ave 6764 max 6726 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 165107 ave 166433 max 163419 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 660428
Ave neighs/atom = 20.6384
Neighbor list builds = 50
Dangerous builds = 0
Total wall time: 0:00:00

74
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00185037 secs
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.95
ghost atom cutoff = 5.95
binsize = 2.975, bins = 25 25 25
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam, 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) = 16.83 | 16.83 | 16.83 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 3.92295 on 1 procs for 100 steps with 32000 atoms
Performance: 11.012 ns/day, 2.179 hours/ns, 25.491 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3913 | 3.3913 | 3.3913 | 0.0 | 86.45
Neigh | 0.48107 | 0.48107 | 0.48107 | 0.0 | 12.26
Comm | 0.01729 | 0.01729 | 0.01729 | 0.0 | 0.44
Output | 0.00011253 | 0.00011253 | 0.00011253 | 0.0 | 0.00
Modify | 0.024349 | 0.024349 | 0.024349 | 0.0 | 0.62
Other | | 0.008847 | | | 0.23
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:03

74
bench/POTENTIALS/log.16Mar18.eam.4 Normal file
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@ -0,0 +1,74 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Cu in EAM
units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000595331 secs
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.95
ghost atom cutoff = 5.95
binsize = 2.975, bins = 25 25 25
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam, 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) = 7.381 | 7.381 | 7.381 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 1.04497 on 4 procs for 100 steps with 32000 atoms
Performance: 41.341 ns/day, 0.581 hours/ns, 95.697 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88513 | 0.88724 | 0.89191 | 0.3 | 84.91
Neigh | 0.12418 | 0.12458 | 0.12511 | 0.1 | 11.92
Comm | 0.015654 | 0.020543 | 0.022984 | 2.0 | 1.97
Output | 4.8637e-05 | 5.8711e-05 | 8.6546e-05 | 0.0 | 0.01
Modify | 0.0085199 | 0.0085896 | 0.0086446 | 0.1 | 0.82
Other | | 0.003959 | | | 0.38
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9130.25 ave 9138 max 9122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 301946 ave 302392 max 301360 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0
Total wall time: 0:00:01

47
bench/POTENTIALS/log.26Jun12.eff.1 → bench/POTENTIALS/log.16Mar18.eff.1
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@ -1,4 +1,6 @@
LAMMPS (29 Jun 2012)
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
units electron
@ -7,15 +9,17 @@ atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style eff/cut 12
pair_coeff * *
pair_coeff * *
neigh_modify one 6000 page 60000
communicate single vel yes
comm_modify vel yes
compute effTemp all temp/eff
@ -26,7 +30,19 @@ thermo_modify temp effTemp
fix 1 all nve/eff
run 100
Memory usage per processor = 367.578 Mbytes
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 6000, page size: 60000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 370.9 | 370.9 | 370.9 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -49,13 +65,20 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 691.429 on 1 procs for 100 steps with 32000 atoms
Loop time of 323.031 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 690.897 (99.923)
Neigh time (%) = 0 (0)
Comm time (%) = 0.380233 (0.0549924)
Outpt time (%) = 0.00317478 (0.000459162)
Other time (%) = 0.148708 (0.0215073)
Performance: 26.747 fs/day, 0.897 hours/fs, 0.310 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 | 322.78 | 322.78 | 322.78 | 0.0 | 99.92
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.1876 | 0.1876 | 0.1876 | 0.0 | 0.06
Output | 0.0027025 | 0.0027025 | 0.0027025 | 0.0 | 0.00
Modify | 0.032475 | 0.032475 | 0.032475 | 0.0 | 0.01
Other | | 0.02538 | | | 0.01
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -68,3 +91,7 @@ Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:05:27

47
bench/POTENTIALS/log.26Jun12.eff.4 → bench/POTENTIALS/log.16Mar18.eff.4
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@ -1,4 +1,6 @@
LAMMPS (29 Jun 2012)
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# eFF benchmark of H plasma
units electron
@ -7,15 +9,17 @@ atom_style electron
read_data data.eff
orthogonal box = (0 0 0) to (41.9118 41.9118 41.9118)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style eff/cut 12
pair_coeff * *
pair_coeff * *
neigh_modify one 6000 page 60000
communicate single vel yes
comm_modify vel yes
compute effTemp all temp/eff
@ -26,7 +30,19 @@ thermo_modify temp effTemp
fix 1 all nve/eff
run 100
Memory usage per processor = 98.5462 Mbytes
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 6000, page size: 60000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 101.4 | 104.8 | 108.3 Mbytes
Step TotEng PotEng KinEng Temp Press
0 4046.5854 796.63785 3249.9475 42763.133 4.4764483e+12
5 4046.5854 796.95799 3249.6274 42758.92 4.4728546e+12
@ -49,13 +65,20 @@ Step TotEng PotEng KinEng Temp Press
90 4046.5857 864.14162 3182.4441 41874.916 4.3868277e+12
95 4046.5857 871.30234 3175.2834 41780.695 4.3805068e+12
100 4046.5858 878.76023 3167.8255 41682.563 4.3740731e+12
Loop time of 186.181 on 4 procs for 100 steps with 32000 atoms
Loop time of 90.1636 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 176.315 (94.701)
Neigh time (%) = 0 (0)
Comm time (%) = 9.78075 (5.25336)
Outpt time (%) = 0.00258493 (0.0013884)
Other time (%) = 0.082338 (0.0442248)
Performance: 95.826 fs/day, 0.250 hours/fs, 1.109 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 83.772 | 86.516 | 89.593 | 29.5 | 95.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.51677 | 3.5934 | 6.3368 | 144.6 | 3.99
Output | 0.0012872 | 0.0018208 | 0.0024981 | 1.0 | 0.00
Modify | 0.017231 | 0.018405 | 0.01983 | 0.8 | 0.02
Other | | 0.03431 | | | 0.04
Nlocal: 8000 ave 8112 max 7875 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -68,3 +91,7 @@ Total # of neighbors = 81057159
Ave neighs/atom = 2533.04
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:31

77
bench/POTENTIALS/log.16Mar18.eim.1 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
# crystal can be annealed to the correct NaCl type of NaCl polycrystals
units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0 every 1
timestep 0.0005
thermo_style custom step pe pxx pyy pzz temp
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
# anneal in much longer run
#fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.906
ghost atom cutoff = 7.906
binsize = 3.953, bins = 19 37 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eim, 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) = 17.72 | 17.72 | 17.72 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 11.4536 on 1 procs for 100 steps with 32000 atoms
Performance: 0.377 ns/day, 63.631 hours/ns, 8.731 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 | 9.8277 | 9.8277 | 9.8277 | 0.0 | 85.80
Neigh | 1.484 | 1.484 | 1.484 | 0.0 | 12.96
Comm | 0.028584 | 0.028584 | 0.028584 | 0.0 | 0.25
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.00
Modify | 0.09791 | 0.09791 | 0.09791 | 0.0 | 0.85
Other | | 0.0152 | | | 0.13
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21505 ave 21505 max 21505 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:11

77
bench/POTENTIALS/log.16Mar18.eim.4 Normal file
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@ -0,0 +1,77 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
# crystal can be annealed to the correct NaCl type of NaCl polycrystals
units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
1 by 4 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0 every 1
timestep 0.0005
thermo_style custom step pe pxx pyy pzz temp
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
# anneal in much longer run
#fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.906
ghost atom cutoff = 7.906
binsize = 3.953, bins = 19 37 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eim, 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) = 7.285 | 7.285 | 7.285 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 3.12061 on 4 procs for 100 steps with 32000 atoms
Performance: 1.384 ns/day, 17.337 hours/ns, 32.045 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6504 | 2.6583 | 2.6685 | 0.5 | 85.18
Neigh | 0.36996 | 0.37847 | 0.39396 | 1.5 | 12.13
Comm | 0.037041 | 0.040586 | 0.04504 | 1.4 | 1.30
Output | 7.081e-05 | 8.75e-05 | 0.00012994 | 0.0 | 0.00
Modify | 0.029286 | 0.035978 | 0.047942 | 3.9 | 1.15
Other | | 0.007206 | | | 0.23
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 9460.25 ave 9469 max 9449 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 395975 ave 397239 max 394616 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Neighbor list builds = 37
Dangerous builds = 12
Total wall time: 0:00:03

84
bench/POTENTIALS/log.16Mar18.fene.1 Normal file
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@ -0,0 +1,84 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify delay 5 every 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76, bins = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.18 | 13.18 | 13.18 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 0.66285 on 1 procs for 100 steps with 32000 atoms
Performance: 156415.445 tau/day, 150.864 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 | 0.13075 | 0.13075 | 0.13075 | 0.0 | 19.73
Bond | 0.046363 | 0.046363 | 0.046363 | 0.0 | 6.99
Neigh | 0.3172 | 0.3172 | 0.3172 | 0.0 | 47.85
Comm | 0.016553 | 0.016553 | 0.016553 | 0.0 | 2.50
Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.02
Modify | 0.14515 | 0.14515 | 0.14515 | 0.0 | 21.90
Other | | 0.006728 | | | 1.02
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9493 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155873 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

84
bench/POTENTIALS/log.16Mar18.fene.4 Normal file
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@ -0,0 +1,84 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.fene
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify delay 5 every 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.52
ghost atom cutoff = 1.52
binsize = 0.76, bins = 45 45 45
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.606 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9736748 0.44378481 20.502389 22.40664 4.7809557
Loop time of 0.184782 on 4 procs for 100 steps with 32000 atoms
Performance: 561093.346 tau/day, 541.178 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033747 | 0.034391 | 0.035036 | 0.3 | 18.61
Bond | 0.012475 | 0.012579 | 0.012812 | 0.1 | 6.81
Neigh | 0.083916 | 0.083953 | 0.084022 | 0.0 | 45.43
Comm | 0.012409 | 0.01363 | 0.014534 | 0.7 | 7.38
Output | 4.1246e-05 | 5.9545e-05 | 0.00010443 | 0.0 | 0.03
Modify | 0.036675 | 0.037876 | 0.038357 | 0.4 | 20.50
Other | | 0.002294 | | | 1.24
Nlocal: 8000 ave 8023 max 7978 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 4158.75 ave 4175 max 4145 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 38940 ave 39184 max 38640 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 155760
Ave neighs/atom = 4.8675
Ave special neighs/atom = 1.98
Neighbor list builds = 20
Dangerous builds = 20
Total wall time: 0:00:00

43
bench/POTENTIALS/log.26Jun12.gb.1 → bench/POTENTIALS/log.16Mar18.gb.1
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@ -1,4 +1,6 @@
LAMMPS (30 Jun 2012)
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
# shape: 2 1.5 1
@ -18,7 +20,9 @@ atom_style ellipsoid
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
1 by 1 by 1 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
@ -47,7 +51,19 @@ thermo 20
fix 1 all npt/asphere temp 2.4 2.4 0.2 iso 8.0 8.0 0.2
run 100
Memory usage per processor = 26.9944 Mbytes
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, 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) = 28.91 | 28.91 | 28.91 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
@ -55,13 +71,20 @@ Step Temp E_pair E_mol TotEng Press Volume
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 72.0749 on 1 procs for 100 steps with 32768 atoms
Loop time of 43.7894 on 1 procs for 100 steps with 32768 atoms
Pair time (%) = 70.3565 (97.6157)
Neigh time (%) = 0.493162 (0.684236)
Comm time (%) = 0.132031 (0.183186)
Outpt time (%) = 0.000532866 (0.000739322)
Other time (%) = 1.09272 (1.5161)
Performance: 394.616 tau/day, 2.284 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 | 42.881 | 42.881 | 42.881 | 0.0 | 97.93
Neigh | 0.35071 | 0.35071 | 0.35071 | 0.0 | 0.80
Comm | 0.065153 | 0.065153 | 0.065153 | 0.0 | 0.15
Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.00
Modify | 0.47852 | 0.47852 | 0.47852 | 0.0 | 1.09
Other | | 0.01337 | | | 0.03
Nlocal: 32768 ave 32768 max 32768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -74,3 +97,7 @@ Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:44

