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examples/USER/smtbq/log.smtbq.Al.g++.1 Normal file
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LAMMPS (24 Dec 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
#Constante
variable rac3 equal sqrt(3.0)
variable rac1_2 equal sqrt(0.5)
variable rac3_2 equal sqrt(1.5)
#Structure
variable a equal 4.05
variable nx equal 10
variable ny equal 7
variable nz equal 4
variable bx equal ${a}*${nx}*${rac1_2}
variable bx equal 4.05*${nx}*${rac1_2}
variable bx equal 4.05*10*${rac1_2}
variable bx equal 4.05*10*0.707106781186548
variable by equal ${a}*${ny}*${rac3_2}
variable by equal 4.05*${ny}*${rac3_2}
variable by equal 4.05*7*${rac3_2}
variable by equal 4.05*7*1.22474487139159
variable bz equal ${a}*${nz}*${rac3}
variable bz equal 4.05*${nz}*${rac3}
variable bz equal 4.05*4*${rac3}
variable bz equal 4.05*4*1.73205080756888
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 28.0592230826159 0.0 0.0 0.0
create_box 1 box_vide
Created triclinic box = (0 0 0) to (28.6378 34.7215 28.0592) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
# Aluminium atoms z = [111]
lattice custom ${a} a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 1.73205080756888 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
Lattice spacing in x,y,z = 2.86378 4.96022 7.01481
create_atoms 1 region box_vide
Created 1680 atoms
mass 1 26.98
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.Al Al
Reading potential file ffield.smtbq.Al with DATE: 2015-10-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 4.52298 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653
1 299.98323 729.90439 -5600.8505 65.104695 -5535.7458 28.637825 34.721517 28.059223 27900.653
2 299.93288 731.82072 -5600.8395 65.093767 -5535.7458 28.637825 34.721517 28.059223 27900.653
3 299.84896 735.01448 -5600.8213 65.075556 -5535.7458 28.637825 34.721517 28.059223 27900.653
4 299.7315 739.48472 -5600.7958 65.050064 -5535.7458 28.637825 34.721517 28.059223 27900.653
5 299.58053 745.23012 -5600.7631 65.017299 -5535.7458 28.637825 34.721517 28.059223 27900.653
6 299.39609 752.24896 -5600.723 64.977269 -5535.7458 28.637825 34.721517 28.059223 27900.653
7 299.17822 760.5391 -5600.6757 64.929985 -5535.7458 28.637825 34.721517 28.059223 27900.653
8 298.92698 770.098 -5600.6212 64.875459 -5535.7458 28.637825 34.721517 28.059223 27900.653
9 298.64244 780.92261 -5600.5595 64.813707 -5535.7458 28.637825 34.721517 28.059223 27900.653
10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
Loop time of 5.10475 on 1 procs for 10 steps with 1680 atoms
Performance: 0.034 ns/day, 708.993 hours/ns, 1.959 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 | 5.1037 | 5.1037 | 5.1037 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00044179 | 0.00044179 | 0.00044179 | 0.0 | 0.01
Output | 0.00024772 | 0.00024772 | 0.00024772 | 0.0 | 0.00
Modify | 0.00026011 | 0.00026011 | 0.00026011 | 0.0 | 0.01
Other | | 0.0001063 | | | 0.00
Nlocal: 1680 ave 1680 max 1680 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7518 ave 7518 max 7518 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: 638400 ave 638400 max 638400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#thermo 15
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-8 1.0e-10 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 = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 5.64798 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
11 298.32468 2483.3228 -5600.5212 64.744743 -5535.7764 28.617938 34.697425 28.039771 27842.617
12 298.32468 3102.6624 -5600.6242 64.744743 -5535.8795 28.594201 34.68783 28.048729 27820.715
13 298.32468 1681.0688 -5600.6477 64.744743 -5535.903 28.619779 34.708131 28.055945 27869.065
14 298.32468 949.90841 -5600.6635 64.744743 -5535.9187 28.648416 34.718691 28.044409 27893.966
15 298.32468 2009.1662 -5600.7072 64.744743 -5535.9625 28.652241 34.703261 28.01635 27857.391
16 298.32468 2867.1434 -5600.7192 64.744743 -5535.9744 28.626861 34.69005 28.022309 27828.038
17 298.32468 2480.3207 -5600.7238 64.744743 -5535.9791 28.618046 34.695106 28.040113 27841.2
18 298.32468 2482.4906 -5600.7249 64.744743 -5535.9802 28.614169 34.704237 28.036452 27841.119
19 298.32468 2495.6209 -5600.7261 64.744743 -5535.9813 28.616207 34.697481 28.039453 27840.662
20 298.32468 2210.2897 -5600.7271 64.744743 -5535.9823 28.620852 34.699678 28.042926 27850.393
21 298.32468 2464.137 -5600.734 64.744743 -5535.9893 28.625239 34.687085 28.040022 27841.67
22 298.32468 3091.7034 -5600.7471 64.744743 -5536.0024 28.623565 34.674943 28.02983 27820.181
23 298.32468 2334.9443 -5600.7598 64.744743 -5536.0151 28.634413 34.684598 28.037298 27845.891
24 298.32468 2462.2836 -5600.7767 64.744743 -5536.032 28.615834 34.692433 28.044664 27841.422
25 298.32468 2652.08 -5600.7914 64.744743 -5536.0466 28.61528 34.695645 28.035991 27834.85
26 298.32468 2365.4126 -5600.7923 64.744743 -5536.0476 28.618526 34.699347 28.039662 27844.623
27 298.32468 2334.9429 -5600.7934 64.744743 -5536.0486 28.61826 34.698136 28.041941 27845.656
28 298.32468 2501.1598 -5600.7937 64.744743 -5536.0489 28.616356 34.695993 28.039825 27839.982
29 298.32468 2506.0962 -5600.794 64.744743 -5536.0493 28.617255 34.699031 28.036317 27839.811
30 298.32468 2400.7588 -5600.7942 64.744743 -5536.0495 28.618372 34.698464 28.039299 27843.404
