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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2016-02-15 18:06:11 +00:00
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examples/comb/log.15Feb16.comb.Cu.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 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 = 3 3 3
Memory usage per processor = 6.4805 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.244377 on 1 procs for 10 steps with 256 atoms
Performance: 0.707 ns/day, 33.941 hours/ns, 40.920 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24393 | 0.24393 | 0.24393 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.09
Output | 0.00011015 | 0.00011015 | 0.00011015 | 0.0 | 0.05
Modify | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.02
Other | | 5.984e-05 | | | 0.02
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 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: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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examples/comb/log.15Feb16.comb.Cu.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 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 = 3 3 3
Memory usage per processor = 6.35565 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.0647703 on 4 procs for 10 steps with 256 atoms
Performance: 2.668 ns/day, 8.996 hours/ns, 154.392 timesteps/s
100.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.063009 | 0.063389 | 0.06358 | 0.1 | 97.87
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075269 | 0.00095391 | 0.001322 | 0.7 | 1.47
Output | 0.00029755 | 0.00031668 | 0.00032735 | 0.1 | 0.49
Modify | 1.5736e-05 | 1.7047e-05 | 1.8835e-05 | 0.0 | 0.03
Other | | 9.34e-05 | | | 0.14
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1296 atoms
mass 1 63.54
group type1 type 1
864 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
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.39852 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
Loop time of 0.690546 on 1 procs for 2 steps with 1296 atoms
Performance: 0.050 ns/day, 479.546 hours/ns, 2.896 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27005 | 0.27005 | 0.27005 | 0.0 | 39.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00010324 | 0.00010324 | 0.00010324 | 0.0 | 0.01
Output | 4.9114e-05 | 4.9114e-05 | 4.9114e-05 | 0.0 | 0.01
Modify | 0.4203 | 0.4203 | 0.4203 | 0.0 | 60.86
Other | | 4.387e-05 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds not checked
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 5 5 5
Memory usage per processor = 8.27781 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
Loop time of 29.9485 on 1 procs for 24 steps with 1296 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.04653512838 -3.96876869389 -3.96876869369
Force two-norm initial, final = 32801.4 117.257
Force max component initial, final = 18937.9 67.6917
Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
Iterations, force evaluations = 24 53
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6428 | 7.6428 | 7.6428 | 0.0 | 25.52
Neigh | 0.072307 | 0.072307 | 0.072307 | 0.0 | 0.24
Comm | 0.0033123 | 0.0033123 | 0.0033123 | 0.0 | 0.01
Output | 0.00073075 | 0.00073075 | 0.00073075 | 0.0 | 0.00
Modify | 22.217 | 22.217 | 22.217 | 0.0 | 74.18
Other | | 0.01276 | | | 0.04
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 3
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.65281 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
Loop time of 0.283693 on 1 procs for 1 steps with 1296 atoms
Performance: 0.061 ns/day, 394.018 hours/ns, 3.525 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14656 | 0.14656 | 0.14656 | 0.0 | 51.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 5.8889e-05 | 5.8889e-05 | 5.8889e-05 | 0.0 | 0.02
Output | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01
Modify | 0.13702 | 0.13702 | 0.13702 | 0.0 | 48.30
Other | | 2.337e-05 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom NULL pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
run 10
Memory usage per processor = 7.02781 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
Loop time of 1.61281 on 1 procs for 10 steps with 1296 atoms
Performance: 0.107 ns/day, 224.001 hours/ns, 6.200 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6096 | 1.6096 | 1.6096 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.03
Output | 0.0023828 | 0.0023828 | 0.0023828 | 0.0 | 0.15
Modify | 0.00019932 | 0.00019932 | 0.00019932 | 0.0 | 0.01
Other | | 0.0001204 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 7.77781 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
Loop time of 1.56349 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 217.151 hours/ns, 6.396 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5603 | 1.5603 | 1.5603 | 0.0 | 99.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0005424 | 0.0005424 | 0.0005424 | 0.0 | 0.03
Output | 0.0023627 | 0.0023627 | 0.0023627 | 0.0 | 0.15
Modify | 0.00018978 | 0.00018978 | 0.00018978 | 0.0 | 0.01
