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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13471 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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examples/comb/log.15May15.comb.Cu.g++.1 Normal file
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.242715 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.242278 (99.8201)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000227451 (0.0937113)
Outpt time (%) = 0.000110865 (0.0456769)
Other time (%) = 9.82285e-05 (0.0404707)
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

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examples/comb/log.15May15.comb.Cu.g++.4 Normal file
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.0640531 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.0626674 (97.8367)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00100106 (1.56286)
Outpt time (%) = 0.000276089 (0.431031)
Other time (%) = 0.00010848 (0.16936)
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

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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
Memory usage per processor = 6.39852 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99954481 -3.8453114 -3.8454405 -0.98378999 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.99818299 -3.8453114 -3.8454403 -0.98378324 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.346024 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.123725 (35.7562)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000100136 (0.028939)
Outpt time (%) = 4.79221e-05 (0.0138494)
Other time (%) = 0.222151 (64.201)
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 = 0
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
master list distance cutoff = 12.5
Memory usage per processor = 8.27781 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99818299 -3.8453114 -3.8454403 -0.98377404 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.99818299 -3.8453249 -3.8454539 -0.98259134 -2.8628625 0.72283983 -1.4456797 25.610878 25.610878 25.610878 16798.611
4 0.99818299 -3.8453255 -3.8454544 -0.98248805 -2.8629664 0.7228394 -1.4456788 25.610392 25.610392 25.610392 16797.656
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
Loop time of 24.2523 on 1 procs for 3 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544029724 -3.84545440474 -3.84545441597
Force two-norm initial, final = 14.244 0.733113
Force max component initial, final = 8.22312 0.41081
Final line search alpha, max atom move = 2.38596e-05 9.80177e-06
Iterations, force evaluations = 3 27
Pair time (%) = 1.81002 (7.46331)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00140429 (0.00579032)
Outpt time (%) = 5.60284e-05 (0.000231023)
Other time (%) = 22.4408 (92.5307)
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 = 0
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
master list distance cutoff = 12.5
Memory usage per processor = 6.65281 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
6 0.99600405 -3.8453255 -3.8454541 -0.98252544 -2.8629287 0.72284035 -1.4456807 25.610392 25.610392 25.610392 16797.656
Loop time of 0.333947 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0653648 (19.5734)
Neigh time (%) = 0 (0)
Comm time (%) = 5.126e-05 (0.0153497)
Outpt time (%) = 2.47955e-05 (0.00742499)
Other time (%) = 0.268506 (80.4038)
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 = 0
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:665)
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]
6 25.610392 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
7 25.610648 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
8 25.610904 25.610392 25.610392 0 0 0 -329933.78 -638001.39 -637973.86 -60683.825 -70925.179 -51575.113
9 25.611161 25.610392 25.610392 0 0 0 -1465.948 -617588.28 -617560.74 -60682.607 -70923.756 -51570.007
10 25.611417 25.610392 25.610392 0 0 0 327001.72 -597180.62 -597153.09 -60681.389 -70922.332 -51564.902
11 25.611673 25.610392 25.610392 0 0 0 655469.22 -576778.42 -576750.89 -60680.171 -70920.908 -51559.797
12 25.611929 25.610392 25.610392 0 0 0 983936.56 -556381.68 -556354.15 -60678.953 -70919.485 -51554.692
13 25.612185 25.610392 25.610392 0 0 0 1312403.7 -535990.39 -535962.87 -60677.735 -70918.061 -51549.588
14 25.612441 25.610392 25.610392 0 0 0 1640870.7 -515604.57 -515577.05 -60676.517 -70916.637 -51544.483
15 25.612697 25.610392 25.610392 0 0 0 1969337.6 -495224.2 -495196.68 -60675.299 -70915.213 -51539.378
16 25.612953 25.610392 25.610392 0 0 0 2297804.2 -474849.28 -474821.77 -60674.082 -70913.79 -51534.274