43
bench/POTENTIALS/log.26Jun12.gb.4 → bench/POTENTIALS/log.16Mar18.gb.4
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@ -1,4 +1,6 @@
LAMMPS (30 Jun 2012)
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Gay-Berne benchmark
# biaxial ellipsoid mesogens in isotropic phase
# shape: 2 1.5 1
@ -18,7 +20,9 @@ atom_style ellipsoid
read_data data.gb
orthogonal box = (2.19575 2.19575 2.19575) to (50.8124 50.8124 50.8124)
1 by 2 by 2 MPI processor grid
reading atoms ...
32768 atoms
reading velocities ...
32768 velocities
32768 ellipsoids
@ -47,7 +51,19 @@ thermo 20
fix 1 all npt/asphere temp 2.4 2.4 0.2 iso 8.0 8.0 0.2
run 100
Memory usage per processor = 10.6989 Mbytes
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gayberne, 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) = 11.78 | 11.78 | 11.78 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.4 0.50438568 0 4.1042758 6.7818168 114909.09
20 2.7357818 0.26045557 0 4.364003 6.8299368 111715.16
@ -55,13 +71,20 @@ Step Temp E_pair E_mol TotEng Press Volume
60 2.9820039 0.19733812 0 4.6702075 7.1507065 108393.77
80 3.0148529 0.15114819 0 4.6732895 7.1699502 107672.24
100 3.0206703 0.10567623 0 4.6365433 7.154345 107184.83
Loop time of 19.8423 on 4 procs for 100 steps with 32768 atoms
Loop time of 11.3124 on 4 procs for 100 steps with 32768 atoms
Pair time (%) = 18.0297 (90.865)
Neigh time (%) = 0.126858 (0.639331)
Comm time (%) = 1.38594 (6.98475)
Outpt time (%) = 0.000399113 (0.00201142)
Other time (%) = 0.299395 (1.50887)
Performance: 1527.522 tau/day, 8.840 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.778 | 10.849 | 10.934 | 2.0 | 95.90
Neigh | 0.088265 | 0.08871 | 0.089238 | 0.1 | 0.78
Comm | 0.1384 | 0.22518 | 0.29662 | 14.1 | 1.99
Output | 0.00020599 | 0.00024837 | 0.00036836 | 0.0 | 0.00
Modify | 0.13828 | 0.13899 | 0.13984 | 0.2 | 1.23
Other | | 0.01053 | | | 0.09
Nlocal: 8192 ave 8215 max 8166 min
Histogram: 1 1 0 0 0 0 0 0 0 2
@ -74,3 +97,7 @@ Total # of neighbors = 2304332
Ave neighs/atom = 70.3226
Neighbor list builds = 6
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11

85
bench/POTENTIALS/log.16Mar18.granular.1 Normal file
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@ -0,0 +1,85 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify delay 5 every 1
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55, bins = 73 37 68
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.36 | 23.36 | 23.36 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.292816 on 1 procs for 100 steps with 32000 atoms
Performance: 2950.657 tau/day, 341.511 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17449 | 0.17449 | 0.17449 | 0.0 | 59.59
Neigh | 0.031927 | 0.031927 | 0.031927 | 0.0 | 10.90
Comm | 0.010195 | 0.010195 | 0.010195 | 0.0 | 3.48
Output | 0.00019121 | 0.00019121 | 0.00019121 | 0.0 | 0.07
Modify | 0.064463 | 0.064463 | 0.064463 | 0.0 | 22.01
Other | | 0.01155 | | | 3.94
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115133
Ave neighs/atom = 3.59791
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

85
bench/POTENTIALS/log.16Mar18.granular.4 Normal file
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@ -0,0 +1,85 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# granular chute flow
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify delay 5 every 1
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55, bins = 73 37 68
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair gran/hooke/history, perpetual
attributes: half, newton off, size, history
pair build: half/size/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.41 | 10.42 | 10.42 Mbytes
Step Atoms KinEng c_1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.0903978 on 4 procs for 100 steps with 32000 atoms
Performance: 9557.751 tau/day, 1106.221 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046331 | 0.049088 | 0.052195 | 1.2 | 54.30
Neigh | 0.0090401 | 0.0091327 | 0.0091863 | 0.1 | 10.10
Comm | 0.0073855 | 0.0080023 | 0.0086699 | 0.6 | 8.85
Output | 7.1049e-05 | 0.00010067 | 0.00012088 | 0.0 | 0.11
Modify | 0.017226 | 0.017449 | 0.01803 | 0.3 | 19.30
Other | | 0.006625 | | | 7.33
Nlocal: 8000 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2439 ave 2450 max 2428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 29500.5 ave 30488 max 28513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 118002
Ave neighs/atom = 3.68756
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00

73
bench/POTENTIALS/log.16Mar18.lj.1 Normal file
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@ -0,0 +1,73 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00183916 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 5 every 1
fix 1 all nve
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 15.82 | 15.82 | 15.82 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 1.721 on 1 procs for 100 steps with 32000 atoms
Performance: 25101.720 tau/day, 58.106 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 | 1.2551 | 1.2551 | 1.2551 | 0.0 | 72.93
Neigh | 0.41825 | 0.41825 | 0.41825 | 0.0 | 24.30
Comm | 0.015347 | 0.015347 | 0.015347 | 0.0 | 0.89
Output | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.01
Modify | 0.023436 | 0.023436 | 0.023436 | 0.0 | 1.36
Other | | 0.008766 | | | 0.51
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19669 ave 19669 max 19669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:01

73
bench/POTENTIALS/log.16Mar18.lj.4 Normal file
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@ -0,0 +1,73 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587225 secs
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 5 every 1
fix 1 all nve
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 24 24 24
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, 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) = 6.88 | 6.88 | 6.88 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 0.469936 on 4 procs for 100 steps with 32000 atoms
Performance: 91927.316 tau/day, 212.795 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32713 | 0.32917 | 0.33317 | 0.4 | 70.05
Neigh | 0.10836 | 0.10931 | 0.11007 | 0.2 | 23.26
Comm | 0.015526 | 0.020355 | 0.022399 | 2.0 | 4.33
Output | 4.2439e-05 | 5.8353e-05 | 0.00010061 | 0.0 | 0.01
Modify | 0.0071156 | 0.0072448 | 0.007309 | 0.1 | 1.54
Other | | 0.003793 | | | 0.81
Nlocal: 8000 ave 8041 max 7958 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 9011 ave 9065 max 8961 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300794 ave 304843 max 297317 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:00

84
bench/POTENTIALS/log.16Mar18.meam.1 Normal file
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@ -0,0 +1,84 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00186539 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, 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) = 55.91 | 55.91 | 55.91 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 30.6278 on 1 procs for 100 steps with 32000 atoms
Performance: 1.410 ns/day, 17.015 hours/ns, 3.265 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 | 30.088 | 30.088 | 30.088 | 0.0 | 98.24
Neigh | 0.48914 | 0.48914 | 0.48914 | 0.0 | 1.60
Comm | 0.015916 | 0.015916 | 0.015916 | 0.0 | 0.05
Output | 0.00022554 | 0.00022554 | 0.00022554 | 0.0 | 0.00
Modify | 0.025481 | 0.025481 | 0.025481 | 0.0 | 0.08
Other | | 0.009055 | | | 0.03
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:30

84
bench/POTENTIALS/log.16Mar18.meam.4 Normal file
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@ -0,0 +1,84 @@
LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000587463 secs
pair_style meam
WARNING: The pair_style meam command is unsupported. Please use pair_style meam/c instead (../pair_meam.cpp:51)
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam, 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) = 17.41 | 17.41 | 17.41 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 8.21941 on 4 procs for 100 steps with 32000 atoms
Performance: 5.256 ns/day, 4.566 hours/ns, 12.166 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.0277 | 8.0384 | 8.0504 | 0.3 | 97.80
Neigh | 0.12555 | 0.12645 | 0.12713 | 0.2 | 1.54
Comm | 0.024279 | 0.036776 | 0.048389 | 4.5 | 0.45
Output | 9.4414e-05 | 0.00011903 | 0.00018597 | 0.0 | 0.00
Modify | 0.01252 | 0.012608 | 0.012795 | 0.1 | 0.15
Other | | 0.005028 | | | 0.06
Nlocal: 8000 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:08

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00184226 secs
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/c, 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) = 55.91 | 55.91 | 55.91 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 22.9343 on 1 procs for 100 steps with 32000 atoms
Performance: 1.884 ns/day, 12.741 hours/ns, 4.360 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 | 22.397 | 22.397 | 22.397 | 0.0 | 97.66
Neigh | 0.48781 | 0.48781 | 0.48781 | 0.0 | 2.13
Comm | 0.013967 | 0.013967 | 0.013967 | 0.0 | 0.06
Output | 0.00022793 | 0.00022793 | 0.00022793 | 0.0 | 0.00
Modify | 0.025412 | 0.025412 | 0.025412 | 0.0 | 0.11
Other | | 0.009448 | | | 0.04
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:23

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00058651 secs
pair_style meam/c
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 29 29 29
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/c, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/c, 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) = 17.41 | 17.41 | 17.41 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.431
100 895.50973 -139454.3 0 -135750.3 31804.185
Loop time of 6.45947 on 4 procs for 100 steps with 32000 atoms
Performance: 6.688 ns/day, 3.589 hours/ns, 15.481 timesteps/s
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.22 | 6.2385 | 6.265 | 0.7 | 96.58
Neigh | 0.12657 | 0.12691 | 0.12721 | 0.1 | 1.96
Comm | 0.052339 | 0.07915 | 0.097897 | 5.9 | 1.23
Output | 9.7752e-05 | 0.0001151 | 0.00016594 | 0.0 | 0.00
Modify | 0.010194 | 0.010291 | 0.010442 | 0.1 | 0.16
Other | | 0.004529 | | | 0.07
Nlocal: 8000 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
# Mesh spacing
variable h equal 5.00e-4
# Peridynamic horizon
variable delta equal 3.0*${h}
variable delta equal 3.0*0.0005
# Height of plate (meters)
variable height equal 31.5*${h}
variable height equal 31.5*0.0005
# Width of plate (meters)
variable width equal 39.5*${h}
variable width equal 39.5*0.0005
# Thickness of plate (meters)
variable depth equal 24.5*${h}
variable depth equal 24.5*0.0005
# Height of notch
variable crackheight equal 10*${h}
variable crackheight equal 10*0.0005
# Density of plate
variable mydensity equal 2440.0
# Elastic modulus of material
variable myE equal 72.0e9
# Strain energy release rate at branching
variable myG equal 135.0
# constant, but define it as a variable here
variable pi equal 3.14159265358979323846
units si
boundary s s s
atom_style peri
atom_modify map array
variable myskin equal 2.0*${h}
variable myskin equal 2.0*0.0005
neighbor ${myskin} bin
neighbor 0.001 bin
lattice sc $h
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
variable myxmin equal 0.0
variable myxmax equal ${width}
variable myxmax equal 0.01975
variable myymin equal 0.0
variable myymax equal ${height}
variable myymax equal 0.01575
variable myzmin equal 0.0
variable myzmax equal ${depth}
variable myzmax equal 0.01225
region plate block ${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
1 by 1 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.00362897 secs
pair_style peri/pmb
variable myk equal (2.0/3.0)*${myE}
variable myk equal (2.0/3.0)*72000000000
variable myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.14159265358979*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.14159265358979*(0.0015^4)))
variable mydelta equal (${delta}+(${delta}/100.0))
variable mydelta equal (0.0015+(${delta}/100.0))
variable mydelta equal (0.0015+(0.0015/100.0))
variable mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015))
variable tmpvar1 equal ${myymax}-${crackheight}
variable tmpvar1 equal 0.01575-${crackheight}
variable tmpvar1 equal 0.01575-0.005
variable tmpvar2 equal 0.5*${width}
variable tmpvar2 equal 0.5*0.01975
region topleft block 0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 0 ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 0 0.01225 units box
region topright block ${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
5000 settings made for type
set region topright type 3
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 2 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 3 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 2 3 ${myc} 0.0 ${mys0} 0.0
pair_coeff 2 3 5.43248872420337e+22 0.0 ${mys0} 0.0
pair_coeff 2 3 5.43248872420337e+22 0.0 0.00102062072615966 0.0
pair_coeff 1 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 1 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix F1 all nve
compute C1 all damage/atom
velocity all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 0.01975 units box
variable mystep equal 0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*1.25e-10))
timestep ${mystep}
timestep 2.11931492396226e-08
thermo 20
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.002515
ghost atom cutoff = 0.002515
binsize = 0.0012575, bins = 16 13 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/pmb, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Per MPI rank memory allocation (min/avg/max) = 133.6 | 133.6 | 133.6 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
40 1.3041477e+27 4.6848143e+08 0 1.332729e+09 1.5875756e+14 3.6292128e-06
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 11.0398 on 1 procs for 100 steps with 32000 atoms
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 | 11.005 | 11.005 | 11.005 | 0.0 | 99.68
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.6042e-05 | 6.6042e-05 | 6.6042e-05 | 0.0 | 0.00
Output | 0.00057292 | 0.00057292 | 0.00057292 | 0.0 | 0.01
Modify | 0.0256 | 0.0256 | 0.0256 | 0.0 | 0.23
Other | | 0.008592 | | | 0.08
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Crack growth in notched 3D Peridynamic block
# Mesh spacing
variable h equal 5.00e-4
# Peridynamic horizon
variable delta equal 3.0*${h}
variable delta equal 3.0*0.0005
# Height of plate (meters)
variable height equal 31.5*${h}
variable height equal 31.5*0.0005
# Width of plate (meters)
variable width equal 39.5*${h}
variable width equal 39.5*0.0005
# Thickness of plate (meters)
variable depth equal 24.5*${h}
variable depth equal 24.5*0.0005
# Height of notch
variable crackheight equal 10*${h}
variable crackheight equal 10*0.0005
# Density of plate
variable mydensity equal 2440.0
# Elastic modulus of material
variable myE equal 72.0e9
# Strain energy release rate at branching
variable myG equal 135.0
# constant, but define it as a variable here
variable pi equal 3.14159265358979323846
units si
boundary s s s
atom_style peri
atom_modify map array
variable myskin equal 2.0*${h}
variable myskin equal 2.0*0.0005
neighbor ${myskin} bin
neighbor 0.001 bin
lattice sc $h
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
variable myxmin equal 0.0
variable myxmax equal ${width}
variable myxmax equal 0.01975
variable myymin equal 0.0
variable myymax equal ${height}
variable myymax equal 0.01575
variable myzmin equal 0.0
variable myzmax equal ${depth}
variable myzmax equal 0.01225
region plate block ${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 0.01575 ${myzmin} ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 ${myzmax} units box
region plate block 0 0.01975 0 0.01575 0 0.01225 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
2 by 2 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
Time spent = 0.0011344 secs
pair_style peri/pmb
variable myk equal (2.0/3.0)*${myE}
variable myk equal (2.0/3.0)*72000000000
variable myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.14159265358979*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.14159265358979*(0.0015^4)))
variable mydelta equal (${delta}+(${delta}/100.0))
variable mydelta equal (0.0015+(${delta}/100.0))
variable mydelta equal (0.0015+(0.0015/100.0))
variable mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015))
variable tmpvar1 equal ${myymax}-${crackheight}
variable tmpvar1 equal 0.01575-${crackheight}
variable tmpvar1 equal 0.01575-0.005
variable tmpvar2 equal 0.5*${width}
variable tmpvar2 equal 0.5*0.01975
region topleft block 0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 ${myzmin} ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 0 ${myzmax} units box
region topleft block 0.0 0.009875 0.01075 0.01575 0 0.01225 units box
region topright block ${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 ${myzmin} ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 ${myzmax} units box
region topright block 0.009875 0.01975 0.01075 0.01575 0 0.01225 units box
set region topleft type 2
5000 settings made for type
set region topright type 3
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 1 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 2 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 2 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 3 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 3 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 2 3 ${myc} 0.0 ${mys0} 0.0
pair_coeff 2 3 5.43248872420337e+22 0.0 ${mys0} 0.0
pair_coeff 2 3 5.43248872420337e+22 0.0 0.00102062072615966 0.0
pair_coeff 1 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 2 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
pair_coeff 1 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 ${mys0} 0.0
pair_coeff 1 3 5.43248872420337e+22 0.001515 0.00102062072615966 0.0
set group all density ${mydensity}
set group all density 2440
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.0005)^3
set group all volume ${myvolume}
set group all volume 1.25e-10
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix F1 all nve
compute C1 all damage/atom
velocity all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 0.01975 units box
variable mystep equal 0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.43248872420337e+22/0.0005)*1.25e-10))
timestep ${mystep}
timestep 2.11931492396226e-08
thermo 20
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.002515
ghost atom cutoff = 0.002515
binsize = 0.0012575, bins = 16 13 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair peri/pmb, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix PERI_NEIGH, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Per MPI rank memory allocation (min/avg/max) = 47.63 | 48.11 | 48.78 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
40 1.3041477e+27 4.6848143e+08 0 1.332729e+09 1.5875756e+14 3.6292128e-06
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 2.8928 on 4 procs for 100 steps with 32000 atoms
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 | 2.7472 | 2.7951 | 2.8585 | 2.9 | 96.62
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019592 | 0.083156 | 0.13278 | 17.0 | 2.87
Output | 0.00022125 | 0.00034326 | 0.00058961 | 0.0 | 0.01
Modify | 0.0083542 | 0.0089623 | 0.0095983 | 0.5 | 0.31
Other | | 0.005276 | | | 0.18
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5125 ave 5125 max 5125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
units real
neighbor 2.0 bin
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 1 by 1 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 41070 25600
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 10 13 13
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 140 | 140 | 140 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 23.7567 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 23.7568 on 1 procs for 100 steps with 32000 atoms
Performance: 0.727 ns/day, 32.995 hours/ns, 4.209 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 | 17.905 | 17.905 | 17.905 | 0.0 | 75.37
Bond | 0.73417 | 0.73417 | 0.73417 | 0.0 | 3.09
Kspace | 1.4676 | 1.4676 | 1.4676 | 0.0 | 6.18
Neigh | 2.9907 | 2.9907 | 2.9907 | 0.0 | 12.59
Comm | 0.037427 | 0.037427 | 0.037427 | 0.0 | 0.16
Output | 0.00011754 | 0.00011754 | 0.00011754 | 0.0 | 0.00
Modify | 0.60985 | 0.60985 | 0.60985 | 0.0 | 2.57
Other | | 0.01201 | | | 0.05
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:24

