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add a couple of simple example single/multi-elment inputs for meam/spline pair styles

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Axel Kohlmeyer 2017-05-09 15:51:59 -04:00
parent 390ceb1475
commit d0da0639f0
8 changed files with 979 additions and 0 deletions
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63
examples/USER/misc/meam_spline/Si_1.meam.spline Normal file
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DATE: 2012-02-01 CONTRIBUTOR: Alexander Stukowski, stukowski@mm.tu-darmstadt.de CITATION: Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter and Kress, Modell Simul Mater Sci Eng, 8, 825 (2000) COMMENT: Spline-based MEAM potential for Si. Reference: T. J. Lenosky, B. Sadigh, E. Alonso, V. V. Bulatov, T. D. de la Rubia, J. Kim, A. F. Voter, and J. D. Kress, Modell. Simul. Mater. Sci. Eng. 8, 825 (2000)
10
-4.266966781858503300e+01 0.000000000000000000e+00
1 0 1 0
1.500000000000000000e+00 6.929943430771341000e+00 1.653321602557917600e+02
1.833333333333333300e+00 -4.399503747408950400e-01 3.941543472528634600e+01
2.166666666666666500e+00 -1.701233725061446700e+00 6.871065423413908100e+00
2.500000000000000000e+00 -1.624732919215791800e+00 5.340648014033163800e+00
2.833333333333333000e+00 -9.969641728342462100e-01 1.534811309391571000e+00
3.166666666666667000e+00 -2.739141845072665100e-01 -6.334706186546093900e+00
3.500000000000000000e+00 -2.499156963774082700e-02 -1.798864729909626500e+00
3.833333333333333500e+00 -1.784331481529976400e-02 4.743496636420091500e-01
4.166666666666666100e+00 -9.612303290166881000e-03 -4.006506271304824400e-02
4.500000000000000000e+00 0.000000000000000000e+00 -2.394996574779807200e-01
11
-1.000000000000000000e+00 0.000000000000000000e+00
1 0 0 0
1.500000000000000000e+00 1.374674212682983900e-01 -3.227795813279568500e+00
1.700000000000000000e+00 -1.483141815327918000e-01 -6.411648793604404900e+00
1.899999999999999900e+00 -5.597204896096039700e-01 1.003068519633888300e+01
2.100000000000000100e+00 -7.310964379372824100e-01 2.293461970618954700e+00
2.299999999999999800e+00 -7.628287071954063000e-01 1.742018781618444500e+00
2.500000000000000000e+00 -7.291769685066557000e-01 5.460640949384478700e-01
2.700000000000000200e+00 -6.662022220044453400e-01 4.721760106467195500e-01
2.899999999999999900e+00 -5.732830582550895200e-01 2.056894449546524200e+00
3.100000000000000100e+00 -4.069014309729406300e-01 2.319615721086100800e+00
3.299999999999999800e+00 -1.666155295956388300e-01 -2.497162196179187900e-01
3.500000000000000000e+00 0.000000000000000000e+00 -1.237130660986393100e+01
8
7.351364478015182100e-01 6.165217237728655200e-01
1 1 1 1
-1.770934559908718700e+00 -1.074925682941420000e+00 -1.482768170233858500e-01
-3.881557649503457600e-01 -2.004503493658201000e-01 -1.492100354067345500e-01
9.946230300080272100e-01 4.142241371345077300e-01 -7.012475119623896900e-02
2.377401824966400000e+00 8.793892953828742500e-01 -3.944355024164965900e-02
3.760180619924772900e+00 1.266888024536562100e+00 -1.581431192239436000e-02
5.142959414883146800e+00 1.629979548834614900e+00 2.611224310900800400e-02
6.525738209841518900e+00 1.977379549636293600e+00 -1.378738550324104500e-01
7.908517004799891800e+00 2.396177220616657200e+00 7.494253977092666400e-01
10
-3.618936018538757300e+00 0.000000000000000000e+00
1 0 1 0
1.500000000000000000e+00 1.250311510312851300e+00 2.790400588857243500e+01
1.722222222222222300e+00 8.682060369372680600e-01 -4.522554291731776900e+00
1.944444444444444400e+00 6.084604017544847900e-01 5.052931618779816800e+00
2.166666666666666500e+00 4.875624808097850400e-01 1.180825096539679600e+00
2.388888888888888800e+00 4.416345603457190700e-01 -6.673769465415171400e-01
2.611111111111111200e+00 3.760976313325982700e-01 -8.938118490837722000e-01
2.833333333333333000e+00 2.714524157414608400e-01 -5.090324763524399800e-01
3.055555555555555400e+00 1.481440300150710900e-01 6.623665830603995300e-01
