lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@646 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2007-06-22 23:46:37 +00:00
parent b704a82daf
commit e3fa1c4ef6
42 changed files with 159 additions and 6082 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

42
examples/colloid/in.colloid Normal file
View File

@ -0,0 +1,42 @@
# Big colloid particles and small LJ particles
units lj
atom_style atomic
dimension 2
lattice sq 0.01
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
create_atoms 1 box
set group all type/fraction 2 0.96 23984
mass 1 9
mass 2 1
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
fix 2 all enforce2d
dump 1 all atom 200 dump.colloid
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 10000

154
examples/crack/log.crack.12Feb07.liberty.4
View File

@ -1,154 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
2 by 2 by 1 processor grid
create_atoms 1
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
820 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set leftupper atom 2
820 settings made
set leftlower atom 3
841 settings made
set lower atom 4
302 settings made
set upper atom 5
302 settings made
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.02 0.0
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 1000
thermo_modify temp new
neigh_modify exclude type 2 3
dump 1 all atom 250 dump.crack
run 50000
Memory usage per processor = 1.59725 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.010256158 -3.2595015 0 -3.2500081 -0.10145141 4792.6107
1000 0.0050480673 -3.2546391 0 -3.2499665 -0.12639136 4792.6107
2000 0.0051369915 -3.2543578 0 -3.2496028 -0.15975041 4807.2492
3000 0.0052553075 -3.2540343 0 -3.2491699 -0.1774021 4810.8238
4000 0.0050641166 -3.2533514 0 -3.2486639 -0.19022921 4811.9955
5000 0.0050025515 -3.2525683 0 -3.2479378 -0.24015028 4816.2645
6000 0.0049701482 -3.2516756 0 -3.2470751 -0.30916368 4828.9736
7000 0.0051250335 -3.2507402 0 -3.2459963 -0.39169622 4833.0704
8000 0.0048713476 -3.2493641 0 -3.2448551 -0.47693724 4840.7084
9000 0.0049779793 -3.2481153 0 -3.2435076 -0.53299012 4846.9925
10000 0.0049128574 -3.2466686 0 -3.2421212 -0.55373718 4857.8418
11000 0.0049168986 -3.2450986 0 -3.2405474 -0.55984041 4861.948
12000 0.0048612336 -3.2434103 0 -3.2389106 -0.58141697 4864.2222
13000 0.0047721181 -3.2414759 0 -3.2370587 -0.62552646 4869.2639
14000 0.0048830775 -3.2396196 0 -3.2350997 -0.69800852 4875.2845
15000 0.0048743586 -3.2375595 0 -3.2330476 -0.76818454 4889.0238
16000 0.0046772021 -3.2352919 0 -3.2309626 -0.82750427 4897.7014
17000 0.0047699454 -3.2330635 0 -3.2286483 -0.8579342 4904.3594
18000 0.0047753426 -3.2307014 0 -3.2262813 -0.86808974 4910.4271
19000 0.0047514879 -3.2281706 0 -3.2237725 -0.85125679 4912.8684
20000 0.0048479568 -3.2256981 0 -3.2212107 -0.83903361 4916.6492
21000 0.0050005972 -3.223304 0 -3.2186754 -0.86141301 4923.3107
22000 0.0051837721 -3.2210129 0 -3.2162147 -0.91497358 4935.0337
23000 0.0055014883 -3.2187173 0 -3.213625 -0.98259066 4945.2474
24000 0.0059415321 -3.2164221 0 -3.2109225 -1.0173765 4957.1622
25000 0.0064260911 -3.2142138 0 -3.2082656 -0.99854249 4959.1051
26000 0.0068764456 -3.2118739 0 -3.2055089 -0.96174337 4961.1023
27000 0.0067647514 -3.2089962 0 -3.2027346 -0.91577995 4957.1713
28000 0.0073747742 -3.2067583 0 -3.199932 -0.9190562 4964.7136
29000 0.0081414686 -3.2046855 0 -3.1971496 -0.97705845 4980.1961
30000 0.0088053861 -3.2024749 0 -3.1943244 -0.99081318 4997.4212
31000 0.0093650101 -3.2005673 0 -3.1918989 -1.0220683 5011.6892
32000 0.0098581693 -3.1984747 0 -3.1893498 -1.0266826 5014.6599
33000 0.011028173 -3.1969382 0 -3.1867302 -0.94832256 5010.2518
34000 0.011643915 -3.1949468 0 -3.184169 -0.90746422 5017.2254
35000 0.01332772 -3.1938256 0 -3.1814891 -0.85591111 5047.1343
36000 0.014454124 -3.1918323 0 -3.1784532 -0.86634436 5054.2179
37000 0.016378188 -3.190944 0 -3.175784 -0.92602308 5077.4837
38000 0.017843754 -3.1898052 0 -3.1732887 -0.90546324 5086.0006
39000 0.019366756 -3.1887586 0 -3.1708323 -0.80190332 5089.7603
40000 0.022135202 -3.1894278 0 -3.168939 -0.71192011 5093.5652
41000 0.024807374 -3.1902712 0 -3.1673089 -0.629612 5095.3221
42000 0.027696152 -3.1913199 0 -3.1656837 -0.65566924 5086.8449
43000 0.028906545 -3.1904171 0 -3.1636605 -0.62599838 5095.1026
44000 0.029856229 -3.1894006 0 -3.161765 -0.63227312 5109.8945
45000 0.031334749 -3.1888949 0 -3.1598907 -0.62759443 5122.9902
46000 0.034602854 -3.1903219 0 -3.1582927 -0.67305941 5123.8907
47000 0.034415071 -3.1883711 0 -3.1565157 -0.67895291 5133.6318
48000 0.035822122 -3.188003 0 -3.1548452 -0.56873296 5146.4656
49000 0.035461417 -3.1863792 0 -3.1535553 -0.49114989 5146.0215
50000 0.036039942 -3.1854474 0 -3.152088 -0.47443899 5165.9937
Loop time of 71.7721 on 4 procs for 50000 steps with 8141 atoms
Pair time (%) = 45.6852 (63.6532)
Neigh time (%) = 0.910263 (1.26827)
Comm time (%) = 11.0603 (15.4103)
Outpt time (%) = 3.16426 (4.40877)
Other time (%) = 10.9521 (15.2595)
Nlocal: 2035.25 ave 2093 max 1983 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 201.5 ave 246 max 141 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 17745.5 ave 18295 max 17485 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 70982
Ave neighs/atom = 8.71908
Neighbor list builds = 491
Dangerous builds = 0

154
examples/crack/log.crack.12Feb07.linux.1
View File

@ -1,154 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
1 by 1 by 1 processor grid
create_atoms 1
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
820 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set leftupper atom 2
820 settings made
set leftlower atom 3
841 settings made
set lower atom 4
302 settings made
set upper atom 5
302 settings made
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.02 0.0
velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 1000
thermo_modify temp new
neigh_modify exclude type 2 3
dump 1 all atom 250 dump.crack
run 50000
Memory usage per processor = 2.04243 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.010233422 -3.2595015 0 -3.2500292 -0.10147524 4792.6107
1000 0.0051057052 -3.2546357 0 -3.2499098 -0.13099352 4792.6107
2000 0.0051305159 -3.2543693 0 -3.2496204 -0.16341482 4807.4758
3000 0.005186568 -3.2539935 0 -3.2491927 -0.17782954 4808.2338
4000 0.005087842 -3.2533474 0 -3.248638 -0.18347851 4814.6291
5000 0.004952798 -3.2525326 0 -3.2479482 -0.23680218 4819.1809
6000 0.004991209 -3.2516461 0 -3.2470261 -0.30814679 4826.0224
7000 0.004944807 -3.2506197 0 -3.2460426 -0.39136722 4830.7072
8000 0.0049376929 -3.2494443 0 -3.2448739 -0.48674075 4839.3787
9000 0.0050078092 -3.2482053 0 -3.24357 -0.53039175 4853.1439
10000 0.004983781 -3.2466688 0 -3.2420557 -0.55385151 4857.416
11000 0.0049723432 -3.2451304 0 -3.2405279 -0.56009417 4862.5452
12000 0.0049013912 -3.243408 0 -3.2388712 -0.57381742 4865.356
13000 0.0048043804 -3.2415478 0 -3.2371007 -0.62822628 4866.3058
14000 0.0048263329 -3.2395963 0 -3.2351289 -0.69278151 4872.0789
15000 0.0047872575 -3.2375073 0 -3.2330761 -0.77081332 4885.8904
16000 0.0047945553 -3.2353167 0 -3.2308787 -0.82826028 4893.1664
17000 0.0047216486 -3.2330128 0 -3.2286423 -0.86086905 4902.0617
18000 0.0047886085 -3.2306714 0 -3.226239 -0.86709584 4912.8232
19000 0.0048029287 -3.2282267 0 -3.223781 -0.8478792 4914.5926
20000 0.0049477774 -3.22582 0 -3.2212403 -0.83551748 4917.3514
21000 0.0050097792 -3.2233599 0 -3.2187228 -0.83827951 4924.4496
22000 0.0052037073 -3.2210367 0 -3.21622 -0.87712941 4935.4747
23000 0.005250599 -3.2186209 0 -3.2137608 -0.95723098 4947.854
24000 0.0056583383 -3.2164899 0 -3.2112524 -0.99733057 4959.3194
25000 0.006177144 -3.2143646 0 -3.2086469 -0.99156085 4966.2512
26000 0.0065570098 -3.2120894 0 -3.2060201 -0.94420666 4960.9584
27000 0.0065182894 -3.2093666 0 -3.2033331 -0.87993179 4961.9079
28000 0.0068038044 -3.2067846 0 -3.2004869 -0.86598793 4967.889
29000 0.0077170662 -3.2049416 0 -3.1977985 -0.91334819 4981.938
30000 0.0081816546 -3.2027043 0 -3.1951312 -0.9653003 4996.292
31000 0.0089120184 -3.2008682 0 -3.192619 -0.99183522 5012.9271
32000 0.0095675926 -3.1988646 0 -3.1900086 -0.98991289 5018.881
33000 0.010803233 -3.1974474 0 -3.1874477 -0.94112056 5012.4944
34000 0.011158338 -3.195224 0 -3.1848955 -0.8851475 5006.3799
35000 0.011756558 -3.193118 0 -3.1822359 -0.83787524 5002.794
36000 0.011908028 -3.1908083 0 -3.179786 -0.82041394 5013.2137
37000 0.014248791 -3.1903606 0 -3.1771716 -0.86591483 5045.4357
38000 0.015514642 -3.1889367 0 -3.1745759 -0.84629532 5058.8659
39000 0.017625744 -3.1886096 0 -3.1722948 -0.72912473 5086.8791
40000 0.020166221 -3.1891916 0 -3.1705253 -0.57976268 5092.6354
41000 0.024585629 -3.191961 0 -3.169204 -0.45986861 5092.2489
42000 0.025792679 -3.191911 0 -3.1680367 -0.41104431 5084.743
43000 0.027413976 -3.1918738 0 -3.1664988 -0.317039 5103.4238
44000 0.029084803 -3.1924106 0 -3.165489 -0.35382128 5093.6381
45000 0.028426053 -3.1910339 0 -3.1647221 -0.40685905 5115.0911
46000 0.028866755 -3.190439 0 -3.1637193 -0.44541816 5121.2964
47000 0.02908918 -3.189657 0 -3.1627313 -0.4265388 5149.429
48000 0.028710143 -3.1882276 0 -3.1616528 -0.45494173 5166.6376
49000 0.03082438 -3.1885404 0 -3.1600086 -0.4068 5164.3287
50000 0.032521821 -3.1887517 0 -3.1586487 -0.31047628 5170.302
Loop time of 449.517 on 1 procs for 50000 steps with 8141 atoms
Pair time (%) = 363.166 (80.7903)
Neigh time (%) = 6.23528 (1.38711)
Comm time (%) = 0.552309 (0.122867)
Outpt time (%) = 7.92898 (1.76389)
Other time (%) = 71.6341 (15.9358)
Nlocal: 8141 ave 8141 max 8141 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 70714 ave 70714 max 70714 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 70714
Ave neighs/atom = 8.68616
Neighbor list builds = 488
Dangerous builds = 0