Other | | 0.0001137 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 8.54308 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
Loop time of 1.55801 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 216.390 hours/ns, 6.418 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.555 | 1.555 | 1.555 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052738 | 0.00052738 | 0.00052738 | 0.0 | 0.03
Output | 0.0022299 | 0.0022299 | 0.0022299 | 0.0 | 0.14
Modify | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.01
Other | | 0.0001023 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 9.29308 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
Loop time of 1.56044 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 216.728 hours/ns, 6.408 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5574 | 1.5574 | 1.5574 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00051975 | 0.00051975 | 0.00051975 | 0.0 | 0.03
Output | 0.0022559 | 0.0022559 | 0.0022559 | 0.0 | 0.14
Modify | 0.00019503 | 0.00019503 | 0.00019503 | 0.0 | 0.01
Other | | 0.0001116 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 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: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:44

409
examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
1296 atoms
mass 1 63.54
group type1 type 1
864 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
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.28094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
Loop time of 0.174112 on 4 procs for 2 steps with 1296 atoms
Performance: 0.198 ns/day, 120.911 hours/ns, 11.487 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.067018 | 0.067376 | 0.067552 | 0.1 | 38.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030375 | 0.00049108 | 0.00085974 | 1.0 | 0.28
Output | 7.8678e-05 | 8.1301e-05 | 8.7023e-05 | 0.0 | 0.05
Modify | 0.10611 | 0.10612 | 0.10613 | 0.0 | 60.95
Other | | 4.166e-05 | | | 0.02
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds not checked
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 5 5 5
Memory usage per processor = 8.15594 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
Loop time of 7.73864 on 4 procs for 24 steps with 1296 atoms
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.04653512838 -3.96876869389 -3.96876869369
Force two-norm initial, final = 32801.4 117.257
Force max component initial, final = 18937.9 67.6917
Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
Iterations, force evaluations = 24 53
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8982 | 1.9386 | 1.9643 | 1.8 | 25.05
Neigh | 0.017612 | 0.017903 | 0.018068 | 0.1 | 0.23
Comm | 0.011921 | 0.037696 | 0.078263 | 13.0 | 0.49
Output | 0.00091124 | 0.00094914 | 0.0010424 | 0.2 | 0.01
Modify | 5.736 | 5.7361 | 5.7362 | 0.0 | 74.12
Other | | 0.007425 | | | 0.10
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 3
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.53094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
Loop time of 0.0716895 on 4 procs for 1 steps with 1296 atoms
Performance: 0.241 ns/day, 99.569 hours/ns, 13.949 timesteps/s
100.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035934 | 0.036807 | 0.03732 | 0.3 | 51.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00013494 | 0.00064868 | 0.0015209 | 2.1 | 0.90
Output | 3.6955e-05 | 3.8445e-05 | 4.1962e-05 | 0.0 | 0.05
Modify | 0.034179 | 0.034181 | 0.034182 | 0.0 | 47.68
Other | | 1.472e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom NULL pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
run 10
Memory usage per processor = 6.90594 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
Loop time of 0.40881 on 4 procs for 10 steps with 1296 atoms
Performance: 0.423 ns/day, 56.779 hours/ns, 24.461 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38885 | 0.39776 | 0.40386 | 1.0 | 97.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0020289 | 0.0081917 | 0.017143 | 7.1 | 2.00
Output | 0.0026636 | 0.0027153 | 0.0027769 | 0.1 | 0.66
Modify | 5.6982e-05 | 5.9664e-05 | 6.628e-05 | 0.0 | 0.01
Other | | 8.208e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 7.65594 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
Loop time of 0.407868 on 4 procs for 10 steps with 1296 atoms
Performance: 0.424 ns/day, 56.648 hours/ns, 24.518 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38874 | 0.39706 | 0.40377 | 0.9 | 97.35
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.001327 | 0.0080245 | 0.016345 | 6.6 | 1.97
Output | 0.0026383 | 0.0026469 | 0.0026655 | 0.0 | 0.65
Modify | 5.2929e-05 | 5.6744e-05 | 5.9128e-05 | 0.0 | 0.01
Other | | 7.844e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 8.42123 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
Loop time of 0.408682 on 4 procs for 10 steps with 1296 atoms
Performance: 0.423 ns/day, 56.761 hours/ns, 24.469 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38891 | 0.39738 | 0.40388 | 1.0 | 97.23
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019937 | 0.0084969 | 0.016969 | 6.6 | 2.08