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Rhodopsin model
units real
neighbor 2.0 bin
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 MPI processor grid
reading atoms ...
32000 atoms
reading velocities ...
32000 velocities
scanning bonds ...
4 = max bonds/atom
scanning angles ...
8 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
27723 bonds
reading angles ...
40467 angles
reading dihedrals ...
56829 dihedrals
reading impropers ...
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 10 13 13
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 49.07 | 49.17 | 49.46 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
Volume = 307995.0335
---------------- Step 100 ----- CPU = 6.3997 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6483 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 6.39977 on 4 procs for 100 steps with 32000 atoms
Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4434 | 4.5321 | 4.6846 | 4.3 | 70.82
Bond | 0.17894 | 0.18568 | 0.19951 | 1.9 | 2.90
Kspace | 0.4651 | 0.61064 | 0.69123 | 11.1 | 9.54
Neigh | 0.7739 | 0.77394 | 0.774 | 0.0 | 12.09
Comm | 0.057676 | 0.069183 | 0.07901 | 3.0 | 1.08
Output | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 | 0.0 | 0.00
Modify | 0.21444 | 0.21866 | 0.22524 | 0.9 | 3.42
Other | | 0.009451 | | | 0.15
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
1 by 1 by 1 MPI processor grid
16240 atoms
Time spent = 0.000834942 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 115.8 | 115.8 | 115.8 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.2 22296.712 -29858.677 5721.0921 -1601622.5
10 298.98728 14472.591 -1616093.9 21955.847 -24067.096 7389.148 -1601621.3
20 294.76158 14268.045 -1615890.1 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.377 5833.02 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.9845 19406.33 14947.939 -1601624.6
50 274.84112 13303.787 -1614931.9 -2009.6832 26964.336 13346.855 -1601628.2
60 266.20153 12885.585 -1614519.7 -8441.1641 28485.532 10195.429 -1601634.1
70 259.17085 12545.262 -1614184.2 -11426.993 24941.516 6572.2953 -1601638.9
80 259.73004 12572.33 -1614216.7 -10867.598 16928.461 3033.9021 -1601644.3
90 269.2352 13032.431 -1614679 -7962.3129 4931.5317 -280.22164 -1601646.6
100 280.67181 13586.024 -1615234.3 -3606.1519 -8769.8482 -2527.5887 -1601648.3
Loop time of 358.104 on 1 procs for 100 steps with 16240 atoms
Performance: 0.002 ns/day, 9947.338 hours/ns, 0.279 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 | 358.07 | 358.07 | 358.07 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01623 | 0.01623 | 0.01623 | 0.0 | 0.00
Output | 0.0013328 | 0.0013328 | 0.0013328 | 0.0 | 0.00
Modify | 0.012679 | 0.012679 | 0.012679 | 0.0 | 0.00
Other | | 0.006895 | | | 0.00
Nlocal: 16240 ave 16240 max 16240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 32428 ave 32428 max 32428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6699752
Ave neighs/atom = 412.546
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:02

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
2 by 2 by 1 MPI processor grid
16240 atoms
Time spent = 0.000491619 secs
velocity all create 300.0 9999
pair_style reax
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair reax, perpetual
attributes: half, newton off
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Per MPI rank memory allocation (min/avg/max) = 35.58 | 35.68 | 35.77 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.1 22296.712 -29858.677 5721.0922 -1601622.5
10 298.98728 14472.591 -1616093.8 21955.847 -24067.094 7389.149 -1601621.3
20 294.76158 14268.044 -1615890 19179.258 -10513.494 10789.925 -1601622
30 288.56967 13968.323 -1615591.2 13854.38 5833.0219 13949.731 -1601622.9
40 282.06725 13653.571 -1615278.2 6259.981 19406.327 14947.938 -1601624.7
50 274.84112 13303.787 -1614931.9 -2009.6844 26964.334 13346.855 -1601628.1
60 266.20153 12885.585 -1614519.8 -8441.1628 28485.533 10195.428 -1601634.2
70 259.17085 12545.262 -1614184.2 -11426.992 24941.517 6572.295 -1601639
80 259.73004 12572.33 -1614216.8 -10867.596 16928.464 3033.9024 -1601644.5
90 269.2352 13032.431 -1614679 -7962.3097 4931.5336 -280.21988 -1601646.5
100 280.67181 13586.024 -1615234.3 -3606.1482 -8769.8463 -2527.5874 -1601648.3
Loop time of 97.054 on 4 procs for 100 steps with 16240 atoms
Performance: 0.009 ns/day, 2695.944 hours/ns, 1.030 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 | 94.83 | 95.764 | 96.883 | 9.2 | 98.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.16123 | 1.2801 | 2.2132 | 79.9 | 1.32
Output | 0.00056076 | 0.00066662 | 0.00095987 | 0.0 | 0.00
Modify | 0.0048354 | 0.0049006 | 0.0049515 | 0.1 | 0.01
Other | | 0.004639 | | | 0.00
Nlocal: 4060 ave 4080 max 4040 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 14972 ave 14992 max 14952 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.8135e+06 ave 1.82186e+06 max 1.80514e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 7253988
Ave neighs/atom = 446.674
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:38

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 1 by 1 MPI processor grid
32480 atoms
Time spent = 0.00162625 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 1727 | 1727 | 1727 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5637 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.778 -23987.41 7610.2967 -3203091.6
20 295.5855 28616.735 -3231710.1 18178.568 -10871.882 10603.247 -3203093.3
30 289.48845 28026.457 -3231123.2 12146.362 4985.5572 13364.455 -3203096.8
40 282.66404 27365.76 -3230467.5 4284.2794 18132.771 14133.719 -3203101.7
50 274.97005 26620.876 -3229730.4 -3719.11 25519.692 12551.708 -3203109.5
60 266.11301 25763.393 -3228883.8 -9271.4049 27307.216 9753.2509 -3203120.4
70 259.3263 25106.346 -3228237.2 -11150.726 24238.382 6578.5306 -3203130.8
80 260.33956 25204.444 -3228344.2 -9576.6006 16737.65 3454.5747 -3203139.7
90 269.90199 26130.219 -3229275.5 -5906.376 5246.1572 467.31789 -3203145.3
100 280.76717 27182.117 -3230330.6 -1363.8281 -8133.2509 -1689.7711 -3203148.5
Loop time of 437.886 on 1 procs for 100 steps with 32480 atoms
Performance: 0.002 ns/day, 12163.512 hours/ns, 0.228 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 | 350.29 | 350.29 | 350.29 | 0.0 | 80.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.026264 | 0.026264 | 0.026264 | 0.0 | 0.01
Output | 0.0024614 | 0.0024614 | 0.0024614 | 0.0 | 0.00
Modify | 87.55 | 87.55 | 87.55 | 0.0 | 19.99
Other | | 0.01296 | | | 0.00
Nlocal: 32480 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.414
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:07:24

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
reading atoms ...
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 2 by 2 MPI processor grid
32480 atoms
Time spent = 0.000803709 secs
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax C H O N
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 12 13 12
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 647 | 647 | 647 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22804.879 -29365.593 6302.5638 -3203096.6
10 299.37479 28983.59 -3232075.2 21746.773 -23987.409 7610.2911 -3203091.6
20 295.58552 28616.737 -3231710.1 18178.576 -10871.874 10603.421 -3203093.3
30 289.48843 28026.455 -3231123.3 12146.158 4985.3436 13364.461 -3203096.8
40 282.66409 27365.764 -3230467.5 4284.5077 18133.151 14133.949 -3203101.7
50 274.97008 26620.879 -3229730.3 -3718.536 25520.328 12552.195 -3203109.5
60 266.11301 25763.393 -3228883.7 -9271.0381 27307.591 9753.5339 -3203120.4
70 259.32631 25106.348 -3228237.1 -11150.314 24238.962 6578.8636 -3203130.8
80 260.33966 25204.453 -3228344.1 -9575.5709 16738.467 3455.2525 -3203139.7
90 269.90213 26130.231 -3229275.5 -5906.0456 5246.2122 467.43473 -3203145.2
100 280.76727 27182.127 -3230330.6 -1363.1733 -8132.8726 -1689.3275 -3203148.4
Loop time of 128.275 on 4 procs for 100 steps with 32480 atoms
Performance: 0.007 ns/day, 3563.196 hours/ns, 0.780 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 | 92.314 | 97.932 | 103.53 | 44.1 | 76.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.039458 | 5.6409 | 11.263 | 184.0 | 4.40
Output | 0.00086117 | 0.0010868 | 0.0016167 | 0.9 | 0.00
Modify | 24.687 | 24.688 | 24.69 | 0.0 | 19.25
Other | | 0.01323 | | | 0.01
Nlocal: 8120 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.909
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:10