Loop time of 0.710404 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707336 (99.5681)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000524282 (0.0738006)
Outpt time (%) = 0.00224686 (0.316279)
Other time (%) = 0.00029707 (0.041817)
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 = 0
## 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]
16 25.612953 25.610392 25.610392 0 0 0 2626270.7 -454479.83 -454452.32 -60672.864 -70912.366 -51529.17
17 25.612953 25.610392 25.610648 0 0 0 2626270.7 -454479.83 -454452.32 -60672.864 -70912.366 -51529.17
18 25.612953 25.610392 25.610904 0 0 0 2646636.7 -434056.14 -126036.92 -60666.856 -70910.942 -51528.134
19 25.612953 25.610392 25.611161 0 0 0 2666997.3 -413637.91 202378.33 -60660.849 -70909.518 -51527.099
20 25.612953 25.610392 25.611417 0 0 0 2687352.4 -393225.15 530793.41 -60654.842 -70908.094 -51526.063
21 25.612953 25.610392 25.611673 0 0 0 2707702 -372817.84 859208.34 -60648.835 -70906.671 -51525.028
22 25.612953 25.610392 25.611929 0 0 0 2728046.2 -352415.99 1187623.1 -60642.828 -70905.247 -51523.993
23 25.612953 25.610392 25.612185 0 0 0 2748384.9 -332019.6 1516037.7 -60636.821 -70903.823 -51522.958
24 25.612953 25.610392 25.612441 0 0 0 2768718.2 -311628.66 1844452.1 -60630.815 -70902.399 -51521.923
25 25.612953 25.610392 25.612697 0 0 0 2789045.9 -291243.19 2172866.4 -60624.808 -70900.976 -51520.888
26 25.612953 25.610392 25.612953 0 0 0 2809368.3 -270863.16 2501280.5 -60618.802 -70899.553 -51519.854
Loop time of 0.710274 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707209 (99.5685)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000524759 (0.0738812)
Outpt time (%) = 0.00224233 (0.315699)
Other time (%) = 0.000298023 (0.0419589)
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 = 0
## 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]
26 25.612953 25.610392 25.612953 0 0 0 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
27 25.612953 25.610392 25.612953 0 0 5.1225907e-07 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
28 25.612953 25.610392 25.612953 0 0 1.0245181e-06 2829685.1 -250488.6 2829694.5 -60612.79 -70898.123 -51255.309
29 25.612953 25.610392 25.612953 0 0 1.5367772e-06 2829685.1 -250488.59 2829694.5 -60612.784 -70898.117 -50991.8
30 25.612953 25.610392 25.612953 0 0 2.0490363e-06 2829685.1 -250488.59 2829694.5 -60612.778 -70898.11 -50728.29
31 25.612953 25.610392 25.612953 0 0 2.5612953e-06 2829685.2 -250488.59 2829694.5 -60612.772 -70898.104 -50464.78
32 25.612953 25.610392 25.612953 0 0 3.0735544e-06 2829685.2 -250488.59 2829694.5 -60612.765 -70898.097 -50201.27
33 25.612953 25.610392 25.612953 0 0 3.5858135e-06 2829685.2 -250488.59 2829694.5 -60612.759 -70898.091 -49937.76
34 25.612953 25.610392 25.612953 0 0 4.0980725e-06 2829685.2 -250488.59 2829694.5 -60612.753 -70898.085 -49674.25
35 25.612953 25.610392 25.612953 0 0 4.6103316e-06 2829685.2 -250488.59 2829694.5 -60612.747 -70898.078 -49410.741
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.741 -70898.072 -49147.231
Loop time of 0.693701 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.69068 (99.5645)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00051713 (0.0745465)
Outpt time (%) = 0.00221395 (0.319151)
Other time (%) = 0.000290155 (0.0418272)
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 = 0
## 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]
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
37 25.612953 25.610392 25.612953 5.1220784e-07 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
38 25.612953 25.610392 25.612953 1.0244157e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60349.287 -70898.061 -48883.713
39 25.612953 25.610392 25.612953 1.5366235e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60085.839 -70898.057 -48883.706
40 25.612953 25.610392 25.612953 2.0488314e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -59822.39 -70898.053 -48883.698
41 25.612953 25.610392 25.612953 2.5610392e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59558.942 -70898.048 -48883.691
42 25.612953 25.610392 25.612953 3.0732471e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59295.494 -70898.044 -48883.683
43 25.612953 25.610392 25.612953 3.5854549e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -59032.046 -70898.04 -48883.676
44 25.612953 25.610392 25.612953 4.0976627e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58768.597 -70898.035 -48883.668
45 25.612953 25.610392 25.612953 4.6098706e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58505.149 -70898.031 -48883.661