3.277777777777777700e+00 4.854596610856590900e-02 7.403702452268122700e-01
3.500000000000000000e+00 0.000000000000000000e+00 2.578982318481970500e+00
8
-1.395041572145673000e+01 1.134616739799360700e+00
1 1 1 1
-1.000000000000000900e+00 5.254163992149617700e+00 1.582685381253900500e+01
-7.428367052748285900e-01 2.359149452448745100e+00 3.117611233789983400e+01
-4.856734105496561800e-01 1.195946960915646100e+00 1.658962813584905800e+01
-2.285101158244838800e-01 1.229952028074150000e+00 1.108360928564026400e+01
2.865317890068852500e-02 2.035650777568434500e+00 9.088861456447702400e+00
2.858164736258610400e-01 3.424741418405580000e+00 5.489943377538379500e+00
5.429797683510331200e-01 4.948585892304984100e+00 -1.882291580187675700e+01
8.001430630762056400e-01 5.617988713941801200e+00 -7.718625571850646200e+00

130
examples/USER/misc/meam_spline/TiO.meam.spline Normal file
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# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
meam/spline 2 Ti O
spline3eq
13
-20 0
1.742692837 3.744277175966 99.4865081627958
2.05580176725 0.910839730906 10.8702523265355
2.3689106975 0.388045896634 -1.55322418749562
2.68201962775 -0.018840906533 2.43630041329215
2.995128558 -0.248098929639 2.67912713976835
3.30823748825 -0.264489550297 -0.125056384603077
3.6213464185 -0.227196189283 1.10662555360438
3.93445534875 -0.129293090176 -0.592053676745914
4.247564279 -0.059685366933 -0.470123414607672
4.56067320925 -0.031100025561 -0.0380739973059663
4.8737821395 -0.013847363202 -0.0711547960695406
5.18689106975 -0.003203412728 -0.081768292420175
5.5 0 -0.0571422964883619
spline3eq
5
0.155001355787331 0
1.9 0.533321679606674 0
2.8 0.456402081843862 -1.60311717015859
3.7 -0.324281383502201 1.19940299483249
4.6 -0.474029826906675 1.47909794595154
5.5 0 -2.49521499855605
spline3eq
13
0 0
1.742692837 0 0
2.05580176725 0 0
2.3689106975 0 0
2.68201962775 0 0
2.995128558 0 0
3.30823748825 0 0
3.6213464185 0 0
3.93445534875 0 0
4.247564279 0 0
4.56067320925 0 0
4.8737821395 0 0
5.18689106975 0 0
5.5 0 0
spline3eq
11
-1 0
2.055801767 1.7475279661 -525.869786904802
2.2912215903 -5.8677963945 252.796316927755
2.5266414136 -8.3376288737 71.7318388721015
2.7620612369 -5.8398712842 -1.93587742753693
2.9974810602 -3.1140648231 -39.2999192667503
3.2329008835 -1.7257245065 14.3424136002004
3.4683207068 -0.4428977017 -29.4925534559498
3.7037405301 -0.1466643003 -3.18010534572236
3.9391603534 -0.2095507945 3.33490838803603
4.1745801767 -0.1442384563 3.71918691359508
4.41 0 -9.66717019857564
spline3eq
5
-61.9827585211652 0
1.9 11.2293641315584 0
2.8 -27.9976343076148 122.648031332411
3.7 -8.32979773113248 -54.3340881766381
4.6 -1.00863195297399 3.23150064581724
5.5 0 -5.3514242228123
spline3eq
4
0.00776934946045395 0.105197706160344
-55.14233165 -0.29745568008 0.00152870603877451
-44.7409899033333 -0.15449458722 0.00038933722543571
-34.3396481566667 0.05098657168 0.00038124926922248
-23.93830641 0.57342694704 0.0156639264890892
spline3eq
5
-0.00676745157022662 -0.0159520381982146
-23.9928 0.297607384684645 0
-15.9241175 0.216691597077105 -0.0024248755353942
-7.855435 0.0637598673719069 0.00306245895013358
0.213247499999998 -0.00183450621970427 -0.00177588407633909
8.28193 -0.111277018874367 0
spline3eq
10
2.77327511656661 0
2.055801767 -0.1485215264 72.2010867146919
2.31737934844444 1.6845304918 -47.2744689053404
2.57895692988889 2.0113365977 -15.1859578405326
2.84053451133333 1.1444092747 3.33978204841873
3.10211209277778 0.2861606803 2.587867603808
3.36368967422222 -0.3459281126 6.14070694084556
3.62526725566667 -0.6257480601 3.7397696717154
3.88684483711111 -0.6119510826 4.64749084871402
4.14842241855556 -0.3112059651 2.83275746415936
4.41 0 -15.0612086827734
spline3eq
5
12.3315547862781 0
1.9 2.62105440156724 0
2.8 10.2850803058354 -25.439802988016
3.7 3.23933763743897 -7.20203673434025
4.6 -5.79049355858613 39.5509978688682
5.5 0 -41.221771373642
spline3eq
8
8.33642274810572 -60.4024574736564