Output | 0.0026531 | 0.0026709 | 0.0026915 | 0.0 | 0.65
Modify | 5.1975e-05 | 5.6446e-05 | 5.9366e-05 | 0.0 | 0.01
Other | | 7.963e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 9.17123 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
Loop time of 0.411159 on 4 procs for 10 steps with 1296 atoms
Performance: 0.420 ns/day, 57.105 hours/ns, 24.322 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3889 | 0.39826 | 0.40584 | 1.1 | 96.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0024002 | 0.010008 | 0.019374 | 6.8 | 2.43
Output | 0.0027368 | 0.0027526 | 0.0027771 | 0.0 | 0.67
Modify | 5.6028e-05 | 5.8174e-05 | 6.0081e-05 | 0.0 | 0.01
Other | | 8.059e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 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: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:11

235
examples/comb/log.15Feb16.comb.HfO2.g++.1 Normal file
View File

@ -0,0 +1,235 @@
LAMMPS (15 Feb 2016)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 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
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 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 = 5 5 5
Memory usage per processor = 6.13908 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.169538 on 1 procs for 1 steps with 1500 atoms
Performance: 0.102 ns/day, 235.469 hours/ns, 5.898 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16939 | 0.16939 | 0.16939 | 0.0 | 99.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.04
Output | 2.9802e-05 | 2.9802e-05 | 2.9802e-05 | 0.0 | 0.02
Modify | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.02
Other | | 1.717e-05 | | | 0.01
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 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: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 6.76408 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
Loop time of 1.16742 on 1 procs for 5 steps with 1500 atoms
Performance: 0.074 ns/day, 324.284 hours/ns, 4.283 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85832 | 0.85832 | 0.85832 | 0.0 | 73.52
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00033593 | 0.00033593 | 0.00033593 | 0.0 | 0.03
Output | 0.00015116 | 0.00015116 | 0.00015116 | 0.0 | 0.01
Modify | 0.30852 | 0.30852 | 0.30852 | 0.0 | 26.43
Other | | 9.751e-05 | | | 0.01
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 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: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 5 5 5
Memory usage per processor = 7.88908 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.64676 on 1 procs for 1 steps with 1500 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0414727016 -10.0414727016 -10.0419532985
Force two-norm initial, final = 2625.99 2625.45
Force max component initial, final = 1915.33 1916.61
Final line search alpha, max atom move = 1.04421e-07 0.000200134
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34047 | 0.34047 | 0.34047 | 0.0 | 52.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00012827 | 0.00012827 | 0.00012827 | 0.0 | 0.02
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.30579 | 0.30579 | 0.30579 | 0.0 | 47.28
Other | | 0.0003626 | | | 0.06
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 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: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 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 = 5 5 5
Memory usage per processor = 6.76408 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 2.31943 on 1 procs for 10 steps with 1500 atoms
Performance: 0.075 ns/day, 322.143 hours/ns, 4.311 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7064 | 1.7064 | 1.7064 | 0.0 | 73.57
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00066495 | 0.00066495 | 0.00066495 | 0.0 | 0.03
Output | 0.00035143 | 0.00035143 | 0.00035143 | 0.0 | 0.02
Modify | 0.61178 | 0.61178 | 0.61178 | 0.0 | 26.38
Other | | 0.0002165 | | | 0.01
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 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: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:10

235
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LAMMPS (15 Feb 2016)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 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
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 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 = 5 5 5
Memory usage per processor = 5.96686 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0429993 on 4 procs for 1 steps with 1500 atoms
Performance: 0.402 ns/day, 59.721 hours/ns, 23.256 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042339 | 0.042613 | 0.042762 | 0.1 | 99.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001421 | 0.00029129 | 0.00056505 | 1.0 | 0.68
Output | 3.7909e-05 | 4.0174e-05 | 4.6015e-05 | 0.1 | 0.09
Modify | 2.4796e-05 | 2.4796e-05 | 2.4796e-05 | 0.0 | 0.06
Other | | 3.028e-05 | | | 0.07
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 6.59186 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