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
reading atoms ...
60 atoms
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 = 0.00151849 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) 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) = 34.21 | 34.21 | 34.21 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 5.17257 on 1 procs for 100 steps with 32640 atoms
Performance: 0.835 ns/day, 28.737 hours/ns, 19.333 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 | 3.3427 | 3.3427 | 3.3427 | 0.0 | 64.62
Neigh | 1.7764 | 1.7764 | 1.7764 | 0.0 | 34.34
Comm | 0.017914 | 0.017914 | 0.017914 | 0.0 | 0.35
Output | 0.0011199 | 0.0011199 | 0.0011199 | 0.0 | 0.02
Modify | 0.024357 | 0.024357 | 0.024357 | 0.0 | 0.47
Other | | 0.01004 | | | 0.19
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26460 ave 26460 max 26460 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: 4.90213e+06 ave 4.90213e+06 max 4.90213e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
reading atoms ...
60 atoms
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 = 0.000838995 secs
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 22 21 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) 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) = 11.75 | 11.94 | 12.13 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 179.38052 -137930.92 0 -137174.12 15656.95
20 206.87725 -138046.63 0 -137173.83 -24042.005
30 150.80048 -137807.07 0 -137170.86 -16524.069
40 173.25027 -137902 0 -137171.07 -5716.7297
50 151.80552 -137812.01 0 -137171.55 3481.1096
60 199.08762 -138013.46 0 -137173.53 17882.906
70 217.8592 -138093.51 0 -137174.38 -12269.648
80 202.37612 -138029.05 0 -137175.24 -7622.1573
90 194.905 -137996.68 0 -137174.4 -32267.297
100 185.17966 -137954.16 0 -137172.9 -6902.1493
Loop time of 1.52214 on 4 procs for 100 steps with 32640 atoms
Performance: 2.838 ns/day, 8.456 hours/ns, 65.697 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 | 0.88531 | 0.90632 | 0.92546 | 1.6 | 59.54
Neigh | 0.53954 | 0.54258 | 0.54621 | 0.3 | 35.65
Comm | 0.035654 | 0.058364 | 0.079543 | 7.0 | 3.83
Output | 0.00048494 | 0.00065351 | 0.0011017 | 0.0 | 0.04
Modify | 0.0090034 | 0.0090633 | 0.0091114 | 0.0 | 0.60
Other | | 0.005168 | | | 0.34
Nlocal: 8160 ave 8163 max 8157 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11605.8 ave 11615 max 11593 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.22553e+06 ave 1.22734e+06 max 1.22455e+06 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 4902132
Ave neighs/atom = 150.188
Neighbor list builds = 9
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.0105426 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 91977 55296
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 105.1 | 105.1 | 105.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 20.172 on 1 procs for 100 steps with 36000 atoms
Performance: 0.857 ns/day, 28.017 hours/ns, 4.957 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 | 15.818 | 15.818 | 15.818 | 0.0 | 78.41
Bond | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.00
Kspace | 1.966 | 1.966 | 1.966 | 0.0 | 9.75
Neigh | 2.0639 | 2.0639 | 2.0639 | 0.0 | 10.23
Comm | 0.043918 | 0.043918 | 0.043918 | 0.0 | 0.22
Output | 0.00025153 | 0.00025153 | 0.00025153 | 0.0 | 0.00
Modify | 0.27056 | 0.27056 | 0.27056 | 0.0 | 1.34
Other | | 0.009522 | | | 0.05
Nlocal: 36000 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56963 ave 56963 max 56963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24625e+07 ave 1.24625e+07 max 1.24625e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:20

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
2 by 2 by 1 MPI processor grid
reading atoms ...
4500 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
3000 bonds
reading angles ...
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Time spent = 0.00535488 secs
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.268801
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0331015
estimated relative force accuracy = 9.96841e-05
using double precision FFTs
3d grid and FFT values/proc = 27993 13824
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.8
ghost atom cutoff = 11.8
binsize = 5.9, bins = 13 25 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 37.74 | 37.74 | 37.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 516.17807
50 264.98553 -136986.74 0 -118030.61 -440.29256
100 274.45966 -136364.57 0 -116730.69 -128.61949
Loop time of 5.43807 on 4 procs for 100 steps with 36000 atoms
Performance: 3.178 ns/day, 7.553 hours/ns, 18.389 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0016 | 4.0968 | 4.1706 | 3.3 | 75.34
Bond | 7.1049e-05 | 8.5771e-05 | 0.00010586 | 0.0 | 0.00
Kspace | 0.56386 | 0.63614 | 0.73036 | 8.3 | 11.70
Neigh | 0.52575 | 0.52587 | 0.52594 | 0.0 | 9.67
Comm | 0.045847 | 0.047308 | 0.048331 | 0.4 | 0.87
Output | 9.1314e-05 | 0.00012183 | 0.00021172 | 0.0 | 0.00
Modify | 0.12561 | 0.1258 | 0.12605 | 0.1 | 2.31
Other | | 0.005944 | | | 0.11
Nlocal: 9000 ave 9002 max 8998 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 24134.2 ave 24184 max 24062 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3.11561e+06 ave 3.11676e+06 max 3.11446e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 12462451
Ave neighs/atom = 346.179
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 6
Total wall time: 0:00:05

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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.00191712 secs
pair_style sw
pair_coeff * * Si.sw Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 46 46 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.52 | 12.52 | 12.52 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 5.66634 on 1 procs for 100 steps with 32000 atoms
Performance: 1.525 ns/day, 15.740 hours/ns, 17.648 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 | 5.5464 | 5.5464 | 5.5464 | 0.0 | 97.88
Neigh | 0.075834 | 0.075834 | 0.075834 | 0.0 | 1.34
Comm | 0.0092049 | 0.0092049 | 0.0092049 | 0.0 | 0.16
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.00
Modify | 0.024666 | 0.024666 | 0.024666 | 0.0 | 0.44
Other | | 0.01014 | | | 0.18
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12495 ave 12495 max 12495 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: 894818 ave 894818 max 894818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05

77
bench/POTENTIALS/log.16Mar18.sw.4 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Stillinger-Weber
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000604153 secs
pair_style sw
pair_coeff * * Si.sw Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.77118
ghost atom cutoff = 4.77118
binsize = 2.38559, bins = 46 46 23
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sw, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.104 | 4.104 | 4.104 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 1.47105 on 4 procs for 100 steps with 32000 atoms
Performance: 5.873 ns/day, 4.086 hours/ns, 67.978 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3788 | 1.3929 | 1.4053 | 0.8 | 94.69
Neigh | 0.019134 | 0.019502 | 0.019816 | 0.2 | 1.33
Comm | 0.024183 | 0.035734 | 0.049122 | 4.7 | 2.43
Output | 5.1975e-05 | 6.6102e-05 | 0.00010204 | 0.0 | 0.00
Modify | 0.0063825 | 0.0064374 | 0.0064764 | 0.0 | 0.44
Other | | 0.01638 | | | 1.11
Nlocal: 8000 ave 8015 max 7978 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 4995 ave 5017 max 4980 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 223704 ave 224108 max 223131 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:01

77
bench/POTENTIALS/log.16Mar18.tersoff.1 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.0019412 secs
pair_style tersoff
pair_coeff * * Si.tersoff Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 52 52 26
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.1 | 11.1 | 11.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 8.53088 on 1 procs for 100 steps with 32000 atoms
Performance: 1.013 ns/day, 23.697 hours/ns, 11.722 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 | 8.4236 | 8.4236 | 8.4236 | 0.0 | 98.74
Neigh | 0.065852 | 0.065852 | 0.065852 | 0.0 | 0.77
Comm | 0.0078607 | 0.0078607 | 0.0078607 | 0.0 | 0.09
Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.00
Modify | 0.023968 | 0.023968 | 0.023968 | 0.0 | 0.28
Other | | 0.009521 | | | 0.11
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11537 ave 11537 max 11537 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: 530500 ave 530500 max 530500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:08

77
bench/POTENTIALS/log.16Mar18.tersoff.4 Normal file
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LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# bulk Si via Tersoff
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
Time spent = 0.000605822 secs
pair_style tersoff
pair_coeff * * Si.tersoff Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.2
ghost atom cutoff = 4.2
binsize = 2.1, bins = 52 52 26
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.753 | 3.753 | 3.753 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 2.16161 on 4 procs for 100 steps with 32000 atoms
Performance: 3.997 ns/day, 6.004 hours/ns, 46.262 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1122 | 2.1165 | 2.122 | 0.2 | 97.91
Neigh | 0.016894 | 0.016915 | 0.016955 | 0.0 | 0.78
Comm | 0.012348 | 0.017858 | 0.022105 | 2.7 | 0.83
Output | 4.7684e-05 | 6.2048e-05 | 9.9421e-05 | 0.0 | 0.00
Modify | 0.0064063 | 0.0064579 | 0.0065169 | 0.0 | 0.30
Other | | 0.003793 | | | 0.18
Nlocal: 8000 ave 8005 max 7993 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 4580.25 ave 4593 max 4567 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 132625 ave 132785 max 132562 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:02

52
bench/POTENTIALS/log.26Jun12.adp.1
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LAMMPS (29 Jun 2012)
# bulk Ni in ADP
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style adp
pair_coeff * * Ni.adp Ni
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Memory usage per processor = 25.3022 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 17.8688 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 17.078 (95.5745)
Neigh time (%) = 0.677115 (3.78937)
Comm time (%) = 0.0346231 (0.193763)
Outpt time (%) = 0.000118971 (0.000665802)
Other time (%) = 0.0789182 (0.441653)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.33704e+06 ave 1.33704e+06 max 1.33704e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Neighbor list builds = 13
Dangerous builds = 0

52
bench/POTENTIALS/log.26Jun12.adp.4
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LAMMPS (29 Jun 2012)
# bulk Ni in ADP
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style adp
pair_coeff * * Ni.adp Ni
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Memory usage per processor = 8.14011 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.105
100 793.05485 -139023.13 0 -135742.9 32175.694
Loop time of 4.95441 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 4.6421 (93.6964)
Neigh time (%) = 0.176992 (3.57242)
Comm time (%) = 0.110454 (2.22941)
Outpt time (%) = 7.62939e-05 (0.00153992)
Other time (%) = 0.0247837 (0.500235)
Nlocal: 8000 ave 8044 max 7960 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 9131 ave 9171 max 9087 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 334259 ave 336108 max 332347 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 1337035
Ave neighs/atom = 41.7823
Neighbor list builds = 13
Dangerous builds = 0

63
bench/POTENTIALS/log.26Jun12.airebo.1
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LAMMPS (29 Jun 2012)
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
60 atoms
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Memory usage per processor = 105.507 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 8830.3329
10 143.00954 -138633.58 0 -138030.23 32329.276
20 219.32814 -138956.58 0 -138031.25 -3487.5421
30 120.47567 -138535.14 0 -138026.86 11367.446
40 158.54609 -138696.2 0 -138027.31 13272.949
50 92.336357 -138415.63 0 -138026.07 23805.366
60 182.26046 -138797.42 0 -138028.48 33008.508
70 153.25324 -138676.08 0 -138029.52 3951.7505
80 173.39519 -138762.84 0 -138031.3 20742.112
90 193.98121 -138849.35 0 -138030.96 -10033.519
100 193.18028 -138846.08 0 -138031.07 31990.015
Loop time of 106.235 on 1 procs for 100 steps with 32640 atoms
Pair time (%) = 97.6504 (91.919)
Neigh time (%) = 8.44267 (7.94714)
Comm time (%) = 0.0546622 (0.0514539)
Outpt time (%) = 0.00114608 (0.00107881)
Other time (%) = 0.0864127 (0.0813409)
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48220 ave 48220 max 48220 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: 2.22341e+07 ave 2.22341e+07 max 2.22341e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22234140
Ave neighs/atom = 681.193
Neighbor list builds = 8
Dangerous builds = 0

63
bench/POTENTIALS/log.26Jun12.airebo.4
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LAMMPS (29 Jun 2012)
# AIREBO polyethelene benchmark
units metal
atom_style atomic
read_data data.airebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
60 atoms
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style airebo 3.0 1 1
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Memory usage per processor = 29.8097 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -139299.7 0 -138034.03 8830.3329
10 143.00954 -138633.58 0 -138030.23 32329.276
20 219.32814 -138956.58 0 -138031.25 -3487.5421
30 120.47567 -138535.14 0 -138026.86 11367.446
40 158.54609 -138696.2 0 -138027.31 13272.949
50 92.336357 -138415.63 0 -138026.07 23805.366
60 182.26046 -138797.42 0 -138028.48 33008.508
70 153.25324 -138676.08 0 -138029.52 3951.7505
80 173.39519 -138762.84 0 -138031.3 20742.112
90 193.98121 -138849.35 0 -138030.96 -10033.519
100 193.18028 -138846.08 0 -138031.07 31990.015
Loop time of 29.0637 on 4 procs for 100 steps with 32640 atoms
Pair time (%) = 25.1182 (86.4249)
Neigh time (%) = 2.97429 (10.2337)
Comm time (%) = 0.940242 (3.23511)
Outpt time (%) = 0.000824273 (0.00283609)
Other time (%) = 0.0300676 (0.103454)
Nlocal: 8160 ave 8177 max 8143 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 22625.5 ave 22644 max 22608 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 5.55854e+06 ave 5.57118e+06 max 5.54428e+06 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 22234140
Ave neighs/atom = 681.193
Neighbor list builds = 8
Dangerous builds = 0