-1 0.07651409193 -110.652321293778
-0.724509054371429 0.14155824541 44.8853405500508
-0.449018108742857 0.75788697341 -25.3065115342002
-0.173527163114286 0.63011570378 -2.48510144915082
0.101963782514286 0.09049597305 2.68769386908235
0.377454728142857 -0.35741586657 -1.01558570129633
0.652945673771428 -0.65293217647 13.4224786001212
0.9284366194 -6.00912190653 -452.752542694929
spline3eq
5
0.137191606537625 -1.55094230968985
-1 0.0513843442016519 0
-0.5 0.0179024412245673 -2.44986494990154
0 -0.260650876879273 3.91774583656401
0.5 -0.190163791764901 -4.84414871911743
1 -0.763795416646599 0
spline3eq
8
0 0
-1 0 0
-0.724509054371429 0 0
-0.449018108742857 0 0
-0.173527163114286 0 0
0.101963782514286 0 0
0.377454728142857 0 0
0.652945673771428 0 0
0.9284366194 0 0

22
examples/USER/misc/meam_spline/in.meam-spline.Si Normal file
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@ -0,0 +1,22 @@
# Si fcc phase
units metal
boundary p p p
atom_style atomic
lattice fcc 3.98
region box block 0 5 0 5 0 5
create_box 1 box
create_atoms 1 box
pair_style meam/spline
pair_coeff * * Si_1.meam.spline Si
mass * 28.085
velocity all create 500.0 44226611
fix 1 all nvt temp 500.0 500.0 1.0
thermo 50
run 500

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examples/USER/misc/meam_spline/in.meam-spline.TiO2 Normal file
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#
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 nx equal 6
variable ny equal 6
variable nz equal 11
variable bx equal ${a}*${nx}
variable by equal ${a}*${ny}
variable bz equal ${c}*${nz}
# =======================================================================
units metal
atom_style atomic
dimension 3
boundary p p p
lattice sc 1.0
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
create_box 2 box_vide
#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
create_atoms 2 region box_vide
# 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
create_atoms 1 region box_vide
mass 1 16.00
group Oxy type 1
mass 2 47.867
group Ti type 2
velocity all create ${T_depart} 277387
pair_style meam/spline
pair_coeff * * TiO.meam.spline O Ti
neighbor 0.5 bin
neigh_modify every 2 delay 0 check yes
timestep ${dt}
thermo_style custom step temp press pe ke etotal lx ly lz vol
thermo 10
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 100
unfix 3
fix 1 all box/relax tri 0.0 vmax 0.001
minimize 1.0e-3 1.0e-5 1000 10000
unfix 1
reset_timestep 0
thermo 50
fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
run 500

88
examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.1 Normal file
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LAMMPS (13 Apr 2017)
using 1 OpenMP thread(s) per MPI task
# Si fcc phase
units metal
boundary p p p
atom_style atomic
lattice fcc 3.98
Lattice spacing in x,y,z = 3.98 3.98 3.98
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (19.9 19.9 19.9)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 500 atoms
pair_style meam/spline
pair_coeff * * Si_1.meam.spline Si
Reading potential file Si_1.meam.spline with DATE: 2012-02-01
mass * 28.085
velocity all create 500.0 44226611
fix 1 all nvt temp 500.0 500.0 1.0
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 7 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/spline, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/spline, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.892 | 3.892 | 3.892 Mbytes
Step Temp E_pair E_mol TotEng Press
0 500 -1847.729 0 -1815.4786 1813162.7
50 1934.0932 -1940.8016 0 -1816.051 -48657.676
100 2570.1286 -1984.8725 0 -1819.0971 8002.4248
150 2566.7917 -1990.2724 0 -1824.7123 16819.447
200 2555.1319 -1995.2233 0 -1830.4152 5891.5313
250 2487.2881 -1995.8302 0 -1835.3981 -4339.7172
300 2381.4836 -1994.2492 0 -1840.6415 16508.04
350 2330.8663 -1996.6588 0 -1846.3161 24194.447
400 2212.6035 -1994.9278 0 -1852.2131 -9856.3709
450 2257.7531 -2003.8187 0 -1858.1918 -8029.6019
500 2211.4385 -2006.9846 0 -1864.345 4152.4867