35
examples/dipole/in.dipole Normal file
View File

@ -0,0 +1,35 @@
# Point dipoles in a 2d box
units lj
atom_style dipole
dimension 2
lattice sq2 0.7
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
create_atoms 1 box
mass 1 1.0
shape 1 1 1 1
dipole 1 0.75
set group all dipole/random 98934
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/dipole
fix 2 all enforce2d
timestep 0.005
thermo_style dipole
thermo 500
dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
run 10000

51
examples/ellipse/in.ellipse Normal file
View File

@ -0,0 +1,51 @@
# Ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
create_atoms 1 box
set group all type/fraction 2 0.1 95392
set group all quat/random 18238
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
compute rot all temp/asphere
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
dump 1 all custom 100 dump.ellipse &
tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000

122
examples/flow/log.flow.couette.12Feb07.liberty.4
View File

@ -1,122 +0,0 @@
LAMMPS (12 Feb 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set lower atom 2
60 settings made
set upper atom 3
60 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poisseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236
1000 1 -0.36129869 0 0.3494156 3.254923 366.96236
1500 1.1299217 -0.37859354 0 0.42445794 3.0386512 366.96236
2000 1 -0.34287549 0 0.3678388 3.1412475 366.96236
2500 1.0894638 -0.38358068 0 0.3907168 2.9575357 366.96236
3000 1 -0.38250431 0 0.32820997 2.9128345 366.96236
3500 1.1577825 -0.41389292 0 0.40895962 3.0892503 366.96236
4000 1 -0.42306155 0 0.28765273 2.5216835 366.96236
4500 1.0340697 -0.39435146 0 0.34057665 2.5709158 366.96236
5000 1 -0.43445662 0 0.27625767 2.7074512 366.96236
5500 1.1091102 -0.45430683 0 0.33395366 2.451199 366.96236
6000 1 -0.41166346 0 0.29905082 2.7464633 366.96236
6500 1.0003563 -0.40533723 0 0.30563029 2.5834633 366.96236
7000 1 -0.3904519 0 0.32026238 2.5201459 366.96236
7500 1.1170747 -0.40190088 0 0.39202009 2.6487896 366.96236
8000 1 -0.46477384 0 0.24594045 2.6442771 366.96236
8500 1.1344912 -0.38276439 0 0.4235347 2.7888644 366.96236
9000 1 -0.39709912 0 0.31361516 2.4730908 366.96236
9500 0.99852413 -0.45682444 0 0.25284093 2.3290285 366.96236
10000 1 -0.45069251 0 0.26002177 2.5361799 366.96236
Loop time of 2.01982 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0898595 (4.4489)
Neigh time (%) = 0.0443295 (2.19473)
Comm time (%) = 1.36553 (67.6066)
Outpt time (%) = 0.164397 (8.13922)
Other time (%) = 0.355701 (17.6106)
Nlocal: 105 ave 115 max 96 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 40.25 ave 44 max 37 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 237.5 ave 296 max 179 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 950
Ave neighs/atom = 2.2619
Neighbor list builds = 984
Dangerous builds = 0

122
examples/flow/log.flow.couette.12Feb07.linux.1
View File

@ -1,122 +0,0 @@
LAMMPS (12 Feb 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set lower atom 2
60 settings made
set upper atom 3
60 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poisseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0604224 -0.31549525 0 0.4381621 3.1208962 366.96236
1000 1 -0.34356865 0 0.36714563 3.0305145 366.96236
1500 1.1738082 -0.382026 0 0.45221626 2.9197883 366.96236
2000 1 -0.42682511 0 0.28388918 2.8469183 366.96236
2500 1.0256109 -0.41905835 0 0.30985794 2.9371918 366.96236
3000 1 -0.47521752 0 0.23549677 2.5062527 366.96236
3500 1.1314909 -0.4206347 0 0.38353207 2.7478302 366.96236
4000 1 -0.43576251 0 0.27495178 2.6141195 366.96236
4500 1.0005992 -0.42588084 0 0.28525931 2.7421664 366.96236
5000 1 -0.42282912 0 0.28788516 2.7688981 366.96236
5500 1.0686835 -0.4761288 0 0.28339982 2.5689028 366.96236
6000 1 -0.42978507 0 0.28092922 2.6551983 366.96236
6500 1.0786904 -0.43713715 0 0.3295035 2.5141669 366.96236
7000 1 -0.4121221 0 0.29859218 2.594973 366.96236
7500 1.0939854 -0.40293252 0 0.37457856 2.6974983 366.96236
8000 1 -0.45181425 0 0.25890004 2.6049049 366.96236
8500 1.0257333 -0.400669 0 0.32833428 2.5577387 366.96236
9000 1 -0.42858125 0 0.28213304 2.5725646 366.96236
9500 1.0823613 -0.38920599 0 0.38004366 2.6543624 366.96236
10000 1 -0.42341732 0 0.28729697 2.4806728 366.96236
Loop time of 2.23208 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.69644 (31.2014)
Neigh time (%) = 0.270545 (12.1208)
Comm time (%) = 0.109265 (4.89521)
Outpt time (%) = 0.417752 (18.7158)
Other time (%) = 0.738079 (33.0669)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 50 ave 50 max 50 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 955 ave 955 max 955 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 955
Ave neighs/atom = 2.27381
Neighbor list builds = 1003
Dangerous builds = 0

122
examples/flow/log.flow.poiss.12Feb07.liberty.4
View File

@ -1,122 +0,0 @@
LAMMPS (12 Feb 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set lower atom 2
60 settings made
set upper atom 3
60 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poisseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.0778761 -0.35048279 0 0.41557918 2.8792129 369.20271
1000 1 -0.38740705 0 0.32330724 2.2684877 375.93354
1500 1.2052679 -0.37768559 0 0.47891551 1.6193029 376.17118
2000 1 -0.38060118 0 0.33011311 1.4972142 371.27032
2500 1.2211446 -0.39689946 0 0.47098548 1.5612989 364.09539
3000 1 -0.46394625 0 0.24676803 1.5629864 356.17691
3500 1.2338136 -0.5721878 0 0.30470115 1.8177807 344.96808
4000 1 -0.69530976 0 0.015404522 2.3144776 333.06418
4500 1.2279548 -0.72662695 0 0.14609808 2.9985939 323.55709
5000 1 -0.81185506 0 -0.10114077 3.1833009 321.19482
5500 1.2171627 -0.73966198 0 0.12539291 2.711954 325.39659
6000 1 -0.66983997 0 0.040874311 2.1579634 329.73937
6500 1.2267682 -0.66743744 0 0.20444422 2.1114545 331.88829
7000 1 -0.64509348 0 0.065620807 1.9028431 332.49532
7500 1.2202538 -0.6816503 0 0.18560148 2.1227978 329.88213
8000 1 -0.72110847 0 -0.010394181 2.3587956 327.78501
8500 1.2103845 -0.76502979 0 0.095207788 2.5823624 325.21722
9000 1 -0.75191645 0 -0.041202164 2.4020904 324.81713
9500 1.2094179 -0.74196652 0 0.11758403 2.5289414 326.12345
10000 1 -0.7568777 0 -0.046163412 2.5601376 326.60462
Loop time of 2.55875 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0984794 (3.84874)
Neigh time (%) = 0.0253601 (0.991114)
Comm time (%) = 1.34455 (52.547)
Outpt time (%) = 0.313694 (12.2597)
Other time (%) = 0.776668 (30.3534)
Nlocal: 105 ave 106 max 103 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 43.75 ave 45 max 41 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 276.5 ave 291 max 256 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 1106
Ave neighs/atom = 2.63333
Neighbor list builds = 553
Dangerous builds = 0

122
examples/flow/log.flow.poiss.12Feb07.linux.1
View File

@ -1,122 +0,0 @@
LAMMPS (12 Feb 2007)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set lower atom 2
60 settings made
set upper atom 3
60 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poisseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.54228995 366.96236
500 1.1036177 -0.37435595 0 0.4100009 2.6003586 369.52344
1000 1 -0.40278179 0 0.30793249 2.0566706 375.56836
1500 1.2346487 -0.41204291 0 0.46543956 1.6254791 376.55032
2000 1 -0.40773469 0 0.3029796 1.5174808 374.73899
2500 1.2225527 -0.43831258 0 0.43057311 1.538442 366.48806
3000 1 -0.49535282 0 0.21536146 1.5818917 355.29347
3500 1.2493993 -0.59973642 0 0.28822953 1.7491905 344.52279
4000 1 -0.67338979 0 0.037324493 2.0787539 332.81149
4500 1.1956948 -0.72693321 0 0.12286419 3.0234335 322.85596
5000 1 -0.74958096 0 -0.038866674 3.2864093 320.05477
5500 1.1735028 -0.73256028 0 0.10146491 2.7725647 321.70778
6000 1 -0.68197653 0 0.028737759 2.4161345 328.01856
6500 1.1989708 -0.63163198 0 0.2204937 2.0979387 331.80767
7000 1 -0.65810386 0 0.052610422 2.1889649 331.12128
7500 1.2335065 -0.65237655 0 0.22429412 2.1016554 330.36358
8000 1 -0.68661166 0 0.024102628 2.1253504 327.99967
8500 1.2297323 -0.72995326 0 0.14403503 2.4289517 324.51364
9000 1 -0.72767623 0 -0.016961948 2.4354045 323.49316
9500 1.2252226 -0.75893761 0 0.1118456 2.5476916 324.00783
10000 1 -0.73637225 0 -0.025657963 2.3491973 324.64848
Loop time of 2.7534 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.762382 (27.6888)
Neigh time (%) = 0.157095 (5.70549)
Comm time (%) = 0.098925 (3.59283)
Outpt time (%) = 0.84692 (30.7591)
Other time (%) = 0.888077 (32.2538)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 53 ave 53 max 53 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1128 ave 1128 max 1128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1128
Ave neighs/atom = 2.68571
Neighbor list builds = 558
Dangerous builds = 0