46 25.612953 25.610392 25.612953 5.1220784e-06 0 5.1225907e-06 2829685.2 -250488.55 2829694.6 -58241.701 -70898.027 -48883.653
Loop time of 0.710342 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.707279 (99.5688)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000520468 (0.07327)
Outpt time (%) = 0.00224543 (0.316105)
Other time (%) = 0.000297308 (0.0418542)
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 = 0

329
examples/comb/log.15May15.comb.Cu2O.elastic.g++.4 Normal file
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
Memory usage per processor = 6.28094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99954481 -3.8453114 -3.8454405 -0.98378999 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.99818299 -3.8453114 -3.8454403 -0.98378324 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.0905606 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0316537 (34.9531)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000888228 (0.980812)
Outpt time (%) = 7.83205e-05 (0.0864841)
Other time (%) = 0.0579403 (63.9796)
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 = 0
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
master list distance cutoff = 12.5
Memory usage per processor = 8.15594 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99818299 -3.8453114 -3.8454403 -0.98377404 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.99818299 -3.8453249 -3.8454539 -0.98259134 -2.8628625 0.72283983 -1.4456797 25.610878 25.610878 25.610878 16798.611
4 0.99818299 -3.8453255 -3.8454544 -0.98248805 -2.8629664 0.7228394 -1.4456788 25.610392 25.610392 25.610392 16797.656
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
Loop time of 6.28643 on 4 procs for 3 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544029724 -3.84545440474 -3.84545441597
Force two-norm initial, final = 14.244 0.733113
Force max component initial, final = 8.22312 0.41081
Final line search alpha, max atom move = 2.38596e-05 9.80177e-06
Iterations, force evaluations = 3 27
Pair time (%) = 0.459659 (7.31192)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0115937 (0.184424)
Outpt time (%) = 7.76052e-05 (0.00123449)
Other time (%) = 5.8151 (92.5024)
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: 202608 ave 205160 max 198780 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
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
master list distance cutoff = 12.5
Memory usage per processor = 6.53094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
5 0.99818299 -3.8453255 -3.8454544 -0.98252572 -2.8629287 0.7228403 -1.4456806 25.610392 25.610392 25.610392 16797.656
6 0.99600405 -3.8453255 -3.8454541 -0.98252544 -2.8629287 0.72284035 -1.4456807 25.610392 25.610392 25.610392 16797.656
Loop time of 0.0854127 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0163963 (19.1965)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000354767 (0.415356)
Outpt time (%) = 3.74913e-05 (0.0438943)
Other time (%) = 0.0686242 (80.3442)
Nlocal: 324 ave 329 max 320 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 4943 ave 4947 max 4938 min
Histogram: 1 0 1 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: 202608 ave 205798 max 200056 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
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:665)
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]
6 25.610392 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
7 25.610648 25.610392 25.610392 0 0 0 -658401.77 -658419.97 -658392.44 -60685.043 -70926.603 -51580.218
8 25.610904 25.610392 25.610392 0 0 0 -329933.78 -638001.39 -637973.86 -60683.825 -70925.179 -51575.113
9 25.611161 25.610392 25.610392 0 0 0 -1465.9477 -617588.27 -617560.74 -60682.607 -70923.756 -51570.007
10 25.611417 25.610392 25.610392 0 0 0 327001.72 -597180.62 -597153.09 -60681.389 -70922.332 -51564.902
11 25.611673 25.610392 25.610392 0 0 0 655469.22 -576778.42 -576750.89 -60680.171 -70920.908 -51559.797
12 25.611929 25.610392 25.610392 0 0 0 983936.56 -556381.67 -556354.15 -60678.953 -70919.485 -51554.692
13 25.612185 25.610392 25.610392 0 0 0 1312403.7 -535990.39 -535962.87 -60677.735 -70918.061 -51549.588
14 25.612441 25.610392 25.610392 0 0 0 1640870.7 -515604.56 -515577.05 -60676.517 -70916.637 -51544.483
15 25.612697 25.610392 25.610392 0 0 0 1969337.6 -495224.2 -495196.68 -60675.299 -70915.213 -51539.378
16 25.612953 25.610392 25.610392 0 0 0 2297804.2 -474849.28 -474821.77 -60674.082 -70913.79 -51534.274
Loop time of 0.184534 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.178071 (96.4977)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00348192 (1.88687)
Outpt time (%) = 0.0028165 (1.52628)