Loop time of 5.13837 on 1 procs for 500 steps with 500 atoms
Performance: 8.407 ns/day, 2.855 hours/ns, 97.307 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0952 | 5.0952 | 5.0952 | 0.0 | 99.16
Neigh | 0.026447 | 0.026447 | 0.026447 | 0.0 | 0.51
Comm | 0.0063307 | 0.0063307 | 0.0063307 | 0.0 | 0.12
Output | 0.0001905 | 0.0001905 | 0.0001905 | 0.0 | 0.00
Modify | 0.0082877 | 0.0082877 | 0.0082877 | 0.0 | 0.16
Other | | 0.00187 | | | 0.04
Nlocal: 500 ave 500 max 500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1767 ave 1767 max 1767 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 18059 ave 18059 max 18059 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 36118 ave 36118 max 36118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36118
Ave neighs/atom = 72.236
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:05

88
examples/USER/misc/meam_spline/log.4May2017.meam-spline.Si.g++.4 Normal file
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LAMMPS (13 Apr 2017)
using 1 OpenMP thread(s) per MPI task
# Si fcc phase
units metal
boundary p p p
atom_style atomic
lattice fcc 3.98
Lattice spacing in x,y,z = 3.98 3.98 3.98
region box block 0 5 0 5 0 5
create_box 1 box
Created orthogonal box = (0 0 0) to (19.9 19.9 19.9)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 500 atoms
pair_style meam/spline
pair_coeff * * Si_1.meam.spline Si
Reading potential file Si_1.meam.spline with DATE: 2012-02-01
mass * 28.085
velocity all create 500.0 44226611
fix 1 all nvt temp 500.0 500.0 1.0
thermo 50
run 500
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.5
ghost atom cutoff = 6.5
binsize = 3.25, bins = 7 7 7
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/spline, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/spline, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.861 | 3.861 | 3.861 Mbytes
Step Temp E_pair E_mol TotEng Press
0 500 -1847.729 0 -1815.4786 1813162.7
50 1923.4262 -1940.0936 0 -1816.0311 -38700.835
100 2535.2542 -1982.6249 0 -1819.0989 10216.821
150 2592.8247 -1992.1569 0 -1824.9176 4839.3385
200 2484.7391 -1990.8452 0 -1830.5775 14040.141
250 2597.4401 -2003.1619 0 -1835.625 1261.5199
300 2513.0793 -2002.942 0 -1840.8463 6690.9815
350 2390.933 -2001.0761 0 -1846.859 -4880.1146
400 2269.0782 -1999.3441 0 -1852.9867 -4921.4391
450 2287.5096 -2006.8236 0 -1859.2774 -7313.6151
500 2303.0918 -2014.0693 0 -1865.518 -9995.1789
Loop time of 1.46588 on 4 procs for 500 steps with 500 atoms
Performance: 29.470 ns/day, 0.814 hours/ns, 341.093 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4273 | 1.4292 | 1.432 | 0.1 | 97.50
Neigh | 0.0068567 | 0.0070301 | 0.0073655 | 0.2 | 0.48
Comm | 0.019111 | 0.022127 | 0.024148 | 1.2 | 1.51
Output | 0.00023174 | 0.00024784 | 0.00029206 | 0.0 | 0.02
Modify | 0.005043 | 0.0052016 | 0.0054417 | 0.2 | 0.35
Other | | 0.002066 | | | 0.14
Nlocal: 125 ave 131 max 118 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 979.25 ave 986 max 975 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 4541.75 ave 4712 max 4362 min
Histogram: 1 1 0 0 0 0 0 0 0 2
FullNghs: 9083.5 ave 9485 max 8601 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 36334
Ave neighs/atom = 72.668
Neighbor list builds = 14
Dangerous builds = 0
Total wall time: 0:00:01

248
examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.1 Normal file
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LAMMPS (13 Apr 2017)
using 1 OpenMP thread(s) per MPI task
#
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 atomic
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
mass 2 47.867
group Ti type 2
792 atoms in group Ti
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style meam/spline
pair_coeff * * TiO.meam.spline O Ti
Reading potential file TiO.meam.spline with DATE: 2016-06-05
neighbor 0.5 bin
neigh_modify every 2 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal lx ly lz vol
thermo 10
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 100
Neighbor list info ...