31 298.32468 2499.8528 -5600.7945 64.744743 -5536.0497 28.61702 34.69385 28.040945 27840.021
32 298.32468 2629.5393 -5600.7967 64.744743 -5536.0519 28.619399 34.691546 28.036003 27835.58
33 298.32468 2397.5939 -5600.7973 64.744743 -5536.0526 28.621863 34.69535 28.03848 27843.488
34 298.32468 2222.7714 -5600.8007 64.744743 -5536.056 28.609815 34.705091 28.048395 27849.426
35 298.32468 2748.5871 -5600.8042 64.744743 -5536.0594 28.600322 34.6998 28.043876 27831.457
36 298.32468 2661.1018 -5600.8166 64.744743 -5536.0719 28.615123 34.696499 28.034947 27834.344
37 298.32468 2255.4994 -5600.8185 64.744743 -5536.0737 28.618919 34.702261 28.040497 27848.173
38 298.32468 2260.815 -5600.8239 64.744743 -5536.0791 28.614993 34.70246 28.043972 27847.962
39 298.32468 2549.2876 -5600.8248 64.744743 -5536.0801 28.612892 34.697988 28.039725 27838.113
40 298.32468 2488.3825 -5600.8266 64.744743 -5536.0819 28.623347 34.695524 28.033557 27840.182
41 298.32468 2400.9714 -5600.8283 64.744743 -5536.0835 28.619176 34.695733 28.040468 27843.155
42 298.32468 2496.6566 -5600.8284 64.744743 -5536.0837 28.617629 34.694692 28.039536 27839.89
43 298.32468 2486.2773 -5600.8285 64.744743 -5536.0838 28.617585 34.697413 28.037736 27840.243
44 298.32468 2446.3916 -5600.8287 64.744743 -5536.0839 28.617115 34.696389 28.040393 27841.603
45 298.32468 2547.2311 -5600.8288 64.744743 -5536.0841 28.615267 34.694882 28.039956 27838.161
46 298.32468 2479.9982 -5600.8321 64.744743 -5536.0874 28.603008 34.71581 28.037344 27840.427
47 298.32468 2449.645 -5600.8444 64.744743 -5536.0997 28.612743 34.683541 28.054837 27841.375
48 298.32468 2682.7109 -5600.8695 64.744743 -5536.1248 28.617414 34.683477 28.042139 27833.265
49 298.32468 2350.1707 -5600.8711 64.744743 -5536.1263 28.619236 34.694213 28.043092 27844.6
50 298.32468 2486.1481 -5600.8719 64.744743 -5536.1271 28.615167 34.699435 28.038181 27839.955
51 298.32468 2498.3384 -5600.8721 64.744743 -5536.1274 28.616069 34.696071 28.039596 27839.537
52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
Loop time of 36.8807 on 1 procs for 42 steps with 1680 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 =
-5600.49050006 -5600.87213771 -5600.87218615
Force two-norm initial, final = 50.879 1.39888
Force max component initial, final = 29.3783 0.749036
Final line search alpha, max atom move = 0.0013373 0.00100168
Iterations, force evaluations = 42 71
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 36.86 | 36.86 | 36.86 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0032628 | 0.0032628 | 0.0032628 | 0.0 | 0.01
Output | 0.001102 | 0.001102 | 0.001102 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0159 | | | 0.04
Nlocal: 1680 ave 1680 max 1680 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7518 ave 7518 max 7518 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: 638400 ave 638400 max 638400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 4.52298 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
53 298.28341 2444.4342 -5600.8632 64.735788 -5536.1274 28.617616 34.696737 28.039439 27841.421
54 298.20852 2447.019 -5600.847 64.719534 -5536.1274 28.617616 34.696737 28.039439 27841.421
55 298.1 2450.8786 -5600.8234 64.695982 -5536.1274 28.617616 34.696737 28.039439 27841.421
56 297.95788 2456.0119 -5600.7926 64.665139 -5536.1274 28.617616 34.696737 28.039439 27841.421
57 297.7822 2462.4173 -5600.7545 64.62701 -5536.1274 28.617616 34.696737 28.039439 27841.421
58 297.57298 2470.0928 -5600.709 64.581604 -5536.1274 28.617616 34.696737 28.039439 27841.421
59 297.33028 2479.0363 -5600.6564 64.528932 -5536.1274 28.617616 34.696737 28.039439 27841.421
60 297.05416 2489.245 -5600.5964 64.469006 -5536.1274 28.617616 34.696737 28.039439 27841.421
61 296.74469 2500.7159 -5600.5293 64.401842 -5536.1274 28.617616 34.696737 28.039439 27841.421
62 296.40194 2513.4457 -5600.4549 64.327455 -5536.1274 28.617616 34.696737 28.039439 27841.421
Loop time of 5.13584 on 1 procs for 10 steps with 1680 atoms
Performance: 0.034 ns/day, 713.311 hours/ns, 1.947 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 | 5.1346 | 5.1346 | 5.1346 | 0.0 | 99.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00047112 | 0.00047112 | 0.00047112 | 0.0 | 0.01
Output | 0.00036144 | 0.00036144 | 0.00036144 | 0.0 | 0.01
Modify | 0.00029016 | 0.00029016 | 0.00029016 | 0.0 | 0.01
Other | | 0.0001101 | | | 0.00
Nlocal: 1680 ave 1680 max 1680 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7518 ave 7518 max 7518 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: 638400 ave 638400 max 638400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:49

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LAMMPS (24 Dec 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
#Constante
variable rac3 equal sqrt(3.0)
variable rac1_2 equal sqrt(0.5)
variable rac3_2 equal sqrt(1.5)
#Structure
variable a equal 4.05
variable nx equal 10
variable ny equal 7
variable nz equal 4
variable bx equal ${a}*${nx}*${rac1_2}
variable bx equal 4.05*${nx}*${rac1_2}
variable bx equal 4.05*10*${rac1_2}
variable bx equal 4.05*10*0.707106781186548
variable by equal ${a}*${ny}*${rac3_2}
variable by equal 4.05*${ny}*${rac3_2}
variable by equal 4.05*7*${rac3_2}
variable by equal 4.05*7*1.22474487139159
variable bz equal ${a}*${nz}*${rac3}