Loop time of 0.290755 on 4 procs for 5 steps with 1500 atoms
Performance: 0.297 ns/day, 80.765 hours/ns, 17.197 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21107 | 0.21252 | 0.21354 | 0.2 | 73.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075912 | 0.001812 | 0.0032141 | 2.1 | 0.62
Output | 0.00020814 | 0.00021452 | 0.00023079 | 0.1 | 0.07
Modify | 0.07608 | 0.076133 | 0.076177 | 0.0 | 26.18
Other | | 7.701e-05 | | | 0.03
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 5 5 5
Memory usage per processor = 7.71686 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.161507 on 4 procs for 1 steps with 1500 atoms
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0414727016 -10.0414727016 -10.0419532985
Force two-norm initial, final = 2625.99 2625.45
Force max component initial, final = 1915.33 1916.61
Final line search alpha, max atom move = 1.04421e-07 0.000200134
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.084314 | 0.085016 | 0.085468 | 0.2 | 52.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030208 | 0.00076222 | 0.0014489 | 1.7 | 0.47
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.075456 | 0.075471 | 0.07548 | 0.0 | 46.73
Other | | 0.0002575 | | | 0.16
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 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 = 5 5 5
Memory usage per processor = 6.59186 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.581787 on 4 procs for 10 steps with 1500 atoms
Performance: 0.297 ns/day, 80.804 hours/ns, 17.188 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42265 | 0.42528 | 0.42704 | 0.2 | 73.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015607 | 0.0033906 | 0.0059152 | 2.7 | 0.58
Output | 0.00046325 | 0.00046599 | 0.00046873 | 0.0 | 0.08
Modify | 0.1524 | 0.15252 | 0.1526 | 0.0 | 26.22
Other | | 0.0001305 | | | 0.02
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 4 4 4
Memory usage per processor = 7.60455 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295965 -4.6297255 -4.6297255 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
5 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.206087 on 1 procs for 5 steps with 512 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550325 -4.62972550325
Force two-norm initial, final = 5.86582 2.4862e-12
Force max component initial, final = 3.38663 2.10283e-12
Final line search alpha, max atom move = 1 2.10283e-12
Iterations, force evaluations = 5 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2046 | 0.2046 | 0.2046 | 0.0 | 99.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001161 | | | 0.56
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 5.97955 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
5 1 -4.6295965 -4.6297255 -4.6297255 0
6 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.018579 on 1 procs for 1 steps with 512 atoms
Performance: 0.930 ns/day, 25.804 hours/ns, 53.824 timesteps/s
102.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.018534 | 0.018534 | 0.018534 | 0.0 | 99.76
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.15
Output | 9.0599e-06 | 9.0599e-06 | 9.0599e-06 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.868e-06 | | | 0.04
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom NULL pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
run 10
Memory usage per processor = 6.72955 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06
7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06
8 21.72835 21.727916 21.727916 0 0 0 146204.17 77325.788 77325.788 3.5125695e-06 -1.9487795e-06 5.2972201e-06
9 21.728568 21.727916 21.727916 0 0 0 292407.63 154648.04 154648.04 5.6408383e-06 -2.4472325e-06 6.3046987e-06
10 21.728785 21.727916 21.727916 0 0 0 438610.37 231966.74 231966.74 5.5704989e-06 -1.8785254e-06 -1.4083956e-06
11 21.729002 21.727916 21.727916 0 0 0 584812.4 309281.91 309281.91 -1.2913749e-05 2.0544275e-06 7.547976e-06
12 21.729219 21.727916 21.727916 0 0 0 731013.71 386593.54 386593.54 6.0987798e-06 -2.0790709e-06 7.8755963e-06
13 21.729437 21.727916 21.727916 0 0 0 877214.3 463901.63 463901.63 5.2296156e-06 -2.2013505e-06 2.6034199e-06
14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06
15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06
16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06
Loop time of 0.203248 on 1 procs for 10 steps with 512 atoms
Performance: 0.850 ns/day, 28.229 hours/ns, 49.201 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20165 | 0.20165 | 0.20165 | 0.0 | 99.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.14
Output | 0.0011773 | 0.0011773 | 0.0011773 | 0.0 | 0.58
Modify | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04
Other | | 5.889e-05 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 7.47955 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06
17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06
18 21.730089 21.727916 21.72835 0 0 0 1539307.6 850399.75 919275.09 9.5325273e-06 -6.4331187e-07 4.7453557e-06