57
bench/POTENTIALS/log.26Jun12.bop.1
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LAMMPS (29 Jun 2012)
# bulk CdTe via BOP
units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
1 by 1 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
pair_style bop 4.9
pair_coeff * * CdTe.bop Cd Te
mass 1 112.4
mass 2 127.6
communicate single cutoff 14.7
velocity all create 1000.0 376847 loop geom
neighbor 0.1 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Memory usage per processor = 73.7078 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.48 0 -65403.285 3468.3799
100 572.83068 -67772.68 0 -65403.34 1847.9403
Loop time of 80.268 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 79.1627 (98.623)
Neigh time (%) = 0.973292 (1.21255)
Comm time (%) = 0.051837 (0.0645799)
Outpt time (%) = 0.000120163 (0.000149702)
Other time (%) = 0.0800123 (0.0996815)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 35071 ave 35071 max 35071 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: 141090 ave 141090 max 141090 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 141090
Ave neighs/atom = 4.40906
Neighbor list builds = 14
Dangerous builds = 0

57
bench/POTENTIALS/log.26Jun12.bop.4
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LAMMPS (29 Jun 2012)
# bulk CdTe via BOP
units metal
atom_style atomic
lattice custom 6.82884 basis 0.0 0.0 0.0 basis 0.25 0.25 0.25 basis 0.0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0.0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0.0 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 6.82884 6.82884 6.82884
region box block 0 20 0 20 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (136.577 136.577 68.2884)
2 by 2 by 1 MPI processor grid
create_atoms 1 box basis 2 2 basis 4 2 basis 6 2 basis 8 2
Created 32000 atoms
pair_style bop 4.9
pair_coeff * * CdTe.bop Cd Te
mass 1 112.4
mass 2 127.6
communicate single cutoff 14.7
velocity all create 1000.0 376847 loop geom
neighbor 0.1 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Memory usage per processor = 26.6187 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -69539.48 0 -65403.285 3468.3799
100 572.83068 -67772.68 0 -65403.34 1847.9403
Loop time of 20.6725 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 19.6654 (95.1287)
Neigh time (%) = 0.355175 (1.71811)
Comm time (%) = 0.625993 (3.02815)
Outpt time (%) = 7.26581e-05 (0.000351473)
Other time (%) = 0.025782 (0.124717)
Nlocal: 8000 ave 8005 max 7996 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 15171 ave 15175 max 15166 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 35272.5 ave 35327 max 35221 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 141090
Ave neighs/atom = 4.40906
Neighbor list builds = 14
Dangerous builds = 0

71
bench/POTENTIALS/log.26Jun12.comb.1
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LAMMPS (29 Jun 2012)
# SiO2 for COMB potential
units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
32400 atoms
mass 1 28.0855
group type1 type 1
10800 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
21600 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Si O
neighbor 0.5 bin
neigh_modify every 10 delay 0 check yes
timestep 0.0002
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
thermo_modify norm yes
velocity all create 300.0 3482028
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 10 0.001 file fq.out
thermo 10
run 100
Memory usage per processor = 95.0552 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Press Volume
0 300 -6.800513 -6.8392899 4.6301362 -11.469426 2.8887101 -1.444355 14558.344 462016.62
10 271.62515 -6.8007192 -6.8358285 4.6332165 -11.469045 2.8882392 -1.4441196 14514.953 462016.62
20 238.98408 -6.8009297 -6.8318199 4.6310324 -11.462852 2.8879087 -1.4439543 13651.411 462016.62
30 210.3787 -6.8010518 -6.8282445 4.6294419 -11.457686 2.8878659 -1.4439329 12043.903 462016.62
40 193.1516 -6.8010917 -6.8260577 4.6290792 -11.455137 2.8882154 -1.4441076 9835.5857 462016.62
50 191.94742 -6.8010622 -6.8258726 4.630419 -11.456292 2.8890872 -1.4445436 6942.5175 462016.62
60 207.61185 -6.800982 -6.8278171 4.63437 -11.462187 2.8904146 -1.4452072 3246.4843 462016.62
70 236.98233 -6.8008686 -6.8315 4.6406466 -11.472147 2.8920875 -1.4460437 -1291.732 462016.62
80 273.85158 -6.800735 -6.8361321 4.6488576 -11.48499 2.894141 -1.4470705 -6592.9936 462016.62
90 310.76808 -6.8006054 -6.8407741 4.6597903 -11.500564 2.8962597 -1.4481298 -12439.324 462016.62
100 340.98434 -6.8004987 -6.844573 4.67158 -11.516153 2.8982813 -1.4491406 -18618.072 462016.62
Loop time of 648.075 on 1 procs for 100 steps with 32400 atoms
Pair time (%) = 151.932 (23.4435)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0529873 (0.00817611)
Outpt time (%) = 0.0037415 (0.000577325)
Other time (%) = 496.087 (76.5477)
Nlocal: 32400 ave 32400 max 32400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 42400 ave 42400 max 42400 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: 1.85289e+07 ave 1.85289e+07 max 1.85289e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18528904
Ave neighs/atom = 571.88
Neighbor list builds = 0
Dangerous builds = 0

71
bench/POTENTIALS/log.26Jun12.comb.4
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LAMMPS (29 Jun 2012)
# SiO2 for COMB potential
units metal
atom_style charge
read_data data.comb
triclinic box = (0 0 0) to (74.58 74.58 83.064) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
32400 atoms
mass 1 28.0855
group type1 type 1
10800 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
21600 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Si O
neighbor 0.5 bin
neigh_modify every 10 delay 0 check yes
timestep 0.0002
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 press vol
thermo_modify norm yes
velocity all create 300.0 3482028
fix 1 all nvt temp 300.0 300.0 0.1
fix 2 all qeq/comb 10 0.001 file fq.out
thermo 10
run 100
Memory usage per processor = 26.6527 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Press Volume
0 300 -6.800513 -6.8392899 4.6301362 -11.469426 2.8887101 -1.444355 14558.344 462016.62
10 271.62515 -6.8007192 -6.8358285 4.6332165 -11.469045 2.8882392 -1.4441196 14514.953 462016.62
20 238.98408 -6.8009297 -6.8318199 4.6310324 -11.462852 2.8879087 -1.4439543 13651.411 462016.62
30 210.3787 -6.8010518 -6.8282445 4.6294419 -11.457686 2.8878659 -1.4439329 12043.903 462016.62
40 193.1516 -6.8010917 -6.8260577 4.6290792 -11.455137 2.8882154 -1.4441076 9835.5857 462016.62
50 191.94742 -6.8010622 -6.8258726 4.630419 -11.456292 2.8890872 -1.4445436 6942.5175 462016.62
60 207.61185 -6.800982 -6.8278171 4.63437 -11.462187 2.8904146 -1.4452072 3246.4843 462016.62
70 236.98233 -6.8008686 -6.8315 4.6406466 -11.472147 2.8920875 -1.4460437 -1291.732 462016.62
80 273.85158 -6.800735 -6.8361321 4.6488576 -11.48499 2.894141 -1.4470705 -6592.9936 462016.62
90 310.76808 -6.8006054 -6.8407741 4.6597903 -11.500564 2.8962597 -1.4481298 -12439.324 462016.62
100 340.98434 -6.8004987 -6.844573 4.67158 -11.516153 2.8982813 -1.4491406 -18618.072 462016.62
Loop time of 166.681 on 4 procs for 100 steps with 32400 atoms
Pair time (%) = 38.5193 (23.1097)
Neigh time (%) = 0 (0)
Comm time (%) = 0.700634 (0.420345)
Outpt time (%) = 0.00150448 (0.000902613)
Other time (%) = 127.459 (76.4691)
Nlocal: 8100 ave 8106 max 8094 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 20650 ave 20686 max 20614 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4.63223e+06 ave 4.63577e+06 max 4.62881e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 18528904
Ave neighs/atom = 571.88
Neighbor list builds = 0
Dangerous builds = 0

52
bench/POTENTIALS/log.26Jun12.dpd.1
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LAMMPS (29 Jun 2012)
# DPD benchmark
units lj
atom_style atomic
communicate single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.0 87287 loop geom
pair_style dpd 1.0 1.0 928948
pair_coeff 1 1 25.0 4.5
neighbor 0.5 bin
neigh_modify delay 0 every 1
fix 1 all nve
timestep 0.04
run 100
Memory usage per processor = 11.134 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.880274
100 1.0246036 4.5727353 0 6.1095927 23.859969
Loop time of 3.91185 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 1.94669 (49.7639)
Neigh time (%) = 1.80933 (46.2524)
Comm time (%) = 0.0754168 (1.92791)
Outpt time (%) = 0.00010705 (0.00273656)
Other time (%) = 0.0803113 (2.05303)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14981 ave 14981 max 14981 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 660587 ave 660587 max 660587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 660587
Ave neighs/atom = 20.6433
Neighbor list builds = 50
Dangerous builds = 0

52
bench/POTENTIALS/log.26Jun12.dpd.4
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LAMMPS (29 Jun 2012)
# DPD benchmark
units lj
atom_style atomic
communicate single vel yes
lattice fcc 3.0
Lattice spacing in x,y,z = 1.10064 1.10064 1.10064
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (22.0128 22.0128 22.0128)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.0 87287 loop geom
pair_style dpd 1.0 1.0 928948
pair_coeff 1 1 25.0 4.5
neighbor 0.5 bin
neigh_modify delay 0 every 1
fix 1 all nve
timestep 0.04
run 100
Memory usage per processor = 3.88609 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 3.6872574 0 5.1872105 28.911346
100 1.0219182 4.5817845 0 6.1146139 23.803115
Loop time of 1.10533 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.521759 (47.2037)
Neigh time (%) = 0.488133 (44.1616)
Comm time (%) = 0.0682133 (6.17129)
Outpt time (%) = 7.55787e-05 (0.00683763)
Other time (%) = 0.0271527 (2.45652)
Nlocal: 8000 ave 8014 max 7986 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6744 ave 6764 max 6726 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 165107 ave 166433 max 163419 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 660428
Ave neighs/atom = 20.6384
Neighbor list builds = 50
Dangerous builds = 0

51
bench/POTENTIALS/log.26Jun12.eam.1
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LAMMPS (29 Jun 2012)
# bulk Cu in EAM
units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Memory usage per processor = 15.3728 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 5.98814 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 5.27792 (88.1396)
Neigh time (%) = 0.601851 (10.0507)
Comm time (%) = 0.0318148 (0.531297)
Outpt time (%) = 0.000111103 (0.00185539)
Other time (%) = 0.0764399 (1.27652)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19909 ave 19909 max 19909 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0

51
bench/POTENTIALS/log.26Jun12.eam.4
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LAMMPS (29 Jun 2012)
# bulk Cu in EAM
units metal
atom_style atomic
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (72.3 72.3 72.3)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
run 100
Memory usage per processor = 4.92442 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 1.56165 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 1.35187 (86.5672)
Neigh time (%) = 0.153887 (9.85413)
Comm time (%) = 0.0361158 (2.31267)
Outpt time (%) = 6.85453e-05 (0.0043893)
Other time (%) = 0.0197011 (1.26156)
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9130.25 ave 9138 max 9122 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 301946 ave 302392 max 301360 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 1207784
Ave neighs/atom = 37.7433
Neighbor list builds = 13
Dangerous builds = 0

53
bench/POTENTIALS/log.26Jun12.eim.1
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LAMMPS (29 Jun 2012)
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
# crystal can be annealed to the correct NaCl type of NaCl polycrystals
units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0 every 1
timestep 0.0005
thermo_style custom step pe pxx pyy pzz temp
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
# anneal in much longer run
#fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Memory usage per processor = 16.2156 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 17.9236 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 15.6228 (87.1633)
Neigh time (%) = 2.00511 (11.187)
Comm time (%) = 0.0502045 (0.280103)
Outpt time (%) = 0.000332117 (0.00185296)
Other time (%) = 0.245142 (1.36771)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 21505 ave 21505 max 21505 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.5839e+06 ave 1.5839e+06 max 1.5839e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Neighbor list builds = 37
Dangerous builds = 12