variable bz equal 4.05*${nz}*${rac3}
variable bz equal 4.05*4*${rac3}
variable bz equal 4.05*4*1.73205080756888
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 28.0592230826159 0.0 0.0 0.0
create_box 1 box_vide
Created triclinic box = (0 0 0) to (28.6378 34.7215 28.0592) with tilt (0 0 0)
2 by 2 by 1 MPI processor grid
# Aluminium atoms z = [111]
lattice custom ${a} a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 1.73205080756888 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
Lattice spacing in x,y,z = 2.86378 4.96022 7.01481
create_atoms 1 region box_vide
Created 1680 atoms
mass 1 26.98
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.Al Al
Reading potential file ffield.smtbq.Al with DATE: 2015-10-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 4.2858 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653
1 299.98339 729.897 -5600.8505 65.104731 -5535.7458 28.637825 34.721517 28.059223 27900.653
2 299.93356 731.7909 -5600.8397 65.093915 -5535.7458 28.637825 34.721517 28.059223 27900.653
3 299.8505 734.94708 -5600.8217 65.07589 -5535.7458 28.637825 34.721517 28.059223 27900.653
4 299.73426 739.36449 -5600.7964 65.050662 -5535.7458 28.637825 34.721517 28.059223 27900.653
5 299.58486 745.04171 -5600.764 65.018238 -5535.7458 28.637825 34.721517 28.059223 27900.653
6 299.40234 751.97694 -5600.7244 64.978627 -5535.7458 28.637825 34.721517 28.059223 27900.653
7 299.18677 760.16798 -5600.6776 64.931841 -5535.7458 28.637825 34.721517 28.059223 27900.653
8 298.9382 769.6122 -5600.6237 64.877894 -5535.7458 28.637825 34.721517 28.059223 27900.653
9 298.65669 780.3065 -5600.5626 64.8168 -5535.7458 28.637825 34.721517 28.059223 27900.653
10 298.34234 792.24735 -5600.4943 64.748578 -5535.7458 28.637825 34.721517 28.059223 27900.653
Loop time of 1.49703 on 4 procs for 10 steps with 1680 atoms
Performance: 0.115 ns/day, 207.920 hours/ns, 6.680 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4956 | 1.4957 | 1.4957 | 0.0 | 99.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00078988 | 0.00090927 | 0.0010064 | 0.3 | 0.06
Output | 0.00022459 | 0.00027347 | 0.00034189 | 0.3 | 0.02
Modify | 6.4373e-05 | 7.8619e-05 | 9.3222e-05 | 0.1 | 0.01
Other | | 8.106e-05 | | | 0.01
Nlocal: 420 ave 484 max 360 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 4305 ave 4365 max 4241 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 159600 ave 183920 max 136800 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#thermo 15
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-8 1.0e-10 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 = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 5.4127 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
10 298.34234 792.24735 -5600.4943 64.748578 -5535.7458 28.637825 34.721517 28.059223 27900.653
11 298.34234 2483.41 -5600.5251 64.748578 -5535.7765 28.617939 34.697415 28.039749 27842.588
12 298.34234 3212.2068 -5600.6294 64.748578 -5535.8809 28.605195 34.685635 28.035928 27816.95
13 298.34234 1756.312 -5600.6529 64.748578 -5535.9044 28.62806 34.701751 28.05036 27866.456
14 298.34234 845.30512 -5600.6668 64.748578 -5535.9182 28.652683 34.704776 28.055059 27897.528
15 298.34234 1950.7901 -5600.7433 64.748578 -5535.9948 28.66644 34.670055 28.031028 27859.115
16 298.34234 2860.9521 -5600.7579 64.748578 -5536.0093 28.637802 34.669634 28.028024 27827.963
17 298.34234 2406.0293 -5600.7642 64.748578 -5536.0156 28.624953 34.689277 28.040313 27843.439
18 298.34234 2531.6658 -5600.7645 64.748578 -5536.0159 28.619984 34.690929 28.039526 27839.151
19 298.34234 2410.8263 -5600.7651 64.748578 -5536.0166 28.615355 34.70117 28.039934 27843.27
20 298.34234 2538.4705 -5600.7654 64.748578 -5536.0169 28.613142 34.700755 28.038049 27838.913
21 298.34234 2455.2909 -5600.7657 64.748578 -5536.0171 28.615273 34.700334 28.039158 27841.749
22 298.34234 2578.5637 -5600.766 64.748578 -5536.0174 28.614997 34.695849 28.038814 27837.541
23 298.34234 2413.5858 -5600.7667 64.748578 -5536.0181 28.617591 34.695982 28.041829 27843.164
24 298.34234 2575.34 -5600.7677 64.748578 -5536.0191 28.614711 34.696953 28.038299 27837.636
25 298.34234 2313.5501 -5600.7689 64.748578 -5536.0203 28.618801 34.702208 28.039031 27846.559
26 298.34234 2589.6554 -5600.7724 64.748578 -5536.0239 28.622807 34.692685 28.033282 27837.106
27 298.34234 2258.4841 -5600.7755 64.748578 -5536.0269 28.633037 34.683012 28.042438 27848.382
28 298.34234 2668.7002 -5600.7789 64.748578 -5536.0303 28.632179 34.665065 28.043666 27834.358
29 298.34234 2339.309 -5600.8141 64.748578 -5536.0655 28.626885 34.675842 28.051214 27845.356
30 298.34234 2846.4227 -5600.8223 64.748578 -5536.0737 28.612492 34.69364 28.033449 27828.006
31 298.34234 2534.6985 -5600.8246 64.748578 -5536.076 28.611965 34.709562 28.031793 27838.619
32 298.34234 2278.6053 -5600.8262 64.748578 -5536.0776 28.617042 34.703828 28.040241 27847.349
33 298.34234 2477.381 -5600.8269 64.748578 -5536.0783 28.616395 34.695005 28.041167 27840.56
34 298.34234 2561.8128 -5600.8271 64.748578 -5536.0785 28.615917 34.69647 28.037549 27837.678
35 298.34234 2470.4145 -5600.8273 64.748578 -5536.0787 28.617208 34.699332 28.037111 27840.795
36 298.34234 2415.0452 -5600.8276 64.748578 -5536.079 28.617651 34.69562 28.041578 27842.683