140
examples/friction/log.friction.12Feb07.liberty.4
View File

@ -1,140 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
2 by 2 by 1 processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 110 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
860 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1422 atoms in group mobile
set lo-fixed atom 4
150 settings made
set hi-fixed atom 4
150 settings made
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
dump 1 all atom 100 dump.friction
run 20000
Memory usage per processor = 1.46023 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128
1000 0.088860957 -3.0636883 0 -3.0270758 0.0047805196 1384.4128
2000 0.087112073 -3.066344 0 -3.030452 -0.63632956 1384.4128
3000 0.10058239 -3.0642114 0 -3.0227694 -0.25555813 1384.4128
4000 0.093260137 -3.0555323 0 -3.0171072 -0.40761447 1384.4128
5000 0.11067201 -3.0399212 0 -2.994322 0.066689705 1384.4128
6000 0.10526463 -3.0390544 0 -2.9956832 -0.51522958 1384.4128
7000 0.11541593 -3.0403447 0 -2.992791 -0.41397003 1384.4128
8000 0.10197576 -3.0347747 0 -2.9927585 -0.5486861 1384.4128
9000 0.11134064 -3.0333357 0 -2.9874611 -0.35496419 1384.4128
10000 0.11080628 -3.0436254 0 -2.9979709 -0.46700659 1384.4128
11000 0.11943821 -3.0413975 0 -2.9921865 -0.30699848 1384.4128
12000 0.10413208 -3.0510277 0 -3.0081231 -0.36572201 1384.4128
13000 0.099296169 -3.039397 0 -2.9984849 -0.4947437 1384.4128
14000 0.10330462 -3.0420671 0 -2.9995034 -0.39995589 1384.4128
15000 0.10870951 -3.038746 0 -2.9939554 -0.50477181 1384.4128
16000 0.11417657 -3.0464982 0 -2.9994551 -0.32657064 1384.4128
17000 0.10800189 -3.047902 0 -3.0034029 -0.41936081 1384.4128
18000 0.10829723 -3.0458306 0 -3.0012098 -0.41668893 1384.4128
19000 0.10404908 -3.0526816 0 -3.0098112 -0.41121519 1384.4128
20000 0.10691019 -3.0411759 0 -2.9971266 -0.23642395 1384.4128
Loop time of 9.48287 on 4 procs for 20000 steps with 1722 atoms
Pair time (%) = 3.73598 (39.3971)
Neigh time (%) = 0.214309 (2.25996)
Comm time (%) = 3.45572 (36.4417)
Outpt time (%) = 0.605395 (6.38409)
Other time (%) = 1.47147 (15.5171)
Nlocal: 430.5 ave 482 max 375 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 92 ave 117 max 76 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Neighs: 3601.25 ave 4057 max 3129 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 14405
Ave neighs/atom = 8.36527
Neighbor list builds = 750
Dangerous builds = 0

140
examples/friction/log.friction.12Feb07.linux.1
View File

@ -1,140 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 110 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
860 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1422 atoms in group mobile
set lo-fixed atom 4
150 settings made
set hi-fixed atom 4
150 settings made
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
dump 1 all atom 100 dump.friction
run 20000
Memory usage per processor = 1.53816 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128
1000 0.088253389 -3.0560474 0 -3.0196852 0.050420633 1384.4128
2000 0.087864125 -3.0547262 0 -3.0185243 -0.67004561 1384.4128
3000 0.10557467 -3.0607837 0 -3.0172848 -0.221612 1384.4128
4000 0.085491315 -3.0478702 0 -3.012646 -0.42154648 1384.4128
5000 0.10534884 -3.051862 0 -3.0084561 -0.087935136 1384.4128
6000 0.10556767 -3.0559544 0 -3.0124583 -0.54210169 1384.4128
7000 0.098711954 -3.0590419 0 -3.0183705 -0.42838742 1384.4128
8000 0.11529691 -3.0366296 0 -2.9891248 -0.4457814 1384.4128
9000 0.1 -3.0333227 0 -2.9921206 -0.49174903 1384.4128
10000 0.11644796 -3.04181 0 -2.993831 -0.41991946 1384.4128
11000 0.1051652 -3.0340308 0 -2.9907005 -0.61535665 1384.4128
12000 0.10761127 -3.0351207 0 -2.9907826 -0.30937044 1384.4128
13000 0.11361189 -3.0354003 0 -2.9885898 -0.44289723 1384.4128
14000 0.11530172 -3.037545 0 -2.9900383 -0.31673329 1384.4128
15000 0.098629121 -3.0397602 0 -2.9991229 -0.44569024 1384.4128
16000 0.10525229 -3.0429476 0 -2.9995815 -0.29935796 1384.4128
17000 0.10467455 -3.0381932 0 -2.9950651 -0.48920299 1384.4128
18000 0.10817926 -3.0402364 0 -2.9956643 -0.37596363 1384.4128
19000 0.10816167 -3.0452456 0 -3.0006808 -0.35822139 1384.4128
20000 0.11364667 -3.0448494 0 -2.9980246 -0.40159119 1384.4128
Loop time of 39.1823 on 1 procs for 20000 steps with 1722 atoms
Pair time (%) = 28.9006 (73.7594)
Neigh time (%) = 1.39861 (3.5695)
Comm time (%) = 0.380868 (0.972041)
Outpt time (%) = 3.67569 (9.381)
Other time (%) = 4.82651 (12.3181)
Nlocal: 1722 ave 1722 max 1722 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 146 ave 146 max 146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14398 ave 14398 max 14398 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14398
Ave neighs/atom = 8.36121
Neighbor list builds = 728
Dangerous builds = 0

169
examples/indent/log.indent.12Feb07.liberty.4
View File

@ -1,169 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set lower atom 2
60 settings made
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.44615 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681
2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856
3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439
4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265
5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573
6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734648 249.1402
7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327
8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825
9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265
10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407
11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776
12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714
13000 0.11341039 -3.0596733 0 -2.9628694 1.1566167 249.36303
14000 0.1176102 -3.058063 0 -2.9576743 1.2083863 249.05567
15000 0.12582683 -3.054119 0 -2.9467168 1.052489 254.01804
16000 0.11716129 -3.0359809 0 -2.9359753 1.1111189 259.94912
17000 0.11836208 -3.0276209 0 -2.9265904 1.0821166 257.9832
18000 0.12271609 -3.0171547 0 -2.9124077 1.511924 264.99507
19000 0.11746326 -3.0102961 0 -2.9100328 1.6305608 267.60875
20000 0.12091083 -2.996777 0 -2.893571 1.7996398 268.87085
21000 0.1263182 -2.9950013 0 -2.8871797 1.8539429 271.55393
22000 0.12425331 -2.9761891 0 -2.87013 1.5415686 276.54337
23000 0.11563313 -2.9874945 0 -2.8887934 1.2018805 279.40748
24000 0.11553831 -2.9945403 0 -2.8959201 1.5305748 278.38798
25000 0.11085112 -2.9896742 0 -2.8950548 1.8815906 275.87487
26000 0.12077848 -2.986181 0 -2.883088 1.9122673 275.91918
27000 0.12399848 -2.9814354 0 -2.8755938 1.9167983 278.64025
28000 0.12143106 -3.0225278 0 -2.9188777 0.56589243 290.55803
29000 0.11959029 -3.0121799 0 -2.9101011 0.49660855 295.49221
30000 0.11931566 -3.0215043 0 -2.9196598 0.83146141 294.35452
Loop time of 7.1529 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.4201 (19.8535)
Neigh time (%) = 0.0487321 (0.681291)
Comm time (%) = 4.28154 (59.8574)
Outpt time (%) = 0.109681 (1.53338)
Other time (%) = 1.29285 (18.0744)
Nlocal: 105 ave 125 max 79 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 92.75 ave 104 max 77 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 901 ave 1133 max 620 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3604
Ave neighs/atom = 8.58095
Neighbor list builds = 622
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.4468 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11931566 -3.0215043 0 -2.9196598 0.83281489 293.87614
31000 0.1167364 -3.0429651 0 -2.9433222 -0.36091255 293.88145
32000 0.12641731 -3.0639714 0 -2.9560652 -0.46898184 290.09909
33000 0.10706313 -3.0741804 0 -2.9827944 0.00022078579 285.15883
34000 0.11367315 -3.0688054 0 -2.9717772 -0.76240201 289.87707
35000 0.10655807 -3.0627342 0 -2.9717793 -0.26051048 288.22641
36000 0.11703008 -3.0716705 0 -2.971777 -0.1853764 285.83663
37000 0.11221734 -3.0675632 0 -2.9717776 -0.73386022 290.12632
38000 0.11874224 -3.0731334 0 -2.9717784 -0.12687563 285.36376
39000 0.1189778 -3.0733361 0 -2.9717801 -0.25499323 287.084
40000 0.11898338 -3.0620885 0 -2.9605277 -0.62541843 288.73621
41000 0.1167364 -3.0735602 0 -2.9739173 -0.11692923 283.98124
42000 0.11266172 -3.0700831 0 -2.9739183 -0.39632943 286.59658
43000 0.11902827 -3.0755188 0 -2.9739196 -0.57312115 287.53858
44000 0.12554232 -3.0810812 0 -2.9739219 -0.070954433 286.20995
45000 0.11075688 -3.0684563 0 -2.9739174 -0.55071995 288.55119
46000 0.12586051 -3.0707391 0 -2.9633081 -0.48923571 289.30041
47000 0.11671697 -3.0736442 0 -2.9740179 -0.12378289 285.31819
48000 0.10853944 -3.0666634 0 -2.9740172 -0.57661015 289.17231
49000 0.1167364 -3.0679033 0 -2.9682604 -0.28913991 286.84813
50000 0.10777198 -3.0602483 0 -2.9682572 -0.2607135 286.76228
51000 0.10971818 -3.0619099 0 -2.9682576 -0.50602899 289.54807
52000 0.12283301 -3.0731069 0 -2.9682602 -0.17101974 286.39074
53000 0.11323492 -3.0762744 0 -2.9796203 -0.39853784 289.81061
54000 0.12076965 -3.0709553 0 -2.9678698 -0.3939254 288.24037
55000 0.12319168 -3.0730238 0 -2.9678709 -0.17986864 284.15611
56000 0.12040501 -3.0706451 0 -2.9678708 -0.34825544 286.68764
57000 0.12192823 -3.0719452 0 -2.9678707 -0.42539274 287.8374
58000 0.11878678 -3.0692629 0 -2.9678699 -0.24575165 286.73167
59000 0.11418711 -3.0653342 0 -2.9678674 -0.51388179 287.99512
60000 0.11462897 -3.0657114 0 -2.9678673 -0.4538483 288.11403
Loop time of 7.11751 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.39714 (19.6297)
Neigh time (%) = 0.0485521 (0.68215)
Comm time (%) = 4.35769 (61.2249)
Outpt time (%) = 0.111284 (1.56352)
Other time (%) = 1.20284 (16.8997)
Nlocal: 105 ave 122 max 82 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 92 ave 101 max 82 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 888.5 ave 1097 max 643 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3554
Ave neighs/atom = 8.4619
Neighbor list builds = 630
Dangerous builds = 0