update every 2 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 10 10 11
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/spline, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/spline, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 5.146 | 5.146 | 5.146 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15
10 301.41345 23612.297 -14374.507 92.531772 -14281.975 27.5622 27.5622 32.5457 24724.15
20 305.11674 25127.832 -14375.643 93.668657 -14281.974 27.5622 27.5622 32.5457 24724.15
30 313.28903 26655.89 -14378.151 96.17749 -14281.974 27.5622 27.5622 32.5457 24724.15
40 328.94567 26999.049 -14382.957 100.98397 -14281.974 27.5622 27.5622 32.5457 24724.15
50 354.05827 23023.294 -14390.667 108.69336 -14281.974 27.5622 27.5622 32.5457 24724.15
60 390.48404 13594.655 -14401.849 119.87581 -14281.973 27.5622 27.5622 32.5457 24724.15
70 442.69928 151.15709 -14417.877 135.90551 -14281.972 27.5622 27.5622 32.5457 24724.15
80 516.89551 -14984.124 -14440.654 158.68322 -14281.971 27.5622 27.5622 32.5457 24724.15
90 618.22135 -29948.066 -14471.76 189.78953 -14281.971 27.5622 27.5622 32.5457 24724.15
100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15
Loop time of 38.7948 on 1 procs for 100 steps with 2376 atoms
Performance: 0.045 ns/day, 538.817 hours/ns, 2.578 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 38.774 | 38.774 | 38.774 | 0.0 | 99.95
Neigh | 0.010751 | 0.010751 | 0.010751 | 0.0 | 0.03
Comm | 0.0039313 | 0.0039313 | 0.0039313 | 0.0 | 0.01
Output | 0.00048804 | 0.00048804 | 0.00048804 | 0.0 | 0.00
Modify | 0.0039241 | 0.0039241 | 0.0039241 | 0.0 | 0.01
Other | | 0.001809 | | | 0.00
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4479 ave 4479 max 4479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 106396 ave 106396 max 106396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212792 ave 212792 max 212792 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212792
Ave neighs/atom = 89.5589
Neighbor list builds = 1
Dangerous builds = 0
unfix 3
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)
Per MPI rank memory allocation (min/avg/max) = 6.271 | 6.271 | 6.271 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
100 747.6193 -41964.291 -14511.487 229.51378 -14281.973 27.5622 27.5622 32.5457 24724.15
101 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789
Loop time of 0.814693 on 1 procs for 1 steps with 2376 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-14511.4866189 -14511.4866189 -14517.4235162
Force two-norm initial, final = 5602.25 5486.97
Force max component initial, final = 5232.05 5109.43
Final line search alpha, max atom move = 1.9113e-07 0.000976563
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.81429 | 0.81429 | 0.81429 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.01
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0003347 | | | 0.04
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4449 ave 4449 max 4449 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 105639 ave 105639 max 105639 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 211278 ave 211278 max 211278 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 211278