Other time (%) = 0.000164449 (0.0891159)
Nlocal: 324 ave 329 max 319 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 4943 ave 4948 max 4938 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 205798 max 199418 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## 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]
16 25.612953 25.610392 25.610392 0 0 0 2626270.7 -454479.82 -454452.32 -60672.864 -70912.366 -51529.17
17 25.612953 25.610392 25.610648 0 0 0 2626270.7 -454479.82 -454452.32 -60672.864 -70912.366 -51529.17
18 25.612953 25.610392 25.610904 0 0 0 2646636.7 -434056.14 -126036.92 -60666.856 -70910.942 -51528.134
19 25.612953 25.610392 25.611161 0 0 0 2666997.3 -413637.91 202378.33 -60660.849 -70909.518 -51527.099
20 25.612953 25.610392 25.611417 0 0 0 2687352.4 -393225.15 530793.41 -60654.842 -70908.094 -51526.063
21 25.612953 25.610392 25.611673 0 0 0 2707702 -372817.84 859208.34 -60648.835 -70906.671 -51525.028
22 25.612953 25.610392 25.611929 0 0 0 2728046.2 -352415.99 1187623.1 -60642.828 -70905.247 -51523.993
23 25.612953 25.610392 25.612185 0 0 0 2748384.9 -332019.6 1516037.7 -60636.821 -70903.823 -51522.958
24 25.612953 25.610392 25.612441 0 0 0 2768718.2 -311628.66 1844452.1 -60630.815 -70902.399 -51521.923
25 25.612953 25.610392 25.612697 0 0 0 2789045.9 -291243.19 2172866.4 -60624.808 -70900.976 -51520.888
26 25.612953 25.610392 25.612953 0 0 0 2809368.3 -270863.16 2501280.5 -60618.802 -70899.553 -51519.854
Loop time of 0.185136 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.17822 (96.2646)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00373882 (2.0195)
Outpt time (%) = 0.0030095 (1.62556)
Other time (%) = 0.00016731 (0.0903717)
Nlocal: 324 ave 329 max 319 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 4943 ave 4948 max 4938 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 205798 max 199418 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## 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]
26 25.612953 25.610392 25.612953 0 0 0 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
27 25.612953 25.610392 25.612953 0 0 5.1225907e-07 2829685.1 -250488.6 2829694.5 -60612.796 -70898.13 -51518.819
28 25.612953 25.610392 25.612953 0 0 1.0245181e-06 2829685.1 -250488.59 2829694.5 -60612.79 -70898.123 -51255.309
29 25.612953 25.610392 25.612953 0 0 1.5367772e-06 2829685.1 -250488.59 2829694.5 -60612.784 -70898.117 -50991.8
30 25.612953 25.610392 25.612953 0 0 2.0490363e-06 2829685.1 -250488.59 2829694.5 -60612.778 -70898.11 -50728.29
31 25.612953 25.610392 25.612953 0 0 2.5612953e-06 2829685.2 -250488.59 2829694.5 -60612.772 -70898.104 -50464.78
32 25.612953 25.610392 25.612953 0 0 3.0735544e-06 2829685.2 -250488.59 2829694.5 -60612.765 -70898.097 -50201.27
33 25.612953 25.610392 25.612953 0 0 3.5858135e-06 2829685.2 -250488.59 2829694.5 -60612.759 -70898.091 -49937.76
34 25.612953 25.610392 25.612953 0 0 4.0980725e-06 2829685.2 -250488.59 2829694.5 -60612.753 -70898.085 -49674.25
35 25.612953 25.610392 25.612953 0 0 4.6103316e-06 2829685.2 -250488.59 2829694.5 -60612.747 -70898.078 -49410.741
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.741 -70898.072 -49147.231
Loop time of 0.184386 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.177878 (96.4706)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00345647 (1.87459)
Outpt time (%) = 0.00290865 (1.57748)
Other time (%) = 0.000142515 (0.0772917)
Nlocal: 324 ave 329 max 319 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 4943 ave 4948 max 4938 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 205798 max 199418 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## 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]
36 25.612953 25.610392 25.612953 0 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
37 25.612953 25.610392 25.612953 5.1220784e-07 0 5.1225907e-06 2829685.2 -250488.59 2829694.5 -60612.735 -70898.065 -48883.721
38 25.612953 25.610392 25.612953 1.0244157e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60349.287 -70898.061 -48883.713
39 25.612953 25.610392 25.612953 1.5366235e-06 0 5.1225907e-06 2829685.2 -250488.58 2829694.5 -60085.839 -70898.057 -48883.706
40 25.612953 25.610392 25.612953 2.0488314e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59822.39 -70898.053 -48883.698
41 25.612953 25.610392 25.612953 2.5610392e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59558.942 -70898.048 -48883.691
42 25.612953 25.610392 25.612953 3.0732471e-06 0 5.1225907e-06 2829685.2 -250488.57 2829694.5 -59295.494 -70898.044 -48883.683