169
examples/indent/log.indent.12Feb07.linux.1
View File

@ -1,169 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 processor grid
create_atoms 1
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set lower atom 2
60 settings made
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282
1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001
2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098
3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041
4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717
5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708
6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216
7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979
8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714
9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256
10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836
11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926
12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761
13000 0.12031568 -3.0583679 0 -2.9556699 1.2700141 247.59077
14000 0.1167364 -3.0548463 0 -2.9552034 1.0859392 250.18904
15000 0.1167364 -3.0549235 0 -2.9552806 1.2995977 251.78491
16000 0.12471796 -3.0524621 0 -2.9460064 1.6452633 249.66328
17000 0.12078141 -3.0356474 0 -2.9325519 1.9172375 248.00713
18000 0.11737951 -3.0294793 0 -2.9292875 1.984307 254.03132
19000 0.12273273 -3.016492 0 -2.9117309 1.9954892 251.8583
20000 0.12551089 -3.0011944 0 -2.8940619 1.7797455 260.26155
21000 0.12037224 -2.9934253 0 -2.890679 1.3694744 269.07586
22000 0.12174807 -3.0193123 0 -2.9153916 0.94134986 270.00347
23000 0.12706029 -3.0244275 0 -2.9159725 1.1867392 266.05204
24000 0.11467621 -3.0095158 0 -2.9116314 0.73011254 267.48776
25000 0.11535618 -3.0158848 0 -2.91742 1.2611256 266.59514
26000 0.10710521 -3.0133947 0 -2.9219727 0.67441358 268.32045
27000 0.12422208 -3.0164988 0 -2.9104663 1.1543726 268.18532
28000 0.11139527 -3.0072089 0 -2.9121251 1.4607146 265.23157
29000 0.1167364 -3.0085086 0 -2.9088658 1.6594744 265.37526
30000 0.11102647 -3.0064551 0 -2.9116861 1.3943384 268.60718
Loop time of 15.887 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 10.9921 (69.1889)
Neigh time (%) = 0.333033 (2.09625)
Comm time (%) = 0.347973 (2.19029)
Outpt time (%) = 1.87511 (11.8028)
Other time (%) = 2.33885 (14.7218)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 109 ave 109 max 109 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3655 ave 3655 max 3655 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3655
Ave neighs/atom = 8.70238
Neighbor list builds = 616
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.45035 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11102647 -3.0064551 0 -2.9116861 1.3929673 268.87157
31000 0.12620212 -3.0510755 0 -2.943353 -0.18214813 273.9697
32000 0.11450566 -3.0412855 0 -2.9435467 -0.36947207 273.74363
33000 0.11300395 -3.0666261 0 -2.9701691 -0.36891232 262.29844
34000 0.11360641 -3.0910465 0 -2.9940753 -0.2930611 263.47461
35000 0.11792208 -3.0826962 0 -2.9820413 -0.53020156 264.92677
36000 0.1167364 -3.0791913 0 -2.9795484 -0.28901516 264.42654
37000 0.11195363 -3.075108 0 -2.9795476 -0.35271906 264.6512
38000 0.11608571 -3.0786363 0 -2.9795489 -0.5028598 264.60065
39000 0.1177969 -3.0800557 0 -2.9795076 -0.32434056 263.66269
40000 0.11466668 -3.0774252 0 -2.979549 -0.40950185 263.65927
41000 0.11118976 -3.0744545 0 -2.9795461 -0.58454381 264.39108
42000 0.11460312 -3.0773684 0 -2.9795464 -0.20755902 262.35795
43000 0.11677527 -3.0792261 0 -2.97955 -0.49949012 264.53893
44000 0.11158159 -3.0747894 0 -2.9795466 -0.37452501 263.88851
45000 0.12176422 -3.0834855 0 -2.979551 -0.16070447 262.66164
46000 0.11682005 -3.0792615 0 -2.9795472 -0.63716759 266.07809
47000 0.11262188 -3.0756805 0 -2.9795497 -0.15500292 263.19673
48000 0.12119234 -3.0829975 0 -2.9795512 -0.39672723 263.37224
49000 0.11784014 -3.0801322 0 -2.9795473 -0.42268487 265.07121
50000 0.11675902 -3.0792108 0 -2.9795486 -0.1111771 261.69863
51000 0.11170649 -3.0748959 0 -2.9795465 -0.46340258 263.55401
52000 0.12175858 -3.0834809 0 -2.9795513 -0.48539416 263.47789
53000 0.12074224 -3.0964747 0 -2.9934126 -0.4846085 262.58631
54000 0.11099551 -3.0767379 0 -2.9819953 -0.39099317 263.38816
55000 0.11519489 -3.0803219 0 -2.9819948 -0.38576064 263.5242
56000 0.11716036 -3.0820002 0 -2.9819954 -0.26199121 262.69272
57000 0.10872156 -3.0792099 0 -2.9864083 -0.49564243 267.348
58000 0.12397214 -3.0923068 0 -2.9864877 -0.37680531 262.14403
59000 0.11456625 -3.0842744 0 -2.9864839 -0.30718293 263.3254
60000 0.11413467 -3.0839074 0 -2.9864853 -0.54302442 263.54231
Loop time of 13.8006 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 10.8642 (78.7224)
Neigh time (%) = 0.336436 (2.43783)
Comm time (%) = 0.357799 (2.59263)
Outpt time (%) = 0.267058 (1.93512)
Other time (%) = 1.97515 (14.312)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 101 ave 101 max 101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3570 ave 3570 max 3570 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3570
Ave neighs/atom = 8.5
Neighbor list builds = 630
Dangerous builds = 0

59
examples/meam/log.meam.12Feb07.liberty.4
View File

@ -1,59 +0,0 @@
LAMMPS (12 Feb 2007)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
2 by 1 by 2 processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C sic.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.40047 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.182669 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.149615 (81.905)
Neigh time (%) = 0.00144577 (0.791468)
Comm time (%) = 0.0237137 (12.9818)
Outpt time (%) = 0.00633347 (3.46718)
Other time (%) = 0.00156116 (0.854639)
Nlocal: 32 ave 33 max 31 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 291.25 ave 297 max 284 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 384.25 ave 419 max 351 min
Histogram: 1 0 0 0 2 0 0 0 0 1
FullNghs: 768.5 ave 805 max 731 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10

59
examples/meam/log.meam.12Feb07.linux.1
View File

@ -1,59 +0,0 @@
LAMMPS (12 Feb 2007)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
1 by 1 by 1 processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C sic.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
dump 1 all atom 10 dump.meam
run 100
Memory usage per processor = 4.5032 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.93784 0 -636.93784 -76401.859
10 1777.5718 -666.27518 0 -637.0945 -150596.32
20 1908.6646 -668.42203 0 -637.08932 -120846.06
30 1937.3373 -668.90047 0 -637.09706 -101367.81
40 2110.906 -671.75978 0 -637.10706 -110475.14
50 2057.8682 -670.89589 0 -637.11385 -107817.44
60 1887.9614 -668.08977 0 -637.09693 -108906.46
70 2036.4427 -670.53667 0 -637.10635 -113836.91
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.452112 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.425796 (94.1793)
Neigh time (%) = 0.008883 (1.96478)
Comm time (%) = 0.004133 (0.914154)
Outpt time (%) = 0.009616 (2.12691)
Other time (%) = 0.003684 (0.814842)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 541 ave 541 max 541 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1537 ave 1537 max 1537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3074 ave 3074 max 3074 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3074
Ave neighs/atom = 24.0156
Neighbor list builds = 10
Dangerous builds = 10

163
examples/meam/log.meam.shear.12Feb07.liberty.4
View File

@ -1,163 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 5.05583 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346
50 300 -8152.0635 0 -8098.4335 10060.658 19678.279
75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8
100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128
Loop time of 1.77507 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 1.7326 (97.6074)
Neigh time (%) = 0.00833803 (0.469729)
Comm time (%) = 0.0229964 (1.29552)
Outpt time (%) = 0.000789106 (0.0444549)
Other time (%) = 0.0103461 (0.582853)
Nlocal: 478 ave 486 max 469 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 809 ave 818 max 801 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 5932.75 ave 6076 max 5807 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 11865.5 ave 12111 max 11653 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 47462
Ave neighs/atom = 24.8232
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.meam.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 5.10101 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
100 304.48468 -8173.0606 0 -8136.7859 425.54216 19949.638
200 292.7057 -8176.0355 0 -8141.1641 -420.37567 19967.921
300 300 -8174.2457 0 -8138.5052 -2225.0957 20035.454
400 301.8783 -8169.8228 0 -8133.8586 -954.54062 20072.806
500 297.3529 -8163.9704 0 -8128.5453 -636.90863 20224.627
600 300.21575 -8158.4937 0 -8122.7275 426.04354 20300.212
700 294.62668 -8149.3419 0 -8114.2416 2914.3315 20397.69
800 297.68293 -8140.221 0 -8104.7566 4382.9813 20500.434
900 307.34872 -8129.6288 0 -8093.0129 6273.2975 20626.218
1000 299.54856 -8114.9745 0 -8079.2878 9036.1509 20758.108
1100 298.61047 -8098.7531 0 -8063.1782 10485.79 20872.901
1200 293.03092 -8082.1069 0 -8047.1967 11405.523 21004.792
1300 307.76805 -8065.4274 0 -8028.7615 11979.925 21120.806
1400 300 -8051.592 0 -8015.8516 12466.399 21238.042
1500 308.53314 -8037.7116 0 -8000.9546 15186.116 21363.826
1600 300 -8031.857 0 -7996.1166 16229.579 21487.167
1700 300 -8022.9424 0 -7987.202 18187.876 21605.624
1800 300 -8009.2389 0 -7973.4984 18721.834 21735.072
1900 300.26712 -7997.956 0 -7962.1837 18855.604 21848.644
2000 300 -7987.6035 0 -7951.8631 18711.312 21976.871
2100 300 -7996.1806 0 -7960.4401 16424.414 22100.212
2200 305.54436 -8006.7713 0 -7970.3703 13205.691 22211.342
2300 300 -8010.5965 0 -7974.8561 11455.319 22342.011
2400 300 -8012.9434 0 -7977.2029 12543.014 22469.016
2500 300 -8014.3999 0 -7978.6595 12003.377 22583.809
2600 296.98849 -8009.1337 0 -7973.7521 11080.253 22707.151
2700 300 -8002.4065 0 -7966.666 8890.8608 22836.599
2800 300 -8005.4907 0 -7969.7503 7724.8308 22956.277
2900 308.79197 -8003.0392 0 -7966.2514 8308.48 23072.291
3000 300 -8014.1797 0 -7978.4393 5468.9701 23199.297
Loop time of 57.0237 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 54.0924 (94.8594)
Neigh time (%) = 0.376733 (0.660661)
Comm time (%) = 0.885298 (1.55251)
Outpt time (%) = 1.00536 (1.76305)
Other time (%) = 0.663957 (1.16435)
Nlocal: 478 ave 521 max 447 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 790.5 ave 838 max 745 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 5842.25 ave 6343 max 5608 min
Histogram: 1 2 0 0 0 0 0 0 0 1
FullNghs: 11684.5 ave 12654 max 11231 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 46738
Ave neighs/atom = 24.4446
Neighbor list builds = 225
Dangerous builds = 0