Ave neighs/atom = 88.9217
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
reset_timestep 0
thermo 50
fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
run 500
Per MPI rank memory allocation (min/avg/max) = 5.162 | 5.162 | 5.162 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 747.6193 -39284.65 -14517.424 229.51378 -14287.91 27.569615 27.569695 32.513154 24712.789
50 1155.2849 30650.319 -14678.807 354.6642 -14324.143 27.608688 27.60914 32.375311 24678.15
100 790.03926 99869.991 -14678.858 242.5364 -14436.322 27.777994 27.77799 32.017001 24704.857
150 938.86463 -21488.442 -14803.782 288.22472 -14515.557 27.996584 27.995139 31.67008 24822.003
200 420.11331 -790.80799 -14671.687 128.97178 -14542.715 28.126911 28.125909 31.431033 24864.93
250 352.18149 -3244.2491 -14665.007 108.1172 -14556.889 28.222686 28.223673 31.238649 24883.078
300 622.91245 3657.7097 -14758.201 191.22967 -14566.972 28.301771 28.30503 31.07216 24891.363
350 888.25374 26274.358 -14852.568 272.68754 -14579.881 28.370312 28.375107 30.937051 24904.656
400 735.44163 63109.066 -14823.872 225.77532 -14598.097 28.446905 28.45227 30.838015 24959.642
450 804.81905 6221.0364 -14861.113 247.07369 -14614.039 28.543942 28.548719 30.775793 25078.977
500 628.19106 -33912.026 -14814.726 192.85016 -14621.876 28.611997 28.615169 30.74081 25168.642
Loop time of 176.167 on 1 procs for 500 steps with 2376 atoms
Performance: 0.049 ns/day, 489.353 hours/ns, 2.838 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 175.9 | 175.9 | 175.9 | 0.0 | 99.85
Neigh | 0.17043 | 0.17043 | 0.17043 | 0.0 | 0.10
Comm | 0.018243 | 0.018243 | 0.018243 | 0.0 | 0.01
Output | 0.00040984 | 0.00040984 | 0.00040984 | 0.0 | 0.00
Modify | 0.067142 | 0.067142 | 0.067142 | 0.0 | 0.04
Other | | 0.00828 | | | 0.00
Nlocal: 2376 ave 2376 max 2376 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4358 ave 4358 max 4358 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 102634 ave 102634 max 102634 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 205268 ave 205268 max 205268 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 205268
Ave neighs/atom = 86.3923
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:03:37

248
examples/USER/misc/meam_spline/log.4May2017.meam-spline.TiO2.g++.4 Normal file
View File

@ -0,0 +1,248 @@
LAMMPS (13 Apr 2017)
using 1 OpenMP thread(s) per MPI task
#
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 atomic
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
mass 2 47.867
group Ti type 2
792 atoms in group Ti
velocity all create ${T_depart} 277387
velocity all create 300 277387
pair_style meam/spline
pair_coeff * * TiO.meam.spline O Ti
Reading potential file TiO.meam.spline with DATE: 2016-06-05
neighbor 0.5 bin
neigh_modify every 2 delay 0 check yes
timestep ${dt}
timestep 0.0002
thermo_style custom step temp press pe ke etotal lx ly lz vol
thermo 10
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
fix 3 all nve
run 100
Neighbor list info ...