37 298.34234 2514.0703 -5600.8277 64.748578 -5536.0791 28.616929 34.693138 28.040886 27839.303
38 298.34234 2515.7338 -5600.828 64.748578 -5536.0794 28.619947 34.694884 28.03646 27839.244
39 298.34234 2402.2948 -5600.8281 64.748578 -5536.0796 28.620623 34.69709 28.037911 27843.113
40 298.34234 2457.1081 -5600.8289 64.748578 -5536.0804 28.612617 34.697892 28.043218 27841.237
41 298.34234 2729.4589 -5600.8299 64.748578 -5536.0814 28.610746 34.694899 28.038106 27831.941
42 298.34234 2487.8313 -5600.8331 64.748578 -5536.0845 28.620239 34.701333 28.031882 27840.157
43 298.34234 1959.1329 -5600.8393 64.748578 -5536.0908 28.609631 34.719775 28.045509 27858.164
44 298.34234 2535.5621 -5600.8461 64.748578 -5536.0975 28.587496 34.720535 28.046731 27838.433
45 298.34234 2978.3628 -5600.858 64.748578 -5536.1095 28.609197 34.699148 28.027451 27823.264
46 298.34234 2351.5532 -5600.8632 64.748578 -5536.1146 28.624986 34.701661 28.031447 27844.605
47 298.34234 2294.1629 -5600.8704 64.748578 -5536.1218 28.614261 34.700247 28.045027 27846.522
48 298.34234 2528.0548 -5600.871 64.748578 -5536.1225 28.612265 34.696612 28.041878 27838.536
49 298.34234 2516.2649 -5600.8715 64.748578 -5536.1229 28.618047 34.695729 28.037328 27838.936
50 298.34234 2461.5711 -5600.8715 64.748578 -5536.1229 28.61865 34.696255 28.038191 27840.802
Loop time of 10.0107 on 4 procs for 40 steps with 1680 atoms
98.5% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-5600.49433365 -5600.87146764 -5600.87150075
Force two-norm initial, final = 50.9055 1.01476
Force max component initial, final = 29.378 0.811083
Final line search alpha, max atom move = 0.00128157 0.00103946
Iterations, force evaluations = 40 75
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.9932 | 9.9933 | 9.9933 | 0.0 | 99.83
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0059471 | 0.0059789 | 0.0059991 | 0.0 | 0.06
Output | 0.00088 | 0.0010666 | 0.0015972 | 0.9 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01039 | | | 0.10
Nlocal: 420 ave 426 max 416 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 4305 ave 4309 max 4299 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 159600 ave 161880 max 158080 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 6 5
Memory usage per processor = 4.2877 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
50 298.34234 2461.5711 -5600.8715 64.748578 -5536.1229 28.61865 34.696255 28.038191 27840.802
51 298.30489 2462.7206 -5600.8634 64.740449 -5536.1229 28.61865 34.696255 28.038191 27840.802
52 298.23415 2465.1307 -5600.848 64.725096 -5536.1229 28.61865 34.696255 28.038191 27840.802
53 298.13012 2468.8007 -5600.8254 64.702519 -5536.1229 28.61865 34.696255 28.038191 27840.802
54 297.99284 2473.7295 -5600.7956 64.672726 -5536.1229 28.61865 34.696255 28.038191 27840.802
55 297.82234 2479.9155 -5600.7586 64.635722 -5536.1229 28.61865 34.696255 28.038191 27840.802
56 297.61866 2487.3567 -5600.7144 64.591518 -5536.1229 28.61865 34.696255 28.038191 27840.802
57 297.38185 2496.0508 -5600.663 64.540124 -5536.1229 28.61865 34.696255 28.038191 27840.802
58 297.11198 2505.9952 -5600.6045 64.481554 -5536.1229 28.61865 34.696255 28.038191 27840.802
59 296.80911 2517.1867 -5600.5387 64.415823 -5536.1229 28.61865 34.696255 28.038191 27840.802
60 296.47332 2529.6221 -5600.4659 64.342947 -5536.1229 28.61865 34.696255 28.038191 27840.802
Loop time of 1.2969 on 4 procs for 10 steps with 1680 atoms
Performance: 0.133 ns/day, 180.125 hours/ns, 7.711 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2955 | 1.2955 | 1.2955 | 0.0 | 99.89
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00080395 | 0.00095397 | 0.0010161 | 0.3 | 0.07
Output | 0.00023341 | 0.00028217 | 0.00041556 | 0.5 | 0.02
Modify | 7.2241e-05 | 7.993e-05 | 8.8692e-05 | 0.1 | 0.01
Other | | 8.166e-05 | | | 0.01
Nlocal: 420 ave 424 max 416 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 4305 ave 4309 max 4301 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 159600 ave 161120 max 158080 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 638400
Ave neighs/atom = 380
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:13

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LAMMPS (23 Oct 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Alpha
triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1800 atoms
# ^ Orthorombic box of corundum strcture
mass 1 16.00
group Oxy type 1
1080 atoms in group Oxy
compute chargeOxy Oxy property/atom q
compute q_Oxy Oxy reduce ave c_chargeOxy
mass 2 26.98
group Al type 2
720 atoms in group Al
compute chargeAl Al property/atom q
compute q_Al Al reduce ave c_chargeAl
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.Al2O3 O Al
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 4.12573 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78
1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78
2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78
3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78
4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78
5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78
6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78
7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78
8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78
9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