163
examples/meam/log.meam.shear.12Feb07.linux.1
View File

@ -1,163 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 5.90372 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346
25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346
50 300 -8149.7654 0 -8096.1353 10637.302 19676.681
75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029
100 300 -8173.6884 0 -8120.0584 5954.839 19878.848
Loop time of 8.44709 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 8.32882 (98.5999)
Neigh time (%) = 0.064361 (0.761931)
Comm time (%) = 0.015878 (0.18797)
Outpt time (%) = 0.001083 (0.012821)
Other time (%) = 0.036945 (0.43737)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1672 ave 1672 max 1672 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23806 ave 23806 max 23806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47612 ave 47612 max 47612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47612
Ave neighs/atom = 24.9017
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.meam.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 6.13252 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
100 292.43462 -8178.5214 0 -8143.6823 2595.8245 19846.142
200 302.79029 -8177.5966 0 -8141.5238 928.09995 20038.569
300 291.68573 -8173.4974 0 -8138.7474 -1202.8487 20113.221
400 300 -8170.0629 0 -8134.3225 -1617.1537 20115.738
500 308.49792 -8164.7324 0 -8127.9796 -346.62656 20250.005
600 308.95879 -8159.1257 0 -8122.3179 1160.1349 20280.432
700 303.02599 -8150.2418 0 -8114.1409 2807.9227 20434.583
800 305.36804 -8140.8077 0 -8104.4278 3218.2338 20500.434
900 305.593 -8128.943 0 -8092.5363 3121.7248 20628.661
1000 308.39114 -8113.6413 0 -8076.9012 5180.0491 20758.108
1100 304.62199 -8096.7999 0 -8060.5088 8173.3442 20874.123
1200 293.41155 -8082.676 0 -8047.7205 9884.2077 20987.695
1300 303.32764 -8066.7733 0 -8030.6365 10196.38 21108.594
1400 304.17521 -8049.5115 0 -8013.2736 11518.937 21249.033
1500 300 -8038.1747 0 -8002.4342 12554.583 21361.383
1600 304.95273 -8030.5805 0 -7994.2501 12166.296 21483.504
1700 302.82122 -8019.1918 0 -7983.1152 11726.855 21604.403
1800 300 -8010.2021 0 -7974.4617 11039.327 21737.514
1900 309.75034 -7999.8523 0 -7962.9503 10360.771 21859.635
2000 303.95534 -7995.5876 0 -7959.3759 11106.855 21974.428
2100 300 -7998.4845 0 -7962.7441 9592.4431 22092.885
2200 300 -8010.3787 0 -7974.6383 7011.3257 22223.554
2300 300 -8013.8118 0 -7978.0714 7206.5123 22334.684
2400 300 -8016.5277 0 -7980.7872 8333.0814 22469.016
2500 309.73732 -8019.4133 0 -7982.5128 8734.2461 22586.252
2600 300 -8018.1897 0 -7982.4492 9088.9471 22702.266
2700 300.98484 -8016.4337 0 -7980.576 11358.168 22821.944
2800 309.26899 -8013.3976 0 -7976.5529 11582.101 22956.277
2900 305.82563 -8013.711 0 -7977.2765 8649.9858 23077.176
3000 309.93922 -8013.2879 0 -7976.3634 6488.7794 23187.085
Loop time of 283.508 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 272.659 (96.1731)
Neigh time (%) = 2.77687 (0.979467)
Comm time (%) = 0.520133 (0.183463)
Outpt time (%) = 6.37939 (2.25016)
Other time (%) = 1.17315 (0.413799)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1659 ave 1659 max 1659 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23351 ave 23351 max 23351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46702 ave 46702 max 46702 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46702
Ave neighs/atom = 24.4257
Neighbor list builds = 216
Dangerous builds = 0

57
examples/melt/log.melt.12Feb07.liberty.4
View File

@ -1,57 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 2 by 2 processor grid
create_atoms 1
Created 32000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 10 dump.melt
thermo 50
run 250
Memory usage per processor = 4.307 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2735087 -3.7027964
50 1.6751964 -4.793906 0 -2.28119 5.6449888
100 1.6492395 -4.7543479 0 -2.2805659 5.8242183
150 1.6468325 -4.7503201 0 -2.2801485 5.857928
200 1.64095 -4.741475 0 -2.280127 5.8888655
250 1.6425393 -4.7441579 0 -2.2804259 5.8751067
Loop time of 8.2969 on 4 procs for 250 steps with 32000 atoms
Pair time (%) = 4.39721 (52.9983)
Neigh time (%) = 0.378456 (4.56141)
Comm time (%) = 1.61733 (19.4932)
Outpt time (%) = 1.49492 (18.0178)
Other time (%) = 0.408981 (4.92932)
Nlocal: 8000 ave 8011 max 7981 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost: 8616 ave 8628 max 8605 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 303098 ave 306712 max 300441 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 1212392
Ave neighs/atom = 37.8873
Neighbor list builds = 12
Dangerous builds = 0

57
examples/melt/log.melt.12Feb07.linux.1
View File

@ -1,57 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 20 0 20 0 20
create_box 1 box
Created box = (0 0 0) to (33.5919 33.5919 33.5919)
1 by 1 by 1 processor grid
create_atoms 1
Created 32000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
dump id all atom 10 dump.melt
thermo 50
run 250
Memory usage per processor = 14.4987 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2735087 -3.7027964
50 1.6634568 -4.7767061 0 -2.2815989 5.7060587
100 1.6411943 -4.741815 0 -2.2801004 5.8702166
150 1.6434235 -4.7448489 0 -2.2797906 5.868853
200 1.6427413 -4.7436699 0 -2.279635 5.8804726
250 1.6373146 -4.7362602 0 -2.2803651 5.8998494
Loop time of 39.819 on 1 procs for 250 steps with 32000 atoms
Pair time (%) = 30.7479 (77.2193)
Neigh time (%) = 2.71683 (6.82296)
Comm time (%) = 0.67844 (1.70381)
Outpt time (%) = 3.83524 (9.63168)
Other time (%) = 1.84053 (4.62225)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18806 ave 18806 max 18806 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.21276e+06 ave 1.21276e+06 max 1.21276e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1212760
Ave neighs/atom = 37.8987
Neighbor list builds = 12
Dangerous builds = 0

199
examples/micelle/log.micelle.12Feb07.liberty.4
View File

@ -1,199 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
2 by 2 by 1 processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.84779 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
400 0.45 0.68493339 0.090717081 1.225088 14.904536
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
Loop time of 0.303232 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0798574 (26.3354)
Bond time (%) = 0.0064292 (2.12022)
Neigh time (%) = 0.0161344 (5.3208)
Comm time (%) = 0.154442 (50.932)
Outpt time (%) = 0.00368738 (1.21603)
Other time (%) = 0.0426817 (14.0756)
Nlocal: 300 ave 302 max 294 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 101.75 ave 105 max 100 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 794 ave 811 max 774 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 250 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 1.85934 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
1000 0.44914716 -1.9350719 0.071373764 -1.4151124 7.1568301
2000 0.45 -2.017979 0.070742172 -1.4977993 4.8375385
3000 0.46278827 -2.0089553 0.058330549 -1.488415 4.820275
4000 0.46714531 -2.0210549 0.057888529 -1.496605 4.2962188
5000 0.44804799 -2.0254175 0.06916971 -1.5087599 4.4157997
6000 0.45761629 -2.0368567 0.076990577 -1.5028219 4.6540238
7000 0.44640723 -2.0461339 0.064790763 -1.5354939 4.4179413
8000 0.45177284 -2.0324404 0.047705359 -1.5335269 4.54304
9000 0.43975305 -2.06401 0.069375126 -1.5554315 3.2833286
10000 0.45308355 -2.0423211 0.056575039 -1.5332289 4.1729746
11000 0.44229664 -2.0436958 0.065042761 -1.5369092 4.3783133
12000 0.4688876 -2.0591494 0.058270214 -1.5325777 3.6811782
13000 0.45151162 -2.0633938 0.053917641 -1.5585289 3.1767412
14000 0.44571931 -2.0503046 0.0570333 -1.5481092 3.5096724
15000 0.45 -2.0837399 0.060991769 -1.5733106 3.1370759
16000 0.45307444 -2.0804646 0.0670541 -1.5609024 3.2516824
17000 0.45880865 -2.072733 0.061534139 -1.5529637 3.3828133
18000 0.45650845 -2.0811023 0.057626785 -1.5675377 2.8631577
19000 0.45645839 -2.1137579 0.058378793 -1.5994913 2.6678277
20000 0.44760402 -2.109567 0.06512585 -1.5973966 2.3558292
21000 0.43651289 -2.0863769 0.057529291 -1.5928803 3.0018852
22000 0.43440649 -2.0950161 0.063482231 -1.5976704 2.3233803
23000 0.44572794 -2.0887627 0.061323772 -1.5822681 2.9579923
24000 0.44306777 -2.0843912 0.050176466 -1.5917008 2.8496622
25000 0.45 -2.1051658 0.061328265 -1.5944 2.1179388
26000 0.45552583 -2.119375 0.058663998 -1.6057546 2.2945202
27000 0.43912671 -2.1066914 0.051902852 -1.6162108 2.1491613
28000 0.45168054 -2.1078102 0.067816662 -1.5888776 2.4300025
29000 0.44173014 -2.0804191 0.05137384 -1.5878673 3.0500294
30000 0.44407338 -2.0998759 0.053922142 -1.6024355 2.7183453
31000 0.4431566 -2.1102821 0.061544598 -1.6061349 2.7379786
32000 0.45 -2.1163285 0.060739023 -1.606152 2.0727532
33000 0.46444105 -2.1050315 0.062866914 -1.5783041 1.9114822
34000 0.44581302 -2.0954209 0.063239112 -1.5869261 2.3525995
35000 0.45 -2.1261175 0.060452019 -1.616228 2.014967
36000 0.43470345 -2.1034119 0.063748152 -1.6055037 2.6086075
37000 0.44671396 -2.093898 0.057613863 -1.5901286 2.9715819
38000 0.45751276 -2.1085734 0.058845472 -1.592787 2.5044165
39000 0.44786323 -2.1130108 0.056041424 -1.609666 2.1432
40000 0.43937694 -2.1125665 0.04967594 -1.6240628 2.5594741
41000 0.45 -2.1083933 0.0547275 -1.6042283 2.4651511
42000 0.43287348 -2.1009617 0.054318981 -1.6143103 2.1496725
43000 0.44945469 -2.1285428 0.05863553 -1.6210144 2.2786034
44000 0.44737235 -2.0967009 0.058373014 -1.5915148 2.7502707
45000 0.45401167 -2.110646 0.059341015 -1.5978608 1.9203458
46000 0.43451455 -2.1077912 0.060728016 -1.6130918 2.3294588
47000 0.44822719 -2.1295807 0.061997031 -1.6199168 2.1463667
48000 0.43300738 -2.1029353 0.064025843 -1.6064433 2.1373309
49000 0.44657342 -2.1237489 0.060905756 -1.616828 2.0319341
50000 0.4677882 -2.1242266 0.059790209 -1.597233 2.5375996
51000 0.45536082 -2.0986081 0.052858152 -1.5909583 2.562239
52000 0.45919514 -2.1064277 0.057955 -1.5898515 2.3499751
53000 0.46449938 -2.1195508 0.060178993 -1.595453 2.5406265
54000 0.43682602 -2.1035311 0.069334917 -1.5979162 2.6919587
55000 0.45 -2.0965463 0.055320603 -1.5917882 2.5110927
56000 0.44913495 -2.1210973 0.058848556 -1.6136752 1.8246708
57000 0.44307699 -2.1361861 0.066761708 -1.6269012 2.4928119
58000 0.45181349 -2.1311357 0.05656415 -1.6233228 2.1515038
59000 0.45 -2.1345398 0.060573082 -1.6245292 1.715299
60000 0.45068289 -2.1230762 0.055943523 -1.6170131 2.1657885
Loop time of 23.1686 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 7.28988 (31.4644)
Bond time (%) = 0.388005 (1.6747)
Neigh time (%) = 1.50522 (6.49679)
Comm time (%) = 10.6076 (45.7844)
Outpt time (%) = 0.564966 (2.4385)
Other time (%) = 2.81294 (12.1412)
Nlocal: 300 ave 308 max 291 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 207 ave 218 max 195 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 2467.25 ave 2570 max 2397 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 9869
Ave neighs/atom = 8.22417
Ave special neighs/atom = 0.5
Neighbor list builds = 4885
Dangerous builds = 0