19 21.730089 21.727916 21.728568 0 0 0 1616602.2 927697.36 1065450.9 1.3298468e-05 -1.8936338e-06 4.6426389e-06
20 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.4 1211626 1.0653147e-05 -1.4284476e-06 6.3390661e-07
21 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 9.0018044e-06 -1.2309518e-06 5.565611e-06
22 21.730089 21.727916 21.729219 0 0 0 1848464.7 1159569 1503974 7.5031694e-06 -2.7028978e-06 5.6324743e-06
23 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.4 1650146.9 4.3439607e-06 -2.4393614e-06 5.5564577e-06
24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06
25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06
26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06
Loop time of 0.206357 on 1 procs for 10 steps with 512 atoms
Performance: 0.837 ns/day, 28.661 hours/ns, 48.460 timesteps/s
100.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20466 | 0.20466 | 0.20466 | 0.0 | 99.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.13
Output | 0.0012765 | 0.0012765 | 0.0012765 | 0.0 | 0.62
Modify | 7.7963e-05 | 7.7963e-05 | 7.7963e-05 | 0.0 | 0.04
Other | | 6.175e-05 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 8.24482 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06
27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06
28 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 4.7258447e-06 -1.3958256e-06 243.66105
29 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 4.7492097e-06 -2.8958095e-06 487.32212
30 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 4.8744538e-06 -2.3110563e-06 730.98324
31 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 4.3760082e-06 -8.3074269e-07 974.64423
32 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 4.7980741e-06 -5.7372478e-07 1218.3053
33 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 4.8822804e-06 -2.3433596e-06 1461.9664
34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275
35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496
Loop time of 0.203569 on 1 procs for 10 steps with 512 atoms
Performance: 0.849 ns/day, 28.273 hours/ns, 49.123 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20196 | 0.20196 | 0.20196 | 0.0 | 99.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00028515 | 0.00028515 | 0.00028515 | 0.0 | 0.14
Output | 0.0011783 | 0.0011783 | 0.0011783 | 0.0 | 0.58
Modify | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.04
Other | | 6.366e-05 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 8.99482 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106
37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106
38 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64727 -0.00013232165 2436.6106
39 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29458 -0.0002652587 2436.6106
40 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.9419 -0.00039565085 2436.6106
41 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58916 -0.00052768104 2436.6106
42 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00065822936 2436.6106
43 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.0007889991 2436.6106
44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106
45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106
46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106
Loop time of 0.204484 on 1 procs for 10 steps with 512 atoms
Performance: 0.845 ns/day, 28.401 hours/ns, 48.904 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20272 | 0.20272 | 0.20272 | 0.0 | 99.14
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
Output | 0.0013256 | 0.0013256 | 0.0013256 | 0.0 | 0.65
Modify | 7.844e-05 | 7.844e-05 | 7.844e-05 | 0.0 | 0.04
Other | | 6.27e-05 | | | 0.03
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:01

331
examples/comb/log.15Feb16.comb.Si.elastic.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 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 = 4 4 4
Memory usage per processor = 7.52233 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295965 -4.6297255 -4.6297255 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0429027 on 4 procs for 3 steps with 512 atoms
99.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550325 -4.62972550325
Force two-norm initial, final = 5.86582 3.9583e-08
Force max component initial, final = 3.38663 2.28585e-08
Final line search alpha, max atom move = 1 2.28585e-08
Iterations, force evaluations = 3 6
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026284 | 0.032657 | 0.041753 | 3.1 | 76.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052333 | 0.0096034 | 0.015953 | 5.7 | 22.38
Output | 3.5048e-05 | 3.6538e-05 | 4.1008e-05 | 0.0 | 0.09
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006061 | | | 1.41
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 5.89733 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.00605559 on 4 procs for 1 steps with 512 atoms
Performance: 2.854 ns/day, 8.411 hours/ns, 165.137 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0037332 | 0.0046489 | 0.00595 | 1.2 | 76.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.2002e-05 | 0.0013711 | 0.0022838 | 2.2 | 22.64