43 25.612953 25.610392 25.612953 3.5854549e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -59032.046 -70898.04 -48883.676
44 25.612953 25.610392 25.612953 4.0976627e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58768.597 -70898.035 -48883.668
45 25.612953 25.610392 25.612953 4.6098706e-06 0 5.1225907e-06 2829685.2 -250488.56 2829694.6 -58505.149 -70898.031 -48883.661
46 25.612953 25.610392 25.612953 5.1220784e-06 0 5.1225907e-06 2829685.2 -250488.55 2829694.6 -58241.701 -70898.027 -48883.653
Loop time of 0.184383 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.177841 (96.4522)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00349998 (1.89821)
Outpt time (%) = 0.00289482 (1.57)
Other time (%) = 0.000146747 (0.079588)
Nlocal: 324 ave 329 max 319 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 4943 ave 4948 max 4938 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 205798 max 199418 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

197
examples/comb/log.15May15.comb.HfO2.g++.1 Normal file
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LAMMPS (30 Apr 2015)
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
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
master list distance cutoff = 12.5
Memory usage per processor = 6.15435 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.170595 on 1 procs for 1 steps with 1500 atoms
Pair time (%) = 0.170435 (99.9061)
Neigh time (%) = 0 (0)
Comm time (%) = 6.98566e-05 (0.0409488)
Outpt time (%) = 3.21865e-05 (0.0188672)
Other time (%) = 5.81741e-05 (0.0341007)
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 = 6.77935 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
Loop time of 1.14399 on 1 procs for 5 steps with 1500 atoms
Pair time (%) = 0.838658 (73.3097)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000344276 (0.0300943)
Outpt time (%) = 0.000156641 (0.0136925)
Other time (%) = 0.304834 (26.6465)
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
master list distance cutoff = 12.5
Memory usage per processor = 7.88908 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.645571 on 1 procs for 1 steps with 1500 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0941049618 -10.0941049618 -10.0949959801
Force two-norm initial, final = 5418.49 5437.46
Force max component initial, final = 4082.68 4098.38
Final line search alpha, max atom move = 4.89874e-08 0.000200769
Iterations, force evaluations = 1 1
Pair time (%) = 0.338677 (52.4616)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000132084 (0.02046)
Outpt time (%) = 0 (0)
Other time (%) = 0.306762 (47.5179)
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
master list distance cutoff = 12.5
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 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 2.27596 on 1 procs for 10 steps with 1500 atoms
Pair time (%) = 1.67032 (73.3896)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000641346 (0.0281792)
Outpt time (%) = 0.000294447 (0.0129373)
Other time (%) = 0.604706 (26.5693)
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

197
examples/comb/log.15May15.comb.HfO2.g++.4 Normal file
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LAMMPS (30 Apr 2015)
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
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
master list distance cutoff = 12.5
Memory usage per processor = 5.98215 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0435762 on 4 procs for 1 steps with 1500 atoms
Pair time (%) = 0.0425043 (97.5401)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00099206 (2.27661)
Outpt time (%) = 4.17829e-05 (0.0958845)
Other time (%) = 3.80874e-05 (0.087404)
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 = 6.60715 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
Loop time of 0.291155 on 4 procs for 5 steps with 1500 atoms
Pair time (%) = 0.211277 (72.5651)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00291818 (1.00228)
Outpt time (%) = 0.000213385 (0.0732889)
Other time (%) = 0.0767466 (26.3593)
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
master list distance cutoff = 12.5
Memory usage per processor = 7.71686 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.162492 on 4 procs for 1 steps with 1500 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0941049618 -10.0941049618 -10.0949959801
Force two-norm initial, final = 5418.49 5437.46
Force max component initial, final = 4082.68 4098.38
Final line search alpha, max atom move = 4.89874e-08 0.000200769
Iterations, force evaluations = 1 1
Pair time (%) = 0.084424 (51.9557)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00120038 (0.738729)