199
examples/micelle/log.micelle.12Feb07.linux.1
View File

@ -1,199 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
1 by 1 by 1 processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.69411 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 2.6311673
50 0.47417944 0.67716204 0.057387153 1.2081359 4.4581428
100 0.45 0.73037684 0.054821983 1.2346363 7.730955
150 0.67532546 0.72388376 0.043478036 1.4418431 9.580616
200 0.45 0.78466058 0.076912805 1.3110109 10.136457
250 0.66488946 0.69771453 0.081047682 1.4428206 12.303975
300 0.45 0.76794745 0.066716745 1.2841017 12.618422
350 0.67629601 0.62549506 0.072636862 1.3735826 14.282774
400 0.45 0.68493339 0.090717081 1.225088 14.904536
450 0.56732174 0.64322231 0.080690687 1.2905256 15.790896
500 0.45 0.64764573 0.078468194 1.1755514 15.970391
550 0.56476697 0.58160926 0.080519682 1.22619 16.573931
600 0.45 0.58331363 0.088243449 1.1209946 17.103627
650 0.5229482 0.54530348 0.09321673 1.1608147 17.545826
700 0.45 0.52374674 0.085166964 1.0583512 17.640835
750 0.51528063 0.48974532 0.086434828 1.0908167 17.952674
800 0.45 0.50467091 0.090255509 1.0443639 18.600542
850 0.4950534 0.48512921 0.091950432 1.0715142 18.88713
900 0.45 0.48352312 0.097223467 1.0301841 19.049897
950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988
1000 0.45 0.46260893 0.10106179 1.0131082 19.538971
Loop time of 0.878466 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.50753 (57.7746)
Bond time (%) = 0.04176 (4.75374)
Neigh time (%) = 0.106436 (12.1161)
Comm time (%) = 0.026899 (3.06204)
Outpt time (%) = 0.01353 (1.54018)
Other time (%) = 0.182311 (20.7533)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 193 ave 193 max 193 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3176 ave 3176 max 3176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
dump 1 all atom 250 dump.micelle
reset_timestep 0
run 60000
Memory usage per processor = 1.85432 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 12.63785
1000 0.44914708 -1.9350711 0.071372351 -1.4151131 7.156807
2000 0.45270543 -2.0004904 0.066419058 -1.4819318 5.5702827
3000 0.46916283 -2.0213933 0.065872359 -1.4869445 5.0060597
4000 0.43945376 -2.0166598 0.067641209 -1.5101142 4.6396644
5000 0.45495437 -2.0447226 0.066285498 -1.5240515 3.9305266
6000 0.44963328 -2.056045 0.068450242 -1.5385235 3.8603798
7000 0.44856129 -2.0414287 0.058586674 -1.5348414 3.9952578
8000 0.43667749 -2.0567464 0.065334814 -1.5552799 4.2727683
9000 0.45682384 -2.0679034 0.060201786 -1.5514488 3.9267838
10000 0.45 -2.0518982 0.055746513 -1.5467142 4.0952215
11000 0.45708142 -2.0867219 0.069796539 -1.5604153 2.9408563
12000 0.45241478 -2.0660119 0.05984197 -1.5543207 3.1690286
13000 0.44107393 -2.0641661 0.05983938 -1.5638041 3.505816
14000 0.44110861 -2.097022 0.051901352 -1.6045634 3.1530067
15000 0.46350177 -2.0714176 0.060468155 -1.548027 3.1473645
16000 0.44655044 -2.1091366 0.063286789 -1.5998576 3.01513
17000 0.4669612 -2.0818303 0.06033586 -1.5551169 3.5882255
18000 0.46094826 -2.1157008 0.066505672 -1.5888231 2.3269852
19000 0.44560596 -2.0990576 0.065162589 -1.5888461 2.8984257
20000 0.44208903 -2.0909757 0.059515289 -1.589924 2.8119311
21000 0.45155589 -2.0997977 0.059798723 -1.5890075 2.8373688
22000 0.4454493 -2.1064356 0.057219664 -1.6043234 2.5646073
23000 0.44607005 -2.0965713 0.061416631 -1.5896422 2.4608998
24000 0.46538564 -2.1045166 0.05774363 -1.5819691 2.3150363
25000 0.45936625 -2.1067378 0.056323997 -1.5916218 2.048119
26000 0.44475849 -2.1039936 0.062084383 -1.5977067 2.6218634
27000 0.44698457 -2.0984145 0.055709014 -1.5962797 2.9317131
28000 0.43517932 -2.0913271 0.064117709 -1.5925741 2.8086074
29000 0.45647804 -2.1041742 0.062494065 -1.5857727 3.1137153
30000 0.46315669 -2.0956986 0.062535694 -1.5705852 2.7393652
31000 0.45 -2.1057734 0.06440468 -1.5919312 2.6231226
32000 0.45070852 -2.1035845 0.058447795 -1.5949916 2.4537766
33000 0.45666657 -2.1082739 0.062668872 -1.5895093 2.3000181
34000 0.45 -2.1016598 0.058047346 -1.594175 2.7045891
35000 0.45761633 -2.1166321 0.05661317 -1.6029746 2.4867114
36000 0.4472238 -2.1032503 0.058087856 -1.5984977 2.5708579
37000 0.45 -2.0862798 0.060216086 -1.5766262 3.0682877
38000 0.46457862 -2.111786 0.050899355 -1.5968888 2.3837735
39000 0.4461965 -2.0958328 0.065822692 -1.5843713 2.9356665
40000 0.44099466 -2.1082333 0.052068542 -1.6157214 2.7461117
41000 0.44708215 -2.1138114 0.061595428 -1.6056927 2.7512054
42000 0.45300055 -2.1160106 0.060484049 -1.6030923 2.1170549
43000 0.44584477 -2.1016681 0.065545873 -1.5908347 2.7168769
44000 0.44874855 -2.0962255 0.060190909 -1.587847 2.4701379
45000 0.43208001 -2.0985058 0.059429899 -1.607536 3.4135814
46000 0.43328324 -2.068705 0.062466255 -1.5734971 3.1729387
47000 0.46070055 -2.1056376 0.054706613 -1.5908063 2.4710329
48000 0.44818286 -2.1037138 0.060858877 -1.5952323 2.2822087
49000 0.43421688 -2.0920093 0.05524275 -1.6030924 2.9802749
50000 0.44919305 -2.118617 0.054774617 -1.6152108 2.1728215
51000 0.44744615 -2.1090016 0.059814306 -1.6023004 2.3189772
52000 0.45486735 -2.1082261 0.055067991 -1.5988594 2.2933516
53000 0.46483852 -2.1205596 0.059875293 -1.5964269 2.4109235
54000 0.43582273 -2.0939722 0.056892621 -1.6018017 2.9757336
55000 0.45654728 -2.1024753 0.062836674 -1.583662 2.3343503
56000 0.45942073 -2.0961849 0.053090528 -1.584248 2.8313158
57000 0.44650252 -2.092082 0.052991549 -1.5931461 3.0447824
58000 0.46418464 -2.1277093 0.060472378 -1.6036325 1.7271421
59000 0.45 -2.1304819 0.057808836 -1.6232356 1.6864115
60000 0.45599586 -2.1338576 0.053131762 -1.6253 2.201508
Loop time of 82.7474 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 55.7131 (67.3292)
Bond time (%) = 2.54046 (3.07013)
Neigh time (%) = 9.8923 (11.9548)
Comm time (%) = 2.21129 (2.67234)
Outpt time (%) = 1.4498 (1.75208)
Other time (%) = 10.9404 (13.2215)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 396 ave 396 max 396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9650 ave 9650 max 9650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9650
Ave neighs/atom = 8.04167
Ave special neighs/atom = 0.5
Neighbor list builds = 4890
Dangerous builds = 0

108
examples/min/log.min.12Feb07.liberty.4
View File

@ -1,108 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 processor grid
create_atoms 1
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 1.44958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.6248859 0 2.3657391 10.863748
100 3.3056095 -0.90010417 0 2.3993073 34.161569
200 3.3179673 -0.91237776 0 2.3993683 33.885931
300 3.2898718 -0.88383768 0 2.3998656 34.100539
400 3.3040789 -0.8979868 0 2.3998969 33.870872
500 3.3858715 -0.98323293 0 2.39629 33.00502
600 3.3016075 -0.89577331 0 2.3996436 34.094211
700 3.3530103 -0.94642636 0 2.4002971 33.706321
800 3.2765339 -0.87171428 0 2.3986761 34.272397
900 3.4084164 -1.0031926 0 2.398833 32.606983
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
Loop time of 0.377246 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.098482 (26.1055)
Neigh time (%) = 0.0318925 (8.45403)
Comm time (%) = 0.175421 (46.5006)
Outpt time (%) = 0.0234827 (6.22477)
Other time (%) = 0.0479671 (12.7151)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 170.75 ave 175 max 167 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 1943 ave 1984 max 1900 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 7772
Ave neighs/atom = 9.715
Neighbor list builds = 204
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 5
thermo 5
minimize 0.001 100 1000
Memory usage per processor = 1.90765 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3077995 -0.90272314 0 2.3988743 33.989676
1005 3.3077995 -2.4464146 0 0.85518281 11.813681
1010 3.3077995 -2.722905 0 0.5786924 7.0572259
1015 3.3077995 -2.8240967 0 0.47750069 5.2719814
1020 3.3077995 -2.8735068 0 0.42809061 4.4936467
1025 3.3077995 -2.9038631 0 0.39773429 4.0902371
1030 3.3077995 -2.9235394 0 0.37805797 3.8445956
1035 3.3077995 -2.9410562 0 0.36054119 3.6772327
1038 3.3077995 -2.9486794 0 0.35291801 3.5714315
Loop time of 0.0975236 on 4 procs for 38 steps with 800 atoms
Minimization stats:
E initial, next-to-last, final = -0.902723 -2.94694 -2.94868
Gradient 2-norm init/final= 1904.03 22.323
Gradient inf-norm init/final= 304.285 10.0504
Iterations = 38
Force evaluations = 185
Pair time (%) = 0.0225257 (23.0977)
Neigh time (%) = 0.00271821 (2.78723)
Comm time (%) = 0.0309407 (31.7263)
Outpt time (%) = 0.0167403 (17.1654)
Other time (%) = 0.0245988 (25.2234)
Nlocal: 200 ave 201 max 198 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 171 ave 173 max 168 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1817.75 ave 1834 max 1805 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 7271
Ave neighs/atom = 9.08875
Neighbor list builds = 17
Dangerous builds = 0