Output | 2.0027e-05 | 2.3484e-05 | 2.5988e-05 | 0.0 | 0.39
Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 1.186e-05 | | | 0.20
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom NULL pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:680)
run 10
Memory usage per processor = 6.64733 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06
5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06
6 21.72835 21.727916 21.727916 0 0 0 146204.21 77325.824 77325.824 2.3636154e-06 -2.6955085e-06 -5.4243912e-06
7 21.728568 21.727916 21.727916 0 0 0 292407.66 154648.07 154648.07 -1.2891214e-06 -2.3607767e-06 -4.2545106e-06
8 21.728785 21.727916 21.727916 0 0 0 438610.41 231966.78 231966.78 -1.7378096e-06 -2.0714741e-06 -3.8921893e-06
9 21.729002 21.727916 21.727916 0 0 0 584812.43 309281.95 309281.95 2.5425006e-06 9.0454362e-06 -7.1598291e-06
10 21.729219 21.727916 21.727916 0 0 0 731013.74 386593.58 386593.58 -1.6897864e-06 -2.6139147e-06 -5.4137742e-06
11 21.729437 21.727916 21.727916 0 0 0 877214.34 463901.66 463901.66 -1.8806784e-06 -1.8704431e-06 -4.8350021e-06
12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06
13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06
14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06
Loop time of 0.0683999 on 4 procs for 10 steps with 512 atoms
Performance: 2.526 ns/day, 9.500 hours/ns, 146.199 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041408 | 0.051284 | 0.065623 | 3.9 | 74.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0009675 | 0.015306 | 0.025153 | 7.1 | 22.38
Output | 0.0016904 | 0.0017211 | 0.001745 | 0.1 | 2.52
Modify | 2.4557e-05 | 2.9504e-05 | 3.4809e-05 | 0.1 | 0.04
Other | | 5.972e-05 | | | 0.09
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 7.39733 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06
15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06
16 21.730089 21.727916 21.72835 0 0 0 1539307.7 850399.78 919275.13 -1.1741349e-06 8.1321584e-06 -2.1634811e-06
17 21.730089 21.727916 21.728568 0 0 0 1616602.3 927697.4 1065450.9 9.2086349e-07 -2.6001292e-06 -2.9133823e-06
18 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.5 1211626 1.3356364e-06 -2.794764e-06 -9.2778033e-06
19 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 -8.7949961e-07 -3.4755821e-06 -7.1758788e-06
20 21.730089 21.727916 21.729219 0 0 0 1848464.8 1159569 1503974 1.674426e-06 -2.898863e-06 -2.1520562e-06
21 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.5 1650146.9 -1.7524845e-06 -3.4851467e-06 -1.7806669e-06
22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06
23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06
24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06
Loop time of 0.0679641 on 4 procs for 10 steps with 512 atoms
Performance: 2.543 ns/day, 9.439 hours/ns, 147.137 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041426 | 0.05157 | 0.065353 | 3.8 | 75.88
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090528 | 0.014692 | 0.024832 | 7.1 | 21.62
Output | 0.0016062 | 0.0016239 | 0.0016341 | 0.0 | 2.39
Modify | 1.9789e-05 | 2.6107e-05 | 3.4094e-05 | 0.1 | 0.04
Other | | 5.156e-05 | | | 0.08
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 8.16262 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07
25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06
26 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 -5.49227e-06 -4.2895969e-06 243.66104
27 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 -6.5461301e-06 -6.5635547e-06 487.32212
28 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 -6.2913987e-06 -6.8959666e-06 730.98323
29 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 -6.1650242e-06 -6.374019e-06 974.64422
30 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 -6.8112674e-06 -6.9206286e-06 1218.3053
31 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 -6.5914369e-06 -8.6480249e-06 1461.9664
32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275
33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496
Loop time of 0.0681064 on 4 procs for 10 steps with 512 atoms
Performance: 2.537 ns/day, 9.459 hours/ns, 146.829 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041511 | 0.051664 | 0.065403 | 3.8 | 75.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090647 | 0.014658 | 0.024812 | 7.1 | 21.52
Output | 0.0016921 | 0.0017017 | 0.001713 | 0.0 | 2.50
Modify | 2.2173e-05 | 2.7835e-05 | 3.0994e-05 | 0.1 | 0.04
Other | | 5.496e-05 | | | 0.08
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 8.91262 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106
35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106
36 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64726 -0.00014128194 2436.6106
37 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29457 -0.00027206674 2436.6106
38 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.94189 -0.00040462289 2436.6106
39 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58915 -0.00053614117 2436.6106