update every 2 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 10 10 11
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair meam/spline, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair meam/spline, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 3.922 | 3.922 | 3.922 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15
10 301.16725 23582.084 -14374.431 92.456192 -14281.975 27.5622 27.5622 32.5457 24724.15
20 304.58237 25059.749 -14375.479 93.504609 -14281.974 27.5622 27.5622 32.5457 24724.15
30 312.41477 26504.358 -14377.883 95.9091 -14281.974 27.5622 27.5622 32.5457 24724.15
40 327.67099 26687.057 -14382.566 100.59265 -14281.974 27.5622 27.5622 32.5457 24724.15
50 352.32125 22677.292 -14390.134 108.1601 -14281.974 27.5622 27.5622 32.5457 24724.15
60 388.40592 12472.705 -14401.211 119.23784 -14281.973 27.5622 27.5622 32.5457 24724.15
70 439.97199 -1520.4694 -14417.04 135.06825 -14281.972 27.5622 27.5622 32.5457 24724.15
80 513.34361 -16733.316 -14439.564 157.59282 -14281.971 27.5622 27.5622 32.5457 24724.15
90 613.3542 -31099.591 -14470.267 188.29535 -14281.971 27.5622 27.5622 32.5457 24724.15
100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15
Loop time of 8.92317 on 4 procs for 100 steps with 2376 atoms
Performance: 0.194 ns/day, 123.933 hours/ns, 11.207 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.8912 | 8.9 | 8.9064 | 0.2 | 99.74
Neigh | 0.0027034 | 0.0028808 | 0.0032032 | 0.4 | 0.03
Comm | 0.010964 | 0.017648 | 0.026568 | 5.0 | 0.20
Output | 0.00037575 | 0.00047809 | 0.00053835 | 0.0 | 0.01
Modify | 0.00099134 | 0.001001 | 0.0010085 | 0.0 | 0.01
Other | | 0.001162 | | | 0.01
Nlocal: 594 ave 599 max 589 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 2290.25 ave 2296 max 2282 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 26671.5 ave 26934 max 26495 min
Histogram: 1 0 0 2 0 0 0 0 0 1
FullNghs: 53343 ave 53828 max 52922 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 213372
Ave neighs/atom = 89.803
Neighbor list builds = 1
Dangerous builds = 0
unfix 3
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)
Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15
101 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729
Loop time of 0.193516 on 4 procs for 1 steps with 2376 atoms
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-14509.46351 -14509.46351 -14515.3978891
Force two-norm initial, final = 5602.69 5487.77
Force max component initial, final = 5235.27 5113.06
Final line search alpha, max atom move = 1.91012e-07 0.000976657
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19287 | 0.19299 | 0.19318 | 0.0 | 99.73
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00014043 | 0.00033247 | 0.00045896 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0001886 | | | 0.10
Nlocal: 594 ave 601 max 586 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 2263.25 ave 2271 max 2251 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 26425.8 ave 26807 max 26121 min
Histogram: 1 0 0 1 1 0 0 0 0 1
FullNghs: 52851.5 ave 53580 max 52175 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 211406
Ave neighs/atom = 88.9756
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
reset_timestep 0
thermo 50
fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
run 500
Per MPI rank memory allocation (min/avg/max) = 3.937 | 3.937 | 3.937 Mbytes
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
0 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729
50 1157.347 29332.549 -14679.321 355.29725 -14324.024 27.60903 27.609325 32.375509 24678.772
100 777.55858 101883.12 -14674.854 238.70492 -14436.149 27.778518 27.777373 32.017262 24704.976
150 945.49014 -18305.383 -14806.687 290.25871 -14516.428 27.998313 27.99535 31.670225 24823.838
200 427.46608 -4045.0095 -14674.887 131.22903 -14543.658 28.130283 28.127147 31.431578 24869.438
250 362.82166 -7283.1332 -14669.07 111.38365 -14557.687 28.225232 28.222707 31.238451 24884.314
300 626.2858 7228.0309 -14760.128 192.26526 -14567.862 28.302384 28.299949 31.070038 24885.734
350 859.84293 30084.735 -14845.064 263.96563 -14581.099 28.372349 28.369334 30.934424 24899.261
400 755.26136 54745.408 -14830.701 231.85983 -14598.842 28.450301 28.448361 30.836159 24957.691
450 802.52344 5690.2863 -14860.193 246.36895 -14613.824 28.542311 28.541672 30.773339 25069.354
500 631.84734 -31473.795 -14816.101 193.97261 -14622.128 28.605857 28.605891 30.737955 25152.746
Loop time of 39.7881 on 4 procs for 500 steps with 2376 atoms
Performance: 0.217 ns/day, 110.522 hours/ns, 12.567 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 39.617 | 39.633 | 39.653 | 0.2 | 99.61
Neigh | 0.043624 | 0.046792 | 0.051708 | 1.4 | 0.12
Comm | 0.05215 | 0.072616 | 0.092142 | 5.6 | 0.18
Output | 0.00042915 | 0.00045079 | 0.00051546 | 0.0 | 0.00
Modify | 0.029836 | 0.030341 | 0.03094 | 0.2 | 0.08
Other | | 0.004489 | | | 0.01
Nlocal: 594 ave 606 max 582 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 2226 ave 2238 max 2214 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 25652.8 ave 26129 max 25153 min
Histogram: 1 0 0 0 1 1 0 0 0 1
FullNghs: 51305.5 ave 52398 max 50251 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 205222
Ave neighs/atom = 86.3729
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:00:49