Loop time of 169.694 on 1 procs for 10 steps with 1800 atoms
Performance: 0.001 ns/day, 23568.600 hours/ns, 0.059 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 | 169.69 | 169.69 | 169.69 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075507 | 0.00075507 | 0.00075507 | 0.0 | 0.00
Output | 0.00078607 | 0.00078607 | 0.00078607 | 0.0 | 0.00
Modify | 0.00034666 | 0.00034666 | 0.00034666 | 0.0 | 0.00
Other | | 0.0001752 | | | 0.00
Nlocal: 1800 ave 1800 max 1800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11490 ave 11490 max 11490 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: 1.4472e+06 ave 1.4472e+06 max 1.4472e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1447200
Ave neighs/atom = 804
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
thermo 1
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-3 1.0e-5 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 = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 5.50073 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
Loop time of 25.4145 on 1 procs for 1 steps with 1800 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 =
-11492.6369832 -11492.6369832 -11494.7221261
Force two-norm initial, final = 1453.27 1325.26
Force max component initial, final = 968.201 892.249
Final line search alpha, max atom move = 1.03284e-06 0.000921553
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 25.414 | 25.414 | 25.414 | -nan |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00013995 | 0.00013995 | 0.00013995 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005064 | | | 0.00
Nlocal: 1800 ave 1800 max 1800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11408 ave 11408 max 11408 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: 1.44456e+06 ave 1.44456e+06 max 1.44456e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1444562
Ave neighs/atom = 802.534
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 4.37573 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17
13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17
14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17
15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17
16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17
17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17
18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17
19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17
20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17
21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17
Loop time of 170.699 on 1 procs for 10 steps with 1800 atoms
Performance: 0.001 ns/day, 23708.143 hours/ns, 0.059 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 | 170.7 | 170.7 | 170.7 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00068879 | 0.00068879 | 0.00068879 | 0.0 | 0.00
Output | 0.0008359 | 0.0008359 | 0.0008359 | 0.0 | 0.00
Modify | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.00
Other | | 0.0001593 | | | 0.00
Nlocal: 1800 ave 1800 max 1800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11222 ave 11222 max 11222 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: 1.44126e+06 ave 1.44126e+06 max 1.44126e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1441262
Ave neighs/atom = 800.701
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:42

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LAMMPS (24 Dec 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Alpha
triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
1800 atoms
# ^ Orthorombic box of corundum strcture
mass 1 16.00
group Oxy type 1
1080 atoms in group Oxy
compute chargeOxy Oxy property/atom q
compute q_Oxy Oxy reduce ave c_chargeOxy
mass 2 26.98
group Al type 2
720 atoms in group Al
compute chargeAl Al property/atom q
compute q_Al Al reduce ave c_chargeAl
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.Al2O3 O Al
Reading potential file ffield.smtbq.Al2O3 with DATE: 2015-10-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 3.94008 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78
1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78
2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78
3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78
4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78
5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78
6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78
7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78
8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78
9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
Loop time of 43.8203 on 4 procs for 10 steps with 1800 atoms
Performance: 0.004 ns/day, 6086.154 hours/ns, 0.228 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 | 43.817 | 43.817 | 43.817 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0020506 | 0.0024325 | 0.0026755 | 0.5 | 0.01
Output | 0.00047874 | 0.00057358 | 0.00084901 | 0.7 | 0.00
Modify | 9.8944e-05 | 0.00010616 | 0.00011468 | 0.1 | 0.00
Other | | 0.0001459 | | | 0.00
Nlocal: 450 ave 450 max 450 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6820 ave 6820 max 6820 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: 361800 ave 361800 max 361800 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1447200
Ave neighs/atom = 804
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