40 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00066911336 2436.6106
41 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.00080012128 2436.6106
42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106
43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106
44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106
Loop time of 0.0681901 on 4 procs for 10 steps with 512 atoms
Performance: 2.534 ns/day, 9.471 hours/ns, 146.649 timesteps/s
100.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041675 | 0.051819 | 0.065549 | 3.8 | 75.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00088024 | 0.014621 | 0.024764 | 7.2 | 21.44
Output | 0.0016496 | 0.0016653 | 0.0016737 | 0.0 | 2.44
Modify | 2.0027e-05 | 2.4855e-05 | 3.0756e-05 | 0.1 | 0.04
Other | | 6.02e-05 | | | 0.09
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:00

92
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LAMMPS (15 Feb 2016)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 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 = 4 4 4
Memory usage per processor = 6.47955 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.193527 on 1 procs for 10 steps with 512 atoms
Performance: 0.893 ns/day, 26.879 hours/ns, 51.672 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19296 | 0.19296 | 0.19296 | 0.0 | 99.71
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00025725 | 0.00025725 | 0.00025725 | 0.0 | 0.13
Output | 0.00012445 | 0.00012445 | 0.00012445 | 0.0 | 0.06
Modify | 8.3208e-05 | 8.3208e-05 | 8.3208e-05 | 0.0 | 0.04
Other | | 0.000104 | | | 0.05
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 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: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

92
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LAMMPS (15 Feb 2016)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
Reading potential file ffield.comb with DATE: 2011-02-22
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 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 = 4 4 4
Memory usage per processor = 6.39352 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.0531193 on 4 procs for 10 steps with 512 atoms
Performance: 3.253 ns/day, 7.378 hours/ns, 188.255 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046737 | 0.048466 | 0.051893 | 1.0 | 91.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00082636 | 0.0042595 | 0.0059838 | 3.2 | 8.02
Output | 0.00026178 | 0.00027215 | 0.0002954 | 0.1 | 0.51
Modify | 2.3842e-05 | 2.563e-05 | 2.8372e-05 | 0.0 | 0.05
Other | | 9.644e-05 | | | 0.18
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

90
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LAMMPS (15 Feb 2016)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
Reading potential file lib.comb3 with DATE: 2014-02-01
Reading potential file ffield.comb3 with DATE: 2014-02-01
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
#dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 4 4 6
Memory usage per processor = 4.47117 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
Loop time of 45.764 on 1 procs for 100 steps with 682 atoms
Performance: 0.038 ns/day, 635.612 hours/ns, 2.185 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.987 | 10.987 | 10.987 | 0.0 | 24.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00317 | 0.00317 | 0.00317 | 0.0 | 0.01
Output | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.00
Modify | 34.773 | 34.773 | 34.773 | 0.0 | 75.98
Other | | 0.001366 | | | 0.00
Nlocal: 682 ave 682 max 682 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4154 ave 4154 max 4154 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: 355216 ave 355216 max 355216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 355216
Ave neighs/atom = 520.845
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:48

90
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LAMMPS (15 Feb 2016)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
Reading potential file lib.comb3 with DATE: 2014-02-01
Reading potential file ffield.comb3 with DATE: 2014-02-01
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
#dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 4 4 6
Memory usage per processor = 4.95436 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
Loop time of 20.7745 on 4 procs for 100 steps with 682 atoms
Performance: 0.083 ns/day, 288.534 hours/ns, 4.814 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2393 | 3.5206 | 4.856 | 67.7 | 16.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.024316 | 1.3586 | 2.6388 | 108.8 | 6.54
Output | 0.00034308 | 0.00036204 | 0.00038791 | 0.1 | 0.00
Modify | 15.892 | 15.892 | 15.892 | 0.0 | 76.50
Other | | 0.002505 | | | 0.01
Nlocal: 170.5 ave 245 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2872 ave 3583 max 2157 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: 88804 ave 131817 max 47999 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 355216
Ave neighs/atom = 520.845
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:21