Outpt time (%) = 0 (0)
Other time (%) = 0.0768679 (47.3056)
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
master list distance cutoff = 12.5
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 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.582433 on 4 procs for 10 steps with 1500 atoms
Pair time (%) = 0.422252 (72.498)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00646162 (1.10942)
Outpt time (%) = 0.000423133 (0.0726493)
Other time (%) = 0.153296 (26.3199)
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

284
examples/comb/log.15May15.comb.Si.elastic.g++.1 Normal file
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@ -0,0 +1,284 @@
LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.197969 on 1 procs for 5 steps with 512 atoms
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
Pair time (%) = 0.196495 (99.2555)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000294924 (0.148975)
Outpt time (%) = 2.7895e-05 (0.0140906)
Other time (%) = 0.00115108 (0.581447)
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
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
master list distance cutoff = 12.5
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 0.0178819 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0178392 (99.7613)
Neigh time (%) = 0 (0)
Comm time (%) = 2.7895e-05 (0.155996)
Outpt time (%) = 8.82149e-06 (0.049332)
Other time (%) = 5.96046e-06 (0.0333324)
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
### 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:665)
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 0.192462 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.190872 (99.1741)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000279427 (0.145185)
Outpt time (%) = 0.00117064 (0.608242)
Other time (%) = 0.000139475 (0.0724688)
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
## 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 0.199746 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.198035 (99.1436)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000294685 (0.14753)
Outpt time (%) = 0.00126338 (0.632494)
Other time (%) = 0.000152588 (0.076391)
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
## 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 0.199612 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.197943 (99.1638)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000291109 (0.145837)
Outpt time (%) = 0.00122833 (0.61536)
Other time (%) = 0.000149727 (0.0750089)
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
## 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 0.200292 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.198626 (99.1682)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000290871 (0.145223)
Outpt time (%) = 0.00122523 (0.611723)
Other time (%) = 0.000149965 (0.0748733)
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

282
examples/comb/log.15May15.comb.Si.elastic.g++.4 Normal file
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.0429523 on 4 procs for 3 steps with 512 atoms
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
Pair time (%) = 0.0327069 (76.1471)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00961107 (22.3761)
Outpt time (%) = 3.73125e-05 (0.0868696)
Other time (%) = 0.000597 (1.38991)
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 = 0
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
master list distance cutoff = 12.5
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 0.0060575 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.00465924 (76.9168)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00136727 (22.5715)
Outpt time (%) = 2.17557e-05 (0.359153)
Other time (%) = 9.23872e-06 (0.152517)
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 = 0
### 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:665)
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 0.06639 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0500078 (75.3243)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0144862 (21.8198)
Outpt time (%) = 0.00181007 (2.72642)
Other time (%) = 8.59499e-05 (0.129462)
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 = 0
## 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 0.0663998 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0500509 (75.3781)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0145006 (21.8383)
Outpt time (%) = 0.00177175 (2.6683)
Other time (%) = 7.6592e-05 (0.11535)
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 = 0