thermo 1
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-3 1.0e-5 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 = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 5.31508 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
Loop time of 6.48552 on 4 procs for 1 steps with 1800 atoms
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-11492.6369832 -11492.6369832 -11494.7221261
Force two-norm initial, final = 1453.27 1325.26
Force max component initial, final = 968.201 892.249
Final line search alpha, max atom move = 1.03284e-06 0.000921553
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.4848 | 6.4848 | 6.4848 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00037098 | 0.00037396 | 0.00037694 | 0.0 | 0.01
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0003674 | | | 0.01
Nlocal: 450 ave 450 max 450 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6759 ave 6772 max 6750 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 361140 ave 361150 max 361130 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 1444562
Ave neighs/atom = 802.534
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.6714
ghost atom cutoff = 11.6714
binsize = 5.8357 -> bins = 5 5 5
Memory usage per processor = 4.19008 Mbytes
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17
13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17
14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17
15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17
16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17
17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17
18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17
19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17
20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17
21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17
Loop time of 47.1154 on 4 procs for 10 steps with 1800 atoms
Performance: 0.004 ns/day, 6543.802 hours/ns, 0.212 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 | 47.112 | 47.112 | 47.112 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019891 | 0.0023952 | 0.0026395 | 0.5 | 0.01
Output | 0.0004952 | 0.00062233 | 0.00096345 | 0.8 | 0.00
Modify | 0.00010109 | 0.00010723 | 0.00012183 | 0.1 | 0.00
Other | | 0.0001532 | | | 0.00
Nlocal: 450 ave 450 max 450 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6611 ave 6620 max 6600 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: 360316 ave 360333 max 360300 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1441262
Ave neighs/atom = 800.701
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:48

255
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LAMMPS (23 Oct 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
variable a equal 4.5937
variable c equal 2.9587
variable ca equal ${c}/${a}
variable ca equal 2.9587/${a}
variable ca equal 2.9587/4.5937
variable nx equal 6
variable ny equal 6
variable nz equal 11
variable bx equal ${a}*${nx}
variable bx equal 4.5937*${nx}
variable bx equal 4.5937*6
variable by equal ${a}*${ny}
variable by equal 4.5937*${ny}
variable by equal 4.5937*6
variable bz equal ${c}*${nz}
variable bz equal 2.9587*${nz}
variable bz equal 2.9587*11
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
create_box 2 box_vide
Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
#lattice sc 1.0
#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
# titanium atoms
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
create_atoms 2 region box_vide
Created 792 atoms
# Oxygen atoms
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
create_atoms 1 region box_vide
Created 1584 atoms
mass 1 16.00
group Oxy type 1
1584 atoms in group Oxy
compute chargeOxy Oxy property/atom q
compute q_Oxy Oxy reduce ave c_chargeOxy
mass 2 47.867
group Ti type 2
792 atoms in group Ti
compute chargeTi Ti property/atom q
compute q_Ti Ti reduce ave c_chargeTi
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.TiO2 O Ti
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 4.77264 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
1 299.90455 44375.373 -15815.21 92.06855 -15723.142 2.552178 -1.276089 27.5622 27.5622 32.5457 24724.15
2 299.63739 44392.241 -15815.128 91.986534 -15723.142 2.5521725 -1.2760863 27.5622 27.5622 32.5457 24724.15
3 299.19899 44415.606 -15814.994 91.85195 -15723.142 2.5521616 -1.2760808 27.5622 27.5622 32.5457 24724.15
4 298.59012 44445.345 -15814.808 91.665031 -15723.143 2.5521454 -1.2760727 27.5622 27.5622 32.5457 24724.15
5 297.81185 44481.382 -15814.57 91.426105 -15723.144 2.5521238 -1.2760619 27.5622 27.5622 32.5457 24724.15
6 296.86552 44523.683 -15814.28 91.135592 -15723.144 2.5520969 -1.2760484 27.5622 27.5622 32.5457 24724.15
7 295.75281 44572.175 -15813.939 90.793996 -15723.145 2.5520648 -1.2760324 27.5622 27.5622 32.5457 24724.15
8 294.47564 44626.778 -15813.548 90.401913 -15723.147 2.5520274 -1.2760137 27.5622 27.5622 32.5457 24724.15
9 293.03623 44687.401 -15813.108 89.960027 -15723.148 2.5519849 -1.2759925 27.5622 27.5622 32.5457 24724.15
10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
Loop time of 570.52 on 1 procs for 10 steps with 2376 atoms
Performance: 0.000 ns/day, 79238.948 hours/ns, 0.018 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 | 570.52 | 570.52 | 570.52 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00087428 | 0.00087428 | 0.00087428 | 0.0 | 0.00