108
examples/min/log.min.12Feb07.linux.1
View File

@ -1,108 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 processor grid
create_atoms 1
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
dump 1 all atom 100 dump.min
thermo 100
run 1000
Memory usage per processor = 1.47247 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.6248859 0 2.3657391 10.863748
100 3.3056095 -0.90010417 0 2.3993073 34.161569
200 3.3179673 -0.91237776 0 2.3993683 33.885931
300 3.2898718 -0.88383768 0 2.3998656 34.100539
400 3.3040789 -0.8979868 0 2.3998969 33.870872
500 3.3858715 -0.98323293 0 2.39629 33.00502
600 3.3016074 -0.89577327 0 2.3996436 34.094211
700 3.3530108 -0.94642681 0 2.4002971 33.706316
800 3.2765414 -0.87172188 0 2.398676 34.272332
900 3.4086632 -1.003472 0 2.3988 32.603903
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
Loop time of 1.20356 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.766051 (63.649)
Neigh time (%) = 0.224616 (18.6627)
Comm time (%) = 0.040716 (3.38298)
Outpt time (%) = 0.042399 (3.52281)
Other time (%) = 0.129774 (10.7825)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 314 ave 314 max 314 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7777 ave 7777 max 7777 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7777
Ave neighs/atom = 9.72125
Neighbor list builds = 204
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 5
thermo 5
minimize 0.001 100 1000
Memory usage per processor = 1.96838 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3011881 -0.89596181 0 2.3990365 34.054429
1005 3.3011881 -2.4630946 0 0.83190371 11.52248
1010 3.3011881 -2.7249285 0 0.57006988 7.0081459
1015 3.3011881 -2.8249196 0 0.47007872 5.2407114
1020 3.3011881 -2.8748561 0 0.42014222 4.4638989
1025 3.3011881 -2.9048388 0 0.39015958 4.0705858
1030 3.3011881 -2.9246339 0 0.37036444 3.8097613
1035 3.3011881 -2.941932 0 0.35306633 3.6545452
1036 3.3011881 -2.9434242 0 0.3515742 3.6268584
Loop time of 0.234251 on 1 procs for 36 steps with 800 atoms
Minimization stats:
E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
Gradient 2-norm init/final= 1920.78 20.9992
Gradient inf-norm init/final= 304.283 9.61216
Iterations = 36
Force evaluations = 177
Pair time (%) = 0.158737 (67.7636)
Neigh time (%) = 0.016951 (7.23626)
Comm time (%) = 0.004804 (2.05079)
Outpt time (%) = 0.029892 (12.7607)
Other time (%) = 0.023867 (10.1886)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 314 ave 314 max 314 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7295 ave 7295 max 7295 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7295
Ave neighs/atom = 9.11875
Neighbor list builds = 16
Dangerous builds = 0

31
examples/nemd/in.nemd Normal file
View File

@ -0,0 +1,31 @@
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
create_atoms 1 box
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000

134
examples/obstacle/log.obstacle.12Feb07.liberty.4
View File

@ -1,134 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 processor grid
create_atoms 1
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set lower atom 2
120 settings made
set upper atom 3
120 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 35 atoms, new total = 805
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 770
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.44234 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0006918 0 0 0.68683847 0.48039951 733.92473
1000 1 -0.3603446 0 0.32601904 1.5725867 779.90508
2000 1 -0.42832732 0 0.25803632 1.3587382 813.11821
3000 1 -0.47232806 0 0.21403558 1.4341388 844.88084
4000 1 -0.52763648 0 0.15872716 1.5459739 875.13499
5000 1 -0.48314311 0 0.20322052 1.4357888 907.02154
6000 1 -0.472141 0 0.21422264 1.3030726 924.98416
7000 1 -0.44830722 0 0.23805641 1.2882909 928.95817
8000 1 -0.43371728 0 0.25264635 1.132775 927.35692
9000 1 -0.41463177 0 0.27173186 1.1209309 921.76003
10000 1 -0.38315652 0 0.30320712 1.0966664 922.24088
11000 1 -0.37156486 0 0.31479878 1.1423804 919.78903
12000 1 -0.3742195 0 0.31214414 1.0593775 928.05099
13000 1 -0.38124076 0 0.30512288 1.1256769 929.73097
14000 1 -0.38555026 0 0.30081337 1.0946739 933.53885
15000 1 -0.40703488 0 0.27932876 1.0764066 930.2934
16000 1 -0.3725232 0 0.31384044 1.0011147 931.1519
17000 1 -0.38470452 0 0.30165912 0.99838577 928.91833
18000 1 -0.40199729 0 0.28436634 1.0888096 932.68523
19000 1 -0.37259199 0 0.31377165 0.97032094 938.58622
20000 1 -0.44719826 0 0.23916537 1.0118322 936.68972
21000 1 -0.39518804 0 0.29117559 1.0584198 935.59526
22000 1 -0.36368989 0 0.32267374 1.0593392 935.25352
23000 1 -0.41084354 0 0.27552009 0.9952792 936.90123
24000 1 -0.39025763 0 0.29610601 1.014413 941.44567
25000 1 -0.36909647 0 0.31726717 0.9812463 940.90255
Loop time of 4.94495 on 4 procs for 25000 steps with 770 atoms
Pair time (%) = 0.416176 (8.41618)
Neigh time (%) = 0.147718 (2.98725)
Comm time (%) = 2.01956 (40.8409)
Outpt time (%) = 0.358058 (7.24087)
Other time (%) = 2.00344 (40.5148)
Nlocal: 192.5 ave 240 max 158 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 42.5 ave 45 max 37 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 401.25 ave 559 max 288 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 1605
Ave neighs/atom = 2.08442
Neighbor list builds = 1636
Dangerous builds = 0

134
examples/obstacle/log.obstacle.12Feb07.linux.1
View File

@ -1,134 +0,0 @@
LAMMPS (12 Feb 2007)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 processor grid
create_atoms 1
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set lower atom 2
120 settings made
set upper atom 3
120 settings made
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 35 atoms, new total = 805
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 770
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.4637 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0087541 0 0 0.69237216 0.48426997 733.92473
1000 1 -0.37498059 0 0.31138304 1.5619007 780.16609
2000 1 -0.42018277 0 0.26618087 1.381975 813.7446
3000 1 -0.49158436 0 0.19477928 1.4950838 846.60042
4000 1 -0.50974647 0 0.17661717 1.6968335 877.90837
5000 1 -0.48739676 0 0.19896688 1.372862 906.72222
6000 1 -0.45489776 0 0.23146588 1.1850408 922.1588
7000 1 -0.44298261 0 0.24338103 1.2353271 922.55214
8000 1 -0.39106076 0 0.29530287 1.2129774 923.79013
9000 1 -0.36894699 0 0.31741665 1.1022787 925.88908
10000 1 -0.40366483 0 0.28269881 1.0425088 924.55991
11000 1 -0.37662826 0 0.30973537 1.0605386 924.15634
12000 1 -0.39748408 0 0.28887956 1.1069709 926.1591
13000 1 -0.40533845 0 0.28102518 1.0999422 931.71451
14000 1 -0.39364952 0 0.29271412 0.98434706 935.98322
15000 1 -0.38545757 0 0.30090607 1.0288972 936.10741
16000 1 -0.34970581 0 0.33665783 1.0686207 939.12879
17000 1 -0.35935376 0 0.32700987 0.96188021 939.41127
18000 1 -0.38218429 0 0.30417934 0.97219528 939.42804
19000 1 -0.35002145 0 0.33634218 0.96884865 941.93045
20000 1 -0.37936966 0 0.30699398 1.0604325 935.73258
21000 1 -0.3797544 0 0.30660924 1.0525308 936.59648
22000 1 -0.37015981 0 0.31620383 1.0908613 935.05927
23000 1 -0.39940438 0 0.28695925 1.0860163 932.28118
24000 1 -0.36738604 0 0.3189776 0.97212319 936.04359
25000 1 -0.36023241 0 0.32613123 1.0971047 938.21817
Loop time of 12.2357 on 1 procs for 25000 steps with 770 atoms
Pair time (%) = 2.69352 (22.0137)
Neigh time (%) = 0.822182 (6.71956)
Comm time (%) = 0.283775 (2.31925)
Outpt time (%) = 3.9804 (32.5312)
Other time (%) = 4.45578 (36.4163)
Nlocal: 770 ave 770 max 770 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1637 ave 1637 max 1637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1637
Ave neighs/atom = 2.12597
Neighbor list builds = 1632
Dangerous builds = 0

154
examples/peptide/log.peptide.12Feb07.liberty.4
View File

@ -1,154 +0,0 @@
LAMMPS (12 Feb 2007)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
1 by 2 by 2 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 4312 960 3696
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 8.89765 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771
---------------- Step 50 ----- CPU = 1.0231 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80748e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.23399e-07
12 1.08 2.68045e-07
14 0.96 0
18 0.957201 5.38002e-06
31 104.52 0.000502303
---------------- Step 100 ----- CPU = 2.0570 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
---------------- Step 150 ----- CPU = 3.1067 (sec) ----------------
TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18831e-07
6 0.997 1.50909e-07
8 1.08 6.58563e-08
10 1.111 5.56695e-07
12 1.08 1.99338e-07
14 0.96 0
18 0.957201 3.59689e-06
31 104.52 0.000388134
---------------- Step 200 ----- CPU = 4.1845 (sec) ----------------
TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
---------------- Step 250 ----- CPU = 5.2516 (sec) ----------------
TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78173e-06
6 0.997001 3.51761e-06
8 1.08 2.09202e-06
10 1.111 5.64179e-06
12 1.08 2.10252e-06
14 0.96 0
18 0.957202 7.62675e-06
31 104.52 0.00080599
---------------- Step 300 ----- CPU = 6.3128 (sec) ----------------
TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
Loop time of 6.31307 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 3.7478 (59.3657)
Bond time (%) = 0.0190388 (0.301577)
Kspce time (%) = 1.04423 (16.5407)
Neigh time (%) = 0.366191 (5.80052)
Comm time (%) = 0.669456 (10.6043)
Outpt time (%) = 0.0110819 (0.175539)
Other time (%) = 0.455277 (7.21165)
FFT time (% of Kspce) = 0.219916 (21.0601)
FFT Gflps 3d 1d-only = 0.748076 3.75246
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177008 ave 180559 max 170208 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