## 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 0.0663879 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0500835 (75.4407)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0144514 (21.7681)
Outpt time (%) = 0.00177711 (2.67686)
Other time (%) = 7.59363e-05 (0.114383)
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 = 0
## 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 0.0666665 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0502557 (75.3836)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0144997 (21.7496)
Outpt time (%) = 0.00183129 (2.74694)
Other time (%) = 7.98702e-05 (0.119806)
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 = 0

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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.191885 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.191325 (99.7081)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000267744 (0.139534)
Outpt time (%) = 0.000122786 (0.0639891)
Other time (%) = 0.000169516 (0.0883423)
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

80
examples/comb/log.15May15.comb.Si.g++.4 Normal file
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 12.5
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 0.0533678 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0482765 (90.46)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00442249 (8.28681)
Outpt time (%) = 0.000375569 (0.703737)
Other time (%) = 0.000293255 (0.549498)
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

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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 13
Memory usage per processor = 4.47117 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -2.3270126 -2.3657338 -1.7978067 -0.56792713 21594.196 17719.012 21.3 24.6 33.8162
10 482.6079 -2.3269914 -2.3892819 -1.8216169 -0.56766495 24609.01 17719.012 21.3 24.6 33.8162
20 820.79921 -2.3270402 -2.4329813 -1.8652644 -0.56771692 25602.163 17719.012 21.3 24.6 33.8162
30 1073.6779 -2.3271725 -2.4657527 -1.8979246 -0.56782817 24761.203 17719.012 21.3 24.6 33.8162
40 1204.9932 -2.3273986 -2.4829278 -1.9146138 -0.56831399 18340.932 17719.012 21.3 24.6 33.8162
50 1282.8038 -2.3273604 -2.4929327 -1.9238495 -0.56908322 19213.156 17719.012 21.3 24.6 33.8162
60 1457.03 -2.3276351 -2.5156949 -1.9458412 -0.5698537 36108.879 17719.012 21.3 24.6 33.8162
70 1688.2251 -2.3278888 -2.545789 -1.9752368 -0.57055225 48304.346 17719.012 21.3 24.6 33.8162
80 1888.57 -2.3281759 -2.5719348 -2.0006574 -0.57127734 49979.362 17719.012 21.3 24.6 33.8162
90 2014.3066 -2.3285494 -2.5885372 -2.0165723 -0.57196495 51270.039 17719.012 21.3 24.6 33.8162
100 2097.1576 -2.3288708 -2.5995522 -2.0269935 -0.57255868 43335.293 17719.012 21.3 24.6 33.8162
Loop time of 46.9255 on 1 procs for 100 steps with 682 atoms
Pair time (%) = 10.9992 (23.4398)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00288439 (0.00614673)
Outpt time (%) = 0.000174761 (0.000372422)
Other time (%) = 35.9232 (76.5537)
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

77
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LAMMPS (30 Apr 2015)
# 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
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
master list distance cutoff = 13
Memory usage per processor = 4.95436 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -2.3270126 -2.3657338 -1.7978067 -0.56792713 21594.196 17719.012 21.3 24.6 33.8162
10 482.6079 -2.3269914 -2.3892819 -1.8216169 -0.56766495 24609.01 17719.012 21.3 24.6 33.8162
20 820.79921 -2.3270402 -2.4329813 -1.8652644 -0.56771692 25602.163 17719.012 21.3 24.6 33.8162
30 1073.6779 -2.3271725 -2.4657527 -1.8979246 -0.56782817 24761.203 17719.012 21.3 24.6 33.8162
40 1204.9932 -2.3273986 -2.4829278 -1.9146138 -0.56831399 18340.932 17719.012 21.3 24.6 33.8162
50 1282.8038 -2.3273604 -2.4929327 -1.9238495 -0.56908322 19213.156 17719.012 21.3 24.6 33.8162
60 1457.03 -2.3276351 -2.5156949 -1.9458412 -0.5698537 36108.879 17719.012 21.3 24.6 33.8162
70 1688.2251 -2.3278888 -2.545789 -1.9752368 -0.57055225 48304.346 17719.012 21.3 24.6 33.8162
80 1888.57 -2.3281759 -2.5719348 -2.0006574 -0.57127734 49979.362 17719.012 21.3 24.6 33.8162
90 2014.3066 -2.3285494 -2.5885372 -2.0165723 -0.57196495 51270.039 17719.012 21.3 24.6 33.8162
100 2097.1576 -2.3288708 -2.5995522 -2.0269935 -0.57255868 43335.293 17719.012 21.3 24.6 33.8162
Loop time of 20.9145 on 4 procs for 100 steps with 682 atoms
Pair time (%) = 3.49486 (16.7102)
Neigh time (%) = 0 (0)
Comm time (%) = 1.26299 (6.03884)
Outpt time (%) = 0.000371218 (0.00177493)
Other time (%) = 16.1563 (77.2492)
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