Output | 0.00091386 | 0.00091386 | 0.00091386 | 0.0 | 0.00
Modify | 0.00045085 | 0.00045085 | 0.00045085 | 0.0 | 0.00
Other | | 0.0001979 | | | 0.00
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13138 ave 13138 max 13138 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: 1.9705e+06 ave 1.9705e+06 max 1.9705e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1970496
Ave neighs/atom = 829.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#thermo 15
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-3 1.0e-5 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 = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 6.14764 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
Loop time of 80.5411 on 1 procs for 1 steps with 2376 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 =
-15812.6183471 -15812.6183471 -15814.1085593
Force two-norm initial, final = 1104.2 951.386
Force max component initial, final = 759.352 657.815
Final line search alpha, max atom move = 1.31691e-06 0.000866285
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 80.54 | 80.54 | 80.54 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016761 | 0.00016761 | 0.00016761 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006053 | | | 0.00
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13138 ave 13138 max 13138 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: 1.96864e+06 ave 1.96864e+06 max 1.96864e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1968636
Ave neighs/atom = 828.551
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 5.02264 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
12 289.69465 39072.309 -15813.575 88.934185 -15724.641 2.551372 -1.275686 27.582771 27.582775 32.578246 24785.834
13 287.79928 39149.855 -15812.994 88.352321 -15724.642 2.5513146 -1.2756573 27.582771 27.582775 32.578246 24785.834
14 285.75427 39232.968 -15812.368 87.724515 -15724.644 2.5512525 -1.2756262 27.582771 27.582775 32.578246 24785.834
15 283.56312 39321.472 -15811.697 87.05185 -15724.645 2.5511856 -1.2755928 27.582771 27.582775 32.578246 24785.834
16 281.22962 39415.185 -15810.983 86.335481 -15724.647 2.5511143 -1.2755571 27.582771 27.582775 32.578246 24785.834
17 278.75777 39513.921 -15810.226 85.57664 -15724.649 2.5510384 -1.2755192 27.582771 27.582775 32.578246 24785.834
18 276.15182 39617.471 -15809.428 84.776632 -15724.651 2.5509583 -1.2754791 27.582771 27.582775 32.578246 24785.834
19 273.41625 39725.622 -15808.591 83.936831 -15724.654 2.5508739 -1.275437 27.582771 27.582775 32.578246 24785.834
20 270.55575 39838.144 -15807.715 83.058679 -15724.656 2.5507855 -1.2753928 27.582771 27.582775 32.578246 24785.834
21 267.57523 39954.804 -15806.802 82.14368 -15724.659 2.5506932 -1.2753466 27.582771 27.582775 32.578246 24785.834
Loop time of 606.774 on 1 procs for 10 steps with 2376 atoms
Performance: 0.000 ns/day, 84274.222 hours/ns, 0.016 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 | 606.77 | 606.77 | 606.77 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00085855 | 0.00085855 | 0.00085855 | 0.0 | 0.00
Output | 0.00087833 | 0.00087833 | 0.00087833 | 0.0 | 0.00
Modify | 0.00041723 | 0.00041723 | 0.00041723 | 0.0 | 0.00
Other | | 0.0001888 | | | 0.00
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 13138 ave 13138 max 13138 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: 1.96049e+06 ave 1.96049e+06 max 1.96049e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1960492
Ave neighs/atom = 825.123
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:23:48

256
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LAMMPS (24 Dec 2015)
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
variable T_depart equal 300
variable dt equal 0.0002
variable a equal 4.5937
variable c equal 2.9587
variable ca equal ${c}/${a}
variable ca equal 2.9587/${a}
variable ca equal 2.9587/4.5937
variable nx equal 6
variable ny equal 6
variable nz equal 11
variable bx equal ${a}*${nx}
variable bx equal 4.5937*${nx}
variable bx equal 4.5937*6
variable by equal ${a}*${ny}
variable by equal 4.5937*${ny}
variable by equal 4.5937*6
variable bz equal ${c}*${nz}
variable bz equal 2.9587*${nz}
variable bz equal 2.9587*11
# =======================================================================
units metal
atom_style charge
dimension 3
boundary p p p
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
create_box 2 box_vide
Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
#lattice sc 1.0
#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
# titanium atoms
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
create_atoms 2 region box_vide
Created 792 atoms
# Oxygen atoms
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
create_atoms 1 region box_vide
Created 1584 atoms
mass 1 16.00
group Oxy type 1
1584 atoms in group Oxy
compute chargeOxy Oxy property/atom q
compute q_Oxy Oxy reduce ave c_chargeOxy
mass 2 47.867
group Ti type 2
792 atoms in group Ti
compute chargeTi Ti property/atom q
compute q_Ti Ti reduce ave c_chargeTi
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style smtbq
pair_coeff * * ffield.smtbq.TiO2 O Ti
Reading potential file ffield.smtbq.TiO2 with DATE: 2015-10-22
neighbor 0.5 bin