53
bench/POTENTIALS/log.26Jun12.eim.4
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LAMMPS (29 Jun 2012)
# EIM benchmark
# if run long enough (e.g. 1M steps), the unstable CsCl form of a NaCl single
# crystal can be annealed to the correct NaCl type of NaCl polycrystals
units metal
atom_style atomic
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (71.58 143.66 71.58)
1 by 4 by 1 MPI processor grid
32000 atoms
32000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0 every 1
timestep 0.0005
thermo_style custom step pe pxx pyy pzz temp
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 1400.0 0.1 aniso 0.0 0.0 0.1
# anneal in much longer run
#fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
run 100
Memory usage per processor = 4.81914 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -90567.58 -117883.6 -118039.81 -117894.07 1400
100 -91997.012 -4104.7052 -4138.276 -4145.8936 944.10136
Loop time of 4.64014 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 4.00505 (86.3132)
Neigh time (%) = 0.510816 (11.0086)
Comm time (%) = 0.0515542 (1.11105)
Outpt time (%) = 0.000117719 (0.00253697)
Other time (%) = 0.0726004 (1.56462)
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 9460.25 ave 9469 max 9449 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 395975 ave 397239 max 394616 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1583901
Ave neighs/atom = 49.4969
Neighbor list builds = 37
Dangerous builds = 12

58
bench/POTENTIALS/log.26Jun12.fene.1
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LAMMPS (29 Jun 2012)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.fene
1 = max bonds/atom
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify delay 5 every 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
run 100
Memory usage per processor = 11.5156 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 0.916534 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.200358 (21.8604)
Bond time (%) = 0.0873125 (9.52637)
Neigh time (%) = 0.367993 (40.1505)
Comm time (%) = 0.0293641 (3.20382)
Outpt time (%) = 0.000102043 (0.0111336)
Other time (%) = 0.231404 (25.2478)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9493 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155873 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Neighbor list builds = 20
Dangerous builds = 20

58
bench/POTENTIALS/log.26Jun12.fene.4
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LAMMPS (29 Jun 2012)
# FENE beadspring benchmark
units lj
atom_style bond
special_bonds fene
read_data data.fene
1 = max bonds/atom
orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
31680 bonds
2 = max # of 1-2 neighbors
2 = max # of special neighbors
neighbor 0.4 bin
neigh_modify delay 5 every 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
timestep 0.012
run 100
Memory usage per processor = 4.85535 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.9736748 0.44378481 20.502389 22.40664 4.7809557
Loop time of 0.242779 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0495595 (20.4134)
Bond time (%) = 0.0221654 (9.12986)
Neigh time (%) = 0.0930593 (38.3309)
Comm time (%) = 0.019502 (8.03285)
Outpt time (%) = 5.23329e-05 (0.0215558)
Other time (%) = 0.0584403 (24.0714)
Nlocal: 8000 ave 8023 max 7978 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 4158.75 ave 4175 max 4145 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 38940 ave 39184 max 38640 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 155760
Ave neighs/atom = 4.8675
Ave special neighs/atom = 1.98
Neighbor list builds = 20
Dangerous builds = 20

61
bench/POTENTIALS/log.26Jun12.granular.1
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LAMMPS (30 Jun 2012)
# granular chute flow
units lj
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify delay 5 every 1
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
run 100
Memory usage per processor = 35.056 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.666637 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.411868 (61.783)
Neigh time (%) = 0.049587 (7.43838)
Comm time (%) = 0.0233159 (3.49754)
Outpt time (%) = 0.000216007 (0.0324025)
Other time (%) = 0.18165 (27.2487)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5463 ave 5463 max 5463 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 115133 ave 115133 max 115133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 115133
Ave neighs/atom = 3.59791
Neighbor list builds = 2
Dangerous builds = 0

61
bench/POTENTIALS/log.26Jun12.granular.4
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LAMMPS (30 Jun 2012)
# granular chute flow
units lj
atom_style sphere
boundary p p fs
newton off
communicate single vel yes
read_data data.granular
orthogonal box = (0 0 0) to (40 20 37.2886)
2 by 1 by 2 MPI processor grid
32000 atoms
32000 velocities
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify delay 5 every 1
timestep 0.0001
group bottom type 2
912 atoms in group bottom
group active subtract all bottom
31088 atoms in group active
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
run 100
Memory usage per processor = 15.3108 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29833.783
100 32000 784292.08 1571.0968 29834.707
Loop time of 0.155661 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.0724595 (46.5496)
Neigh time (%) = 0.0113012 (7.26016)
Comm time (%) = 0.0168278 (10.8105)
Outpt time (%) = 0.000223458 (0.143554)
Other time (%) = 0.0548489 (35.2362)
Nlocal: 8000 ave 8008 max 7992 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2439 ave 2450 max 2428 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 29500.5 ave 30488 max 28513 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 118002
Ave neighs/atom = 3.68756
Neighbor list builds = 2
Dangerous builds = 0

50
bench/POTENTIALS/log.26Jun12.lj.1
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LAMMPS (29 Jun 2012)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 5 every 1
fix 1 all nve
run 100
Memory usage per processor = 14.4474 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 2.56328 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 1.93274 (75.4008)
Neigh time (%) = 0.53491 (20.8682)
Comm time (%) = 0.0289466 (1.12928)
Outpt time (%) = 0.000109911 (0.0042879)
Other time (%) = 0.0665786 (2.5974)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19669 ave 19669 max 19669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20318e+06 ave 1.20318e+06 max 1.20318e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Neighbor list builds = 11
Dangerous builds = 0

50
bench/POTENTIALS/log.26Jun12.lj.4
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LAMMPS (29 Jun 2012)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 5 every 1
fix 1 all nve
run 100
Memory usage per processor = 4.61801 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.75745998 -5.7584998 0 -4.6223453 0.20729996
Loop time of 0.720234 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.515158 (71.5264)
Neigh time (%) = 0.143012 (19.8563)
Comm time (%) = 0.0423787 (5.88401)
Outpt time (%) = 0.000118494 (0.0164522)
Other time (%) = 0.0195675 (2.71682)
Nlocal: 8000 ave 8041 max 7958 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 9011 ave 9065 max 8961 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 300794 ave 304843 max 297317 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1203176
Ave neighs/atom = 37.5992
Neighbor list builds = 11
Dangerous builds = 0

55
bench/POTENTIALS/log.26Jun12.meam.1
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LAMMPS (29 Jun 2012)
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Memory usage per processor = 56.0952 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 42.1683 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 41.4542 (98.3066)
Neigh time (%) = 0.597845 (1.41776)
Comm time (%) = 0.0312274 (0.0740541)
Outpt time (%) = 0.000230074 (0.000545609)
Other time (%) = 0.084774 (0.201037)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13576 ave 13576 max 13576 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 780360 ave 780360 max 780360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.56072e+06 ave 1.56072e+06 max 1.56072e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0

55
bench/POTENTIALS/log.26Jun12.meam.4
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LAMMPS (29 Jun 2012)
# bulk Ni in MEAM
units metal
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 20 0 20 0 20
create_box 1 box
Created orthogonal box = (0 0 0) to (70.4 70.4 70.4)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.005
thermo 50
run 100
Memory usage per processor = 18.4054 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1600 -142400 0 -135782.09 20259.18
50 885.10702 -139411.51 0 -135750.54 32425.433
100 895.5097 -139454.3 0 -135750.3 31804.187
Loop time of 11.2927 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 10.9598 (97.0519)
Neigh time (%) = 0.155562 (1.37754)
Comm time (%) = 0.149276 (1.32188)
Outpt time (%) = 0.000140548 (0.00124459)
Other time (%) = 0.0279386 (0.247404)
Nlocal: 8000 ave 8045 max 7947 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 6066.75 ave 6120 max 6021 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 195090 ave 196403 max 193697 min
Histogram: 1 0 0 1 0 0 0 1 0 1
FullNghs: 390180 ave 392616 max 387490 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1560720
Ave neighs/atom = 48.7725
Neighbor list builds = 8
Dangerous builds = 0

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bench/POTENTIALS/log.26Jun12.peri.1
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LAMMPS (29 Jun 2012)
# Crack growth in notched 3D Peridynamic block
# Mesh spacing
variable h equal 5.00e-4
# Peridynamic horizon
variable delta equal 3.0*${h}
variable delta equal 3.0*0.00050000000000000001041
# Height of plate (meters)
variable height equal 31.5*${h}
variable height equal 31.5*0.00050000000000000001041
# Width of plate (meters)
variable width equal 39.5*${h}
variable width equal 39.5*0.00050000000000000001041
# Thickness of plate (meters)
variable depth equal 24.5*${h}
variable depth equal 24.5*0.00050000000000000001041
# Height of notch
variable crackheight equal 10*${h}
variable crackheight equal 10*0.00050000000000000001041
# Density of plate
variable mydensity equal 2440.0
# Elastic modulus of material
variable myE equal 72.0e9
# Strain energy release rate at branching
variable myG equal 135.0
# constant, but define it as a variable here
variable pi equal 3.14159265358979323846
units si
boundary s s s
atom_style peri
atom_modify map array
variable myskin equal 2.0*${h}
variable myskin equal 2.0*0.00050000000000000001041
neighbor ${myskin} bin
neighbor 0.0010000000000000000208 bin
lattice sc $h
lattice sc 0.00050000000000000001041
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
variable myxmin equal 0.0
variable myxmax equal ${width}
variable myxmax equal 0.019750000000000000194
variable myymin equal 0.0
variable myymax equal ${height}
variable myymax equal 0.015750000000000000111
variable myzmin equal 0.0
variable myzmax equal ${depth}
variable myzmax equal 0.012250000000000000472
region plate block ${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 0 ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 0 0.012250000000000000472 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
1 by 1 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
pair_style peri/pmb
variable myk equal (2.0/3.0)*${myE}
variable myk equal (2.0/3.0)*72000000000
variable myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.141592653589793116*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.141592653589793116*(0.0015000000000000000312^4)))
variable mydelta equal (${delta}+(${delta}/100.0))
variable mydelta equal (0.0015000000000000000312+(${delta}/100.0))
variable mydelta equal (0.0015000000000000000312+(0.0015000000000000000312/100.0))
variable mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015000000000000000312))
variable tmpvar1 equal ${myymax}-${crackheight}
variable tmpvar1 equal 0.015750000000000000111-${crackheight}
variable tmpvar1 equal 0.015750000000000000111-0.0050000000000000001041
variable tmpvar2 equal 0.5*${width}
variable tmpvar2 equal 0.5*0.019750000000000000194
region topleft block 0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 0 ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 0 0.012250000000000000472 units box
region topright block ${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 0 ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 0 0.012250000000000000472 units box
set region topleft type 2
5000 settings made for type
set region topright type 3
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 2 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 3 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 2 3 ${myc} 0.0 ${mys0} 0.0
pair_coeff 2 3 5.4324887242033602757e+22 0.0 ${mys0} 0.0
pair_coeff 2 3 5.4324887242033602757e+22 0.0 0.0010206207261596576558 0.0
pair_coeff 1 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 1 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
set group all density ${mydensity}
set group all density 2440
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.00050000000000000001041)^3
set group all volume ${myvolume}
set group all volume 1.2500000000000000779e-10
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix F1 all nve
compute C1 all damage/atom
velocity all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 0.019750000000000000194 units box
variable mystep equal 0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/0.00050000000000000001041)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/0.00050000000000000001041)*1.2500000000000000779e-10))
timestep ${mystep}
timestep 2.1193149239622597698e-08
thermo 20
run 100
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Memory usage per processor = 145.482 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
40 1.3041477e+27 4.6848143e+08 0 1.332729e+09 1.5875756e+14 3.6292128e-06
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 23.8636 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 23.7778 (99.6409)
Neigh time (%) = 0 (0)
Comm time (%) = 9.84669e-05 (0.000412625)
Outpt time (%) = 0.000550747 (0.0023079)
Other time (%) = 0.0850549 (0.356422)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.74442e+06 ave 6.74442e+06 max 6.74442e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.34888e+07 ave 1.34888e+07 max 1.34888e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Neighbor list builds = 0
Dangerous builds = 0