neigh_modify every 20 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
thermo_modify flush yes
thermo 1
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 4.60415 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
1 299.90799 44372.657 -15815.211 92.069608 -15723.142 2.5521771 -1.2760885 27.5622 27.5622 32.5457 24724.15
2 299.64406 44386.645 -15815.13 91.988581 -15723.142 2.5521705 -1.2760852 27.5622 27.5622 32.5457 24724.15
3 299.20863 44406.97 -15814.997 91.854908 -15723.142 2.5521584 -1.2760792 27.5622 27.5622 32.5457 24724.15
4 298.60246 44433.509 -15814.812 91.668818 -15723.143 2.552141 -1.2760705 27.5622 27.5622 32.5457 24724.15
5 297.82659 44466.206 -15814.574 91.430631 -15723.144 2.5521181 -1.276059 27.5622 27.5622 32.5457 24724.15
6 296.88235 44505.016 -15814.285 91.140758 -15723.144 2.5520898 -1.2760449 27.5622 27.5622 32.5457 24724.15
7 295.77139 44549.856 -15813.945 90.7997 -15723.145 2.5520562 -1.2760281 27.5622 27.5622 32.5457 24724.15
8 294.49562 44600.663 -15813.555 90.408048 -15723.147 2.5520173 -1.2760087 27.5622 27.5622 32.5457 24724.15
9 293.05725 44657.353 -15813.114 89.966478 -15723.148 2.5519732 -1.2759866 27.5622 27.5622 32.5457 24724.15
10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
Loop time of 161.071 on 4 procs for 10 steps with 2376 atoms
Performance: 0.001 ns/day, 22370.960 hours/ns, 0.062 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 | 161.07 | 161.07 | 161.07 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0021119 | 0.0024694 | 0.0026705 | 0.4 | 0.00
Output | 0.00060225 | 0.00070065 | 0.00098777 | 0.6 | 0.00
Modify | 0.00012326 | 0.00013238 | 0.00014782 | 0.1 | 0.00
Other | | 0.0001593 | | | 0.00
Nlocal: 594 ave 630 max 558 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 7638 ave 7674 max 7602 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: 492624 ave 522720 max 462528 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1970496
Ave neighs/atom = 829.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#thermo 15
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-3 1.0e-5 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 = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 5.97915 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
Loop time of 22.3212 on 4 procs for 1 steps with 2376 atoms
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-15812.6250198 -15812.6250198 -15814.1138993
Force two-norm initial, final = 1103.27 950.466
Force max component initial, final = 758.704 657.184
Final line search alpha, max atom move = 1.31804e-06 0.000866193
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.32 | 22.32 | 22.32 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00042605 | 0.00043178 | 0.00043893 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004204 | | | 0.00
Nlocal: 594 ave 600 max 587 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 7638 ave 7645 max 7632 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 492126 ave 497133 max 486366 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 1968506
Ave neighs/atom = 828.496
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
thermo 1
fix 3 all nve
run 10
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.6744
ghost atom cutoff = 12.6744
binsize = 6.3372 -> bins = 5 5 6
Memory usage per processor = 4.85415 Mbytes
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
12 289.71602 39034.428 -15813.58 88.940745 -15724.639 2.5513568 -1.2756784 27.582769 27.582778 32.578246 24785.835
13 287.81994 39107.705 -15813 88.358662 -15724.641 2.5512976 -1.2756488 27.582769 27.582778 32.578246 24785.835
14 285.77378 39186.429 -15812.373 87.730505 -15724.642 2.5512335 -1.2756168 27.582769 27.582778 32.578246 24785.835
15 283.58105 39270.434 -15811.702 87.057353 -15724.644 2.5511647 -1.2755824 27.582769 27.582778 32.578246 24785.835
16 281.24552 39359.544 -15810.986 86.340362 -15724.646 2.5510913 -1.2755457 27.582769 27.582778 32.578246 24785.835
17 278.77119 39453.574 -15810.229 85.580761 -15724.648 2.5510134 -1.2755067 27.582769 27.582778 32.578246 24785.835
18 276.16232 39552.323 -15809.43 84.779855 -15724.65 2.5509311 -1.2754655 27.582769 27.582778 32.578246 24785.835
19 273.42337 39655.586 -15808.592 83.939017 -15724.652 2.5508445 -1.2754223 27.582769 27.582778 32.578246 24785.835
20 270.55904 39763.139 -15807.715 83.05969 -15724.655 2.5507538 -1.2753769 27.582769 27.582778 32.578246 24785.835
21 267.57425 39874.754 -15806.801 82.14338 -15724.658 2.5506591 -1.2753296 27.582769 27.582778 32.578246 24785.835
Loop time of 170.172 on 4 procs for 10 steps with 2376 atoms
Performance: 0.001 ns/day, 23634.979 hours/ns, 0.059 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 | 170.17 | 170.17 | 170.17 | 0.0 |100.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0025029 | 0.0028628 | 0.0030224 | 0.4 | 0.00
Output | 0.00063372 | 0.00081372 | 0.0011685 | 0.7 | 0.00
Modify | 0.00012541 | 0.0001539 | 0.00021005 | 0.3 | 0.00
Other | | 0.0001655 | | | 0.00
Nlocal: 594 ave 600 max 587 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 7638 ave 7645 max 7632 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 490100 ave 495079 max 484284 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 1960398
Ave neighs/atom = 825.083
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:06:39