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bench/POTENTIALS/log.26Jun12.peri.4
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LAMMPS (29 Jun 2012)
# Crack growth in notched 3D Peridynamic block
# Mesh spacing
variable h equal 5.00e-4
# Peridynamic horizon
variable delta equal 3.0*${h}
variable delta equal 3.0*0.00050000000000000001041
# Height of plate (meters)
variable height equal 31.5*${h}
variable height equal 31.5*0.00050000000000000001041
# Width of plate (meters)
variable width equal 39.5*${h}
variable width equal 39.5*0.00050000000000000001041
# Thickness of plate (meters)
variable depth equal 24.5*${h}
variable depth equal 24.5*0.00050000000000000001041
# Height of notch
variable crackheight equal 10*${h}
variable crackheight equal 10*0.00050000000000000001041
# Density of plate
variable mydensity equal 2440.0
# Elastic modulus of material
variable myE equal 72.0e9
# Strain energy release rate at branching
variable myG equal 135.0
# constant, but define it as a variable here
variable pi equal 3.14159265358979323846
units si
boundary s s s
atom_style peri
atom_modify map array
variable myskin equal 2.0*${h}
variable myskin equal 2.0*0.00050000000000000001041
neighbor ${myskin} bin
neighbor 0.0010000000000000000208 bin
lattice sc $h
lattice sc 0.00050000000000000001041
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
variable myxmin equal 0.0
variable myxmax equal ${width}
variable myxmax equal 0.019750000000000000194
variable myymin equal 0.0
variable myymax equal ${height}
variable myymax equal 0.015750000000000000111
variable myzmin equal 0.0
variable myzmax equal ${depth}
variable myzmax equal 0.012250000000000000472
region plate block ${myxmin} ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 ${myxmax} ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 ${myymin} ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 ${myymax} ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 ${myzmin} ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 0 ${myzmax} units box
region plate block 0 0.019750000000000000194 0 0.015750000000000000111 0 0.012250000000000000472 units box
create_box 3 plate
Created orthogonal box = (0 0 0) to (0.01975 0.01575 0.01225)
2 by 2 by 1 MPI processor grid
create_atoms 1 region plate
Created 32000 atoms
pair_style peri/pmb
variable myk equal (2.0/3.0)*${myE}
variable myk equal (2.0/3.0)*72000000000
variable myc equal ((18.0*${myk})/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(${pi}*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.141592653589793116*(${delta}^4)))
variable myc equal ((18.0*48000000000)/(3.141592653589793116*(0.0015000000000000000312^4)))
variable mydelta equal (${delta}+(${delta}/100.0))
variable mydelta equal (0.0015000000000000000312+(${delta}/100.0))
variable mydelta equal (0.0015000000000000000312+(0.0015000000000000000312/100.0))
variable mys0 equal sqrt((5.0*${myG})/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*${myk}*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*${delta}))
variable mys0 equal sqrt((5.0*135)/(9.0*48000000000*0.0015000000000000000312))
variable tmpvar1 equal ${myymax}-${crackheight}
variable tmpvar1 equal 0.015750000000000000111-${crackheight}
variable tmpvar1 equal 0.015750000000000000111-0.0050000000000000001041
variable tmpvar2 equal 0.5*${width}
variable tmpvar2 equal 0.5*0.019750000000000000194
region topleft block 0.0 ${tmpvar2} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 ${myymax} ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 ${myzmin} ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 0 ${myzmax} units box
region topleft block 0.0 0.0098750000000000000971 0.01074999999999999914 0.015750000000000000111 0 0.012250000000000000472 units box
region topright block ${tmpvar2} ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 ${myxmax} ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 ${tmpvar1} ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 ${myymax} ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 ${myzmin} ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 0 ${myzmax} units box
region topright block 0.0098750000000000000971 0.019750000000000000194 0.01074999999999999914 0.015750000000000000111 0 0.012250000000000000472 units box
set region topleft type 2
5000 settings made for type
set region topright type 3
5000 settings made for type
pair_coeff 1 1 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 1 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 2 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 2 2 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 3 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 3 3 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 2 3 ${myc} 0.0 ${mys0} 0.0
pair_coeff 2 3 5.4324887242033602757e+22 0.0 ${mys0} 0.0
pair_coeff 2 3 5.4324887242033602757e+22 0.0 0.0010206207261596576558 0.0
pair_coeff 1 2 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 2 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
pair_coeff 1 3 ${myc} ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 ${mydelta} ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 0.0015150000000000000706 ${mys0} 0.0
pair_coeff 1 3 5.4324887242033602757e+22 0.0015150000000000000706 0.0010206207261596576558 0.0
set group all density ${mydensity}
set group all density 2440
32000 settings made for density
variable myvolume equal ($h)^3
variable myvolume equal (0.00050000000000000001041)^3
set group all volume ${myvolume}
set group all volume 1.2500000000000000779e-10
32000 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix F1 all nve
compute C1 all damage/atom
velocity all ramp vx -10.0 10.0 x ${myxmin} ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 ${myxmax} units box
velocity all ramp vx -10.0 10.0 x 0 0.019750000000000000194 units box
variable mystep equal 0.8*sqrt((2.0*${mydensity})/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(${myc}/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/$h)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/0.00050000000000000001041)*${myvolume}))
variable mystep equal 0.8*sqrt((2.0*2440)/(512*(5.4324887242033602757e+22/0.00050000000000000001041)*1.2500000000000000779e-10))
timestep ${mystep}
timestep 2.1193149239622597698e-08
thermo 20
run 100
Peridynamic bonds:
total # of bonds = 3457032
bonds/atom = 108.032
Memory usage per processor = 54.0347 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 2.0134233e+27 0 0 1.3342785e+09 2.4509971e+14 3.6292128e-06
20 1.7695805e+27 1.6163291e+08 0 1.3343188e+09 2.1541601e+14 3.6292128e-06
40 1.3041477e+27 4.6848143e+08 0 1.332729e+09 1.5875756e+14 3.6292128e-06
60 9.8975313e+26 5.7284448e+08 0 1.2287455e+09 1.2048543e+14 3.6292128e-06
80 9.3888573e+26 4.0928092e+08 0 1.0314725e+09 1.1429321e+14 3.6292128e-06
100 8.3930314e+26 3.8522361e+08 0 9.4142265e+08 1.0217075e+14 3.6292128e-06
Loop time of 6.30757 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 5.98077 (94.8189)
Neigh time (%) = 0 (0)
Comm time (%) = 0.299014 (4.74056)
Outpt time (%) = 0.000436008 (0.00691246)
Other time (%) = 0.0273517 (0.433634)
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5125 ave 5125 max 5125 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.6861e+06 ave 1.77502e+06 max 1.60625e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 3.37221e+06 ave 3.41832e+06 max 3.3261e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 13488836
Ave neighs/atom = 421.526
Neighbor list builds = 0
Dangerous builds = 0

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bench/POTENTIALS/log.26Jun12.protein.1
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LAMMPS (29 Jun 2012)
# Rhodopsin model
units real
neighbor 2.0 bin
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248831
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.025142
estimated relative force accuracy = 7.57143e-05
using double precision FFTs
brick FFT buffer size/proc = 41070 25600 12321
Memory usage per processor = 139.274 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 100 ----- CPU = 36.1778 (sec) ----------------
TotEng = -25290.7641 KinEng = 21592.0080 Temp = 301.0920
PotEng = -46882.7721 E_bond = 2567.9806 E_angle = 10781.9408
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
E_coul = 206654.9996 E_long = -270400.7390 Press = 6.9875
Volume = 308133.9900
Loop time of 36.1779 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 25.7884 (71.2822)
Bond time (%) = 1.2794 (3.53643)
Kspce time (%) = 3.29168 (9.0986)
Neigh time (%) = 4.43537 (12.2599)
Comm time (%) = 0.0717564 (0.198343)
Outpt time (%) = 0.000114918 (0.000317646)
Other time (%) = 1.31117 (3.62423)
FFT time (% of Kspce) = 0.27822 (8.45222)
FFT Gflps 3d (1d only) = 1.86794 3.25864
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

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bench/POTENTIALS/log.26Jun12.protein.4
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LAMMPS (29 Jun 2012)
# Rhodopsin model
units real
neighbor 2.0 bin
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.protein
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
1617 = # of size 2 clusters
3633 = # of size 3 clusters
747 = # of size 4 clusters
4233 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248831
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.025142
estimated relative force accuracy = 7.57143e-05
using double precision FFTs
brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 54.5952 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 100 ----- CPU = 9.8819 (sec) ----------------
TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
Volume = 308133.9900
Loop time of 9.88193 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 6.69935 (67.794)
Bond time (%) = 0.326266 (3.30164)
Kspce time (%) = 1.20454 (12.1893)
Neigh time (%) = 1.14156 (11.552)
Comm time (%) = 0.0931967 (0.943103)
Outpt time (%) = 7.80225e-05 (0.000789547)
Other time (%) = 0.416932 (4.21914)
FFT time (% of Kspce) = 0.0984144 (8.17028)
FFT Gflps 3d (1d only) = 5.28071 12.3682
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 22733.5 ave 22769 max 22693 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0

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bench/POTENTIALS/log.26Jun12.reax.1
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LAMMPS (30 Jun 2012)
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
1 by 1 by 1 MPI processor grid
16240 atoms
velocity all create 300.0 9999
pair_style reax
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Memory usage per processor = 115.943 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.1 22329.472 -29840.021 5669.6761 -1601622.5
10 297.06023 14379.312 -1616004.6 22568.484 -23569.801 8334.8479 -1601625.3
20 280.26351 13566.26 -1615190.8 19620.298 -9954.808 11866.836 -1601624.5
30 263.50831 12755.218 -1614379.4 13439.231 6176.3474 14246.248 -1601624.2
40 258.87863 12531.117 -1614157.3 5267.3955 19729.505 14332.761 -1601626.1
50 261.68221 12666.825 -1614296.2 -3026.4359 27591.526 12071.625 -1601629.4
60 258.41413 12508.633 -1614143.1 -9016.9098 29528.914 8797.9695 -1601634.5
70 247.72913 11991.421 -1613629.7 -11365.463 26152.599 5655.2121 -1601638.3
80 244.65886 11842.804 -1613485.5 -10507.562 17663.127 2699.8676 -1601642.7
90 259.7204 12571.863 -1614216 -7181.0746 5021.2072 246.67513 -1601644.1
100 283.95637 13745.014 -1615390.6 -2652.4067 -9521.5146 -1343.3691 -1601645.6
Loop time of 460.91 on 1 procs for 100 steps with 16240 atoms
Pair time (%) = 460.833 (99.9831)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0296826 (0.00644)
Outpt time (%) = 0.00197053 (0.00042753)
Other time (%) = 0.0460784 (0.00999727)
Nlocal: 16240 ave 16240 max 16240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 32428 ave 32428 max 32428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.69975e+06 ave 6.69975e+06 max 6.69975e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6699752
Ave neighs/atom = 412.546
Neighbor list builds = 0
Dangerous builds = 0

61
bench/POTENTIALS/log.26Jun12.reax.4
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LAMMPS (30 Jun 2012)
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
58 atoms
#replicate 7 8 10
replicate 7 8 5
orthogonal box = (0 0 0) to (66.4375 75.9285 34.9562)
2 by 2 by 1 MPI processor grid
16240 atoms
velocity all create 300.0 9999
pair_style reax
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 2 all nve
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Memory usage per processor = 33.2558 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 14521.612 -1616144.1 22329.472 -29840.021 5669.6761 -1601622.5
10 297.06023 14379.312 -1616004.6 22568.484 -23569.801 8334.8479 -1601625.3
20 280.26351 13566.26 -1615190.8 19620.298 -9954.8085 11866.836 -1601624.5
30 263.50831 12755.218 -1614379.5 13439.233 6176.348 14246.247 -1601624.2
40 258.87863 12531.117 -1614157.3 5267.387 19729.498 14332.758 -1601626.2
50 261.68221 12666.825 -1614296.2 -3026.4394 27591.523 12071.623 -1601629.4
60 258.41413 12508.633 -1614143.1 -9016.9099 29528.913 8797.9693 -1601634.5
70 247.72913 11991.421 -1613629.7 -11365.462 26152.598 5655.2121 -1601638.3
80 244.65886 11842.804 -1613485.5 -10507.561 17663.127 2699.8679 -1601642.7
90 259.7204 12571.863 -1614216 -7181.0717 5021.2084 246.67603 -1601644.1
100 283.95637 13745.014 -1615390.6 -2652.405 -9521.5134 -1343.3681 -1601645.6
Loop time of 122.083 on 4 procs for 100 steps with 16240 atoms
Pair time (%) = 120.603 (98.7873)
Neigh time (%) = 0 (0)
Comm time (%) = 1.46018 (1.19605)
Outpt time (%) = 0.00101995 (0.000835457)
Other time (%) = 0.0192486 (0.0157668)
Nlocal: 4060 ave 4080 max 4040 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 14972 ave 14992 max 14952 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.8135e+06 ave 1.82186e+06 max 1.80514e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 7253988
Ave neighs/atom = 446.674
Neighbor list builds = 0
Dangerous builds = 0

61
bench/POTENTIALS/log.26Jun12.reaxc.1
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LAMMPS (30 Jun 2012)
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
1 by 1 by 1 MPI processor grid
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 1 by 1 MPI processor grid
32480 atoms
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Memory usage per processor = 290.813 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22822.641 -29350.75 6269.9587 -3203096.6
10 297.46826 28799.011 -3231900.7 22429.993 -23451.647 8632.9947 -3203101.7
20 281.19686 27223.717 -3230326.1 18750.967 -10261.149 11753.374 -3203102.4
30 264.44551 25601.956 -3228706.6 11945.12 5439.3337 13773.491 -3203104.6
40 259.21485 25095.556 -3228205.6 3632.1983 18743.212 13728.05 -3203110.1
50 261.28805 25296.271 -3228414.6 -4398.2677 26482.197 11507.677 -3203118.3
60 257.70779 24949.652 -3228077.4 -9603.7544 28618.606 8576.0388 -3203127.8
70 247.45488 23957.03 -3227092.6 -11047.563 25561.983 5786.1739 -3203135.6
80 245.01202 23720.528 -3226863.5 -9338.6904 17459.913 3182.5255 -3203143
90 260.13701 25184.834 -3228330.7 -5428.6211 5185.3492 974.10222 -3203145.8
100 283.73163 27469.118 -3230613.8 -830.3439 -9143.6599 -640.66249 -3203144.7
Loop time of 354.457 on 1 procs for 100 steps with 32480 atoms
Pair time (%) = 256.137 (72.2618)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0505295 (0.0142555)
Outpt time (%) = 0.0035758 (0.00100881)
Other time (%) = 98.266 (27.7229)
Nlocal: 32480 ave 32480 max 32480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45128 ave 45128 max 45128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.27781e+07 ave 1.27781e+07 max 1.27781e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12778082
Ave neighs/atom = 393.414
Neighbor list builds = 0
Dangerous builds = 0

61
bench/POTENTIALS/log.26Jun12.reaxc.4
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LAMMPS (30 Jun 2012)
# ReaxFF benchmark: simulation of PETN crystal, replicated unit cell
units real
atom_style charge
read_data data.reax
orthogonal box = (0 0 0) to (9.49107 9.49107 6.99123)
2 by 2 by 1 MPI processor grid
58 atoms
replicate 7 8 10
orthogonal box = (0 0 0) to (66.4375 75.9285 69.9123)
1 by 2 by 2 MPI processor grid
32480 atoms
velocity all create 300.0 9999
pair_style reax/c NULL
pair_coeff * * ffield.reax 1 2 3 4
timestep 0.1
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp ke pe pxx pyy pzz etotal
run 100
Memory usage per processor = 93.1709 Mbytes
Step Temp KinEng PotEng Pxx Pyy Pzz TotEng
0 300 29044.119 -3232140.8 22822.641 -29350.75 6269.9587 -3203096.6
10 297.46826 28799.012 -3231900.7 22429.987 -23451.646 8633.0049 -3203101.7
20 281.19693 27223.723 -3230326.1 18751.296 -10260.898 11753.565 -3203102.3
30 264.44558 25601.963 -3228706.6 11944.966 5439.2052 13773.246 -3203104.6
40 259.21484 25095.555 -3228205.6 3631.8687 18742.959 13727.737 -3203110.1
50 261.28801 25296.266 -3228414.6 -4398.3911 26482.009 11507.488 -3203118.3
60 257.70778 24949.652 -3228077.4 -9603.7946 28618.812 8576.0854 -3203127.8
70 247.45493 23957.034 -3227092.6 -11047.674 25561.879 5786.0486 -3203135.6
80 245.01206 23720.532 -3226863.5 -9338.5522 17460.083 3182.5874 -3203143
90 260.13702 25184.835 -3228330.6 -5427.889 5185.8606 974.51576 -3203145.8
100 283.73164 27469.118 -3230613.8 -830.13211 -9143.6107 -640.56137 -3203144.7
Loop time of 111.882 on 4 procs for 100 steps with 32480 atoms
Pair time (%) = 78.4446 (70.1135)
Neigh time (%) = 0 (0)
Comm time (%) = 2.94055 (2.62825)
Outpt time (%) = 0.00161415 (0.00144272)
Other time (%) = 30.4955 (27.2568)
Nlocal: 8120 ave 8120 max 8120 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 21992 ave 21992 max 21992 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.48274e+06 ave 3.48274e+06 max 3.48274e+06 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13930976
Ave neighs/atom = 428.909
Neighbor list builds = 0
Dangerous builds = 0

63
bench/POTENTIALS/log.26Jun12.rebo.1
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LAMMPS (29 Jun 2012)
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 1 MPI processor grid
60 atoms
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Memory usage per processor = 33.1619 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 161.83836 -137855.93 0 -137173.14 14222.57
20 212.11275 -138067.85 0 -137172.96 -26955.685
30 118.6053 -137669.82 0 -137169.43 -14705.957
40 192.52805 -137982.54 0 -137170.28 -6869.6528
50 121.53391 -137682.34 0 -137169.59 4940.722
60 202.88352 -138028.88 0 -137172.93 15911.927
70 195.08113 -137996.06 0 -137173.03 -12031.849
80 230.84583 -138148.96 0 -137175.04 -8565.0012
90 166.26203 -137874.27 0 -137172.83 -31552.577
100 191.03117 -137977.88 0 -137171.94 -1153.5542
Loop time of 10.3821 on 1 procs for 100 steps with 32640 atoms
Pair time (%) = 8.10849 (78.1005)
Neigh time (%) = 2.15209 (20.7288)
Comm time (%) = 0.0356007 (0.342904)
Outpt time (%) = 0.00113368 (0.0109195)
Other time (%) = 0.0848057 (0.816844)
Nlocal: 32640 ave 32640 max 32640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26746 ave 26746 max 26746 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: 4.87269e+06 ave 4.87269e+06 max 4.87269e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4872694
Ave neighs/atom = 149.286
Neighbor list builds = 8
Dangerous builds = 0

63
bench/POTENTIALS/log.26Jun12.rebo.4
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LAMMPS (29 Jun 2012)
# REBO polyethelene benchmark
units metal
atom_style atomic
read_data data.rebo
orthogonal box = (-2.1 -2.1 0) to (2.1 2.1 25.579)
1 by 1 by 4 MPI processor grid
60 atoms
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
neighbor 0.5 bin
neigh_modify delay 5 every 1
pair_style rebo
pair_coeff * * CH.airebo C H
velocity all create 300.0 761341
fix 1 all nve
timestep 0.0005
thermo 10
run 100
Memory usage per processor = 10.6691 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -138442.48 0 -137176.8 2464.5258
10 161.83836 -137855.93 0 -137173.14 14222.57
20 212.11275 -138067.85 0 -137172.96 -26955.685
30 118.6053 -137669.82 0 -137169.43 -14705.957
40 192.52805 -137982.54 0 -137170.28 -6869.6528
50 121.53391 -137682.34 0 -137169.59 4940.722
60 202.88352 -138028.88 0 -137172.93 15911.927
70 195.08113 -137996.06 0 -137173.03 -12031.849
80 230.84583 -138148.96 0 -137175.04 -8565.0012
90 166.26203 -137874.27 0 -137172.83 -31552.577
100 191.03117 -137977.88 0 -137171.94 -1153.5542
Loop time of 2.87679 on 4 procs for 100 steps with 32640 atoms
Pair time (%) = 2.04788 (71.1861)
Neigh time (%) = 0.68543 (23.8262)
Comm time (%) = 0.116537 (4.05095)
Outpt time (%) = 0.000668228 (0.0232282)
Other time (%) = 0.0262787 (0.913474)
Nlocal: 8160 ave 8166 max 8154 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 11696.2 ave 11703 max 11691 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.21817e+06 ave 1.22026e+06 max 1.21648e+06 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 4872694
Ave neighs/atom = 149.286
Neighbor list builds = 8
Dangerous builds = 0

106
bench/POTENTIALS/log.26Jun12.spce.1
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@ -1,106 +0,0 @@
LAMMPS (29 Jun 2012)
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
1 by 1 by 1 MPI processor grid
4500 atoms
3000 bonds
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 1 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
G vector (1/distance) = 0.268811
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0234088
estimated relative force accuracy = 7.0495e-05
using double precision FFTs
brick FFT buffer size/proc = 91977 55296 35604
Memory usage per processor = 102.176 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 -911.71286
50 256.42601 -138687.16 0 -120343.35 -931.69582
100 265.62923 -137828.91 0 -118826.74 -345.32241
Loop time of 31.5847 on 1 procs for 100 steps with 36000 atoms
Pair time (%) = 23.6339 (74.827)
Bond time (%) = 0.000171185 (0.000541985)
Kspce time (%) = 4.19505 (13.2819)
Neigh time (%) = 3.13994 (9.94134)
Comm time (%) = 0.0808184 (0.255878)
Outpt time (%) = 0.000238895 (0.000756364)
Other time (%) = 0.534611 (1.69263)
FFT time (% of Kspce) = 0.933042 (22.2415)
FFT Gflps 3d (1d only) = 1.29439 2.74331
Nlocal: 36000 ave 36000 max 36000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56916 ave 56916 max 56916 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.24624e+07 ave 1.24624e+07 max 1.24624e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12462366
Ave neighs/atom = 346.177
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 8

106
bench/POTENTIALS/log.26Jun12.spce.4
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@ -1,106 +0,0 @@
LAMMPS (29 Jun 2012)
# SPC/E water box benchmark
units real
atom_style full
read_data data.spce
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
2 by 2 by 1 MPI processor grid
4500 atoms
3000 bonds
1500 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
replicate 2 4 1
orthogonal box = (0.02645 0.02645 0.02641) to (71.0392 142.052 35.4736)
1 by 4 by 1 MPI processor grid
36000 atoms
24000 bonds
12000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long 9.8 9.8
kspace_style pppm 1.0e-4
pair_coeff 1 1 0.15535 3.166
pair_coeff * 2 0.0000 0.0000
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
neighbor 2.0 bin
neigh_modify every 1 delay 10 check yes
fix 1 all shake 0.0001 20 0 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
12000 = # of frozen angles
fix 2 all nvt temp 300.0 300.0 100.0
velocity all create 300 432567 dist uniform
timestep 2.0
thermo_style one
thermo 50
run 100
PPPM initialization ...
G vector (1/distance) = 0.268811
grid = 36 64 24
stencil order = 5
estimated absolute RMS force accuracy = 0.0234088
estimated relative force accuracy = 7.0495e-05
using double precision FFTs
brick FFT buffer size/proc = 27993 13824 11997
Memory usage per processor = 32.8945 Mbytes
Step Temp E_pair E_mol TotEng Press
0 300 -133281.51 0 -111820.57 -911.71286
50 256.42601 -138687.16 0 -120343.35 -931.69582
100 265.62923 -137828.91 0 -118826.74 -345.32242
Loop time of 9.11845 on 4 procs for 100 steps with 36000 atoms
Pair time (%) = 6.24637 (68.5026)
Bond time (%) = 0.000142336 (0.00156097)
Kspce time (%) = 1.64891 (18.0832)
Neigh time (%) = 0.828169 (9.08235)
Comm time (%) = 0.158835 (1.74191)
Outpt time (%) = 0.00013268 (0.00145507)
Other time (%) = 0.235892 (2.58697)
FFT time (% of Kspce) = 0.253972 (15.4024)
FFT Gflps 3d (1d only) = 4.75531 10.9225
Nlocal: 9000 ave 9004 max 8992 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 24129.2 ave 24154 max 24097 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 3.11559e+06 ave 3.11731e+06 max 3.11379e+06 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 12462366
Ave neighs/atom = 346.177
Ave special neighs/atom = 2
Neighbor list builds = 9
Dangerous builds = 8

54
bench/POTENTIALS/log.26Jun12.sw.1
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@ -1,54 +0,0 @@
LAMMPS (29 Jun 2012)
# bulk Si via Stillinger-Weber
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style sw
pair_coeff * * Si.sw Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Memory usage per processor = 12.3488 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 10.501 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 10.3268 (98.3417)
Neigh time (%) = 0.0839791 (0.799726)
Comm time (%) = 0.015074 (0.143549)
Outpt time (%) = 0.00010705 (0.00101943)
Other time (%) = 0.0749753 (0.713983)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12495 ave 12495 max 12495 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: 894818 ave 894818 max 894818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Neighbor list builds = 2
Dangerous builds = 0

54
bench/POTENTIALS/log.26Jun12.sw.4
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@ -1,54 +0,0 @@
LAMMPS (29 Jun 2012)
# bulk Si via Stillinger-Weber
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style sw
pair_coeff * * Si.sw Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Memory usage per processor = 4.12361 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -138771.2 0 -134635 6866.6499
100 508.80533 -136736.12 0 -134631.6 6361.7858
Loop time of 2.74532 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 2.62235 (95.5209)
Neigh time (%) = 0.0214692 (0.782031)
Comm time (%) = 0.0812815 (2.96073)
Outpt time (%) = 4.88758e-05 (0.00178033)
Other time (%) = 0.0201654 (0.734538)
Nlocal: 8000 ave 8015 max 7978 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 4995 ave 5017 max 4980 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 223704 ave 224108 max 223131 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 894818
Ave neighs/atom = 27.9631
Neighbor list builds = 2
Dangerous builds = 0

54
bench/POTENTIALS/log.26Jun12.tersoff.1
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@ -1,54 +0,0 @@
LAMMPS (29 Jun 2012)
# bulk Si via Tersoff
units metal
atom_style atomic
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 20 0 20 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (108.62 108.62 54.31)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
pair_style tersoff
pair_coeff * * Si.tersoff Si
mass 1 28.06
velocity all create 1000.0 376847 loop geom
neighbor 1.0 bin
neigh_modify delay 5 every 1
fix 1 all nve
timestep 0.001
run 100
Memory usage per processor = 10.9293 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1000 -148173.19 0 -144036.99 7019.4434
100 430.57813 -145815.61 0 -144034.65 -14550.734
Loop time of 11.972 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 11.8132 (98.6733)
Neigh time (%) = 0.07127 (0.595304)
Comm time (%) = 0.0146098 (0.122033)
Outpt time (%) = 0.000103951 (0.000868278)
Other time (%) = 0.072855 (0.608543)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11537 ave 11537 max 11537 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: 530500 ave 530500 max 530500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 530500
Ave neighs/atom = 16.5781
Neighbor list builds = 2
Dangerous builds = 0

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