154
examples/peptide/log.peptide.12Feb07.linux.1
View File

@ -1,154 +0,0 @@
LAMMPS (12 Feb 2007)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
1 by 1 by 1 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 10648 3375 5808
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 19.9477 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771
---------------- Step 50 ----- CPU = 7.8161 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80748e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.23399e-07
12 1.08 2.68045e-07
14 0.96 0
18 0.957201 5.38002e-06
31 104.52 0.000502303
---------------- Step 100 ----- CPU = 15.6613 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
---------------- Step 150 ----- CPU = 23.6754 (sec) ----------------
TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18831e-07
6 0.997 1.50909e-07
8 1.08 6.58563e-08
10 1.111 5.56695e-07
12 1.08 1.99338e-07
14 0.96 0
18 0.957201 3.59689e-06
31 104.52 0.000388134
---------------- Step 200 ----- CPU = 31.3970 (sec) ----------------
TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
---------------- Step 250 ----- CPU = 39.4151 (sec) ----------------
TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78173e-06
6 0.997001 3.51761e-06
8 1.08 2.09202e-06
10 1.111 5.64179e-06
12 1.08 2.10252e-06
14 0.96 0
18 0.957202 7.62675e-06
31 104.52 0.00080599
---------------- Step 300 ----- CPU = 47.4101 (sec) ----------------
TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
Loop time of 47.4104 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 38.771 (81.7773)
Bond time (%) = 0.074676 (0.15751)
Kspce time (%) = 3.46724 (7.31323)
Neigh time (%) = 4.29476 (9.05867)
Comm time (%) = 0.326736 (0.689165)
Outpt time (%) = 0.019285 (0.0406767)
Other time (%) = 0.456781 (0.963461)
FFT time (% of Kspce) = 1.14174 (32.9294)
FFT Gflps 3d 1d-only = 0.144091 0.210559
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708030 ave 708030 max 708030 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

136
examples/pour/log.pour.12Feb07.liberty.4
View File

@ -1,136 +0,0 @@
LAMMPS (12 Feb 2007)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.50 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 125 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.4319 47.250762 6600
5000 804 1605.2015 60.084404 6600
6000 804 1371.3425 69.247899 6600
7000 1206 1524.3574 74.071529 6600
8000 1206 1418.8997 60.727536 6600
9000 1206 1258.0238 52.045974 6600
10000 1608 1387.2361 50.17452 6600
11000 1608 1226.8131 50.547962 6600
12000 1608 1195.97 41.951622 6600
13000 2010 1312.7197 51.888514 6600
14000 2010 1176.2242 43.086598 6600
15000 2010 972.7316 46.053358 6600
16000 2412 1040.0907 45.535472 6600
17000 2412 1033.3053 37.798831 6600
18000 2412 929.20314 37.574869 6600
19000 2814 1010.9926 38.716555 6600
20000 2814 953.49259 41.76949 6600
21000 2814 768.81045 45.76655 6600
22000 2814 501.98827 42.18076 6600
23000 3000 428.98535 35.914834 6600
24000 3000 365.81359 22.320118 6600
25000 3000 227.404 23.276402 6600
Loop time of 13.8863 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 4.97869 (35.8531)
Neigh time (%) = 0.706881 (5.09047)
Comm time (%) = 3.96635 (28.5629)
Outpt time (%) = 0.637875 (4.59354)
Other time (%) = 3.59655 (25.8999)
Nlocal: 750 ave 766 max 734 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 388.75 ave 395 max 386 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Neighs: 3588.5 ave 3661 max 3520 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 14354
Ave neighs/atom = 4.78467
Neighbor list builds = 1154
Dangerous builds = 0
unfix ins
fix 2 all gravity chute 26.0
run 25000
Memory usage per processor = 6.82853 Mbytes
Step Atoms KinEng RotKEgrn Volume
25000 3000 227.404 23.276402 6600
26000 3000 106.43826 18.101442 6600
27000 3000 113.05348 12.760864 6600
28000 3000 205.07328 11.584573 6600
29000 3000 358.43804 15.113582 6600
30000 3000 598.64933 20.578979 6600
31000 3000 873.5316 28.461109 6600
32000 3000 1170.5204 31.532882 6600
33000 3000 1527.4366 38.434515 6600
34000 3000 1984.9084 46.821444 6600
35000 3000 2510.0466 50.236977 6600
36000 3000 3115.8979 66.529363 6600
37000 3000 3828.8672 78.585843 6600
38000 3000 4614.202 90.003111 6600
39000 3000 5443.9784 97.5867 6600
40000 3000 6277.0696 109.40245 6600
41000 3000 7205.7543 116.90896 6600
42000 3000 8231.9822 123.54846 6600
43000 3000 9341.3262 139.91668 6600
44000 3000 10540.217 154.5832 6600
45000 3000 11634.026 163.89013 6600
46000 3000 12939.113 172.01293 6600
47000 3000 14117.982 183.04471 6600
48000 3000 15405.59 211.29982 6600
49000 3000 16780.191 197.48907 6600
50000 3000 18147.971 232.52213 6600
Loop time of 25.2916 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 11.0239 (43.5871)
Neigh time (%) = 1.08584 (4.29328)
Comm time (%) = 6.05157 (23.9272)
Outpt time (%) = 1.07456 (4.24868)
Other time (%) = 6.05576 (23.9438)
Nlocal: 750 ave 757 max 742 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Nghost: 401.5 ave 412 max 390 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 3645.75 ave 3775 max 3584 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 14583
Ave neighs/atom = 4.861
Neighbor list builds = 825
Dangerous builds = 0

136
examples/pour/log.pour.12Feb07.linux.1
View File

@ -1,136 +0,0 @@
LAMMPS (12 Feb 2007)
# Pour granular particles into chute container, then induce flow
atom_style granular
boundary p p fm
newton off
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/history 2000.0 50.0 0.50 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 125 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1424.6738 13.243803 6600
4000 804 1725.9135 47.193854 6600
5000 804 1605.9404 61.336034 6600
6000 804 1364.6108 67.554058 6600
7000 1206 1511.4113 74.376707 6600
8000 1206 1418.8901 57.72159 6600
9000 1206 1256.2845 48.910044 6600
10000 1608 1398.3246 51.447622 6600
11000 1608 1247.546 48.387594 6600
12000 1608 1182.5307 42.323247 6600
13000 2010 1308.4067 48.900862 6600
14000 2010 1184.2874 44.83509 6600
15000 2010 1005.943 39.943887 6600
16000 2412 1031.9872 47.786837 6600
17000 2412 1032.5851 40.540687 6600
18000 2412 919.78138 36.200329 6600
19000 2814 1017.0854 35.573349 6600
20000 2814 964.17268 41.63371 6600
21000 2814 748.30864 44.884418 6600
22000 2814 531.66082 40.886555 6600
23000 3000 415.96265 35.009259 6600
24000 3000 363.92132 18.910655 6600
25000 3000 223.50386 24.163325 6600
Loop time of 77.9105 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 44.229 (56.769)
Neigh time (%) = 4.82477 (6.19271)
Comm time (%) = 2.59149 (3.32625)
Outpt time (%) = 1.80922 (2.32218)
Other time (%) = 24.456 (31.3899)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 675 ave 675 max 675 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13637 ave 13637 max 13637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13637
Ave neighs/atom = 4.54567
Neighbor list builds = 1153
Dangerous builds = 0
unfix ins
fix 2 all gravity chute 26.0
run 25000
Memory usage per processor = 7.24008 Mbytes
Step Atoms KinEng RotKEgrn Volume
25000 3000 223.50386 24.163325 6600
26000 3000 116.7995 18.613728 6600
27000 3000 122.40388 11.057402 6600
28000 3000 231.29589 11.189183 6600
29000 3000 394.03717 14.367314 6600
30000 3000 647.20427 22.016262 6600
31000 3000 908.91364 28.607326 6600
32000 3000 1271.4653 30.481316 6600
33000 3000 1667.4275 41.693229 6600
34000 3000 2165.6715 50.388564 6600
35000 3000 2742.9875 52.867314 6600
36000 3000 3313.9686 64.802217 6600
37000 3000 4043.4311 73.963901 6600
38000 3000 4826.4345 82.469868 6600
39000 3000 5665.19 95.419726 6600
40000 3000 6555.0312 105.12519 6600
41000 3000 7541.9934 121.4346 6600
42000 3000 8632.6663 129.37799 6600
43000 3000 9666.568 132.68521 6600
44000 3000 10825.138 153.12413 6600
45000 3000 12010.686 165.13241 6600
46000 3000 13364.225 184.80686 6600
47000 3000 14694.757 196.08109 6600
48000 3000 16083.771 220.53678 6600
49000 3000 17548.113 228.11249 6600
50000 3000 19103.087 244.48465 6600
Loop time of 158.137 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 98.0991 (62.0342)
Neigh time (%) = 7.5106 (4.74943)
Comm time (%) = 5.67871 (3.59101)
Outpt time (%) = 2.85027 (1.8024)
Other time (%) = 43.9984 (27.823)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 766 ave 766 max 766 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13994 ave 13994 max 13994 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13994
Ave neighs/atom = 4.66467
Neighbor list builds = 833
Dangerous builds = 0

89
examples/pour/log.pour.2d.12Feb07.liberty.4
View File

@ -1,89 +0,0 @@
LAMMPS (12 Feb 2007)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary p fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created box = (0 0 -0.5) to (100 50 0.5)
2 by 2 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hertzian 2000.0 50.0 0.0 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 90.0 -90.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 100 dump.pour
run 25000
Memory usage per processor = 0.335693 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3310.8798 0 5000
7000 672 3505.2381 0 5000
8000 672 3325.8942 0 5000
9000 672 3165.2505 0 5000
10000 896 3170.2639 0 5000
11000 896 2947.3721 0 5000
12000 896 2860.549 0 5000
13000 1000 2845.3312 0 5000
14000 1000 2632.0994 0 5000
15000 1000 2195.3133 0 5000
16000 1000 1551.8485 0 5000
17000 1000 941.82431 0 5000
18000 1000 684.95986 0 5000
19000 1000 346.24904 0 5000
20000 1000 100.47441 0 5000
21000 1000 55.606283 0 5000
22000 1000 47.410559 0 5000
23000 1000 38.365449 0 5000
24000 1000 27.535477 0 5000
25000 1000 16.082932 0 5000
Loop time of 7.63049 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.21044 (15.8632)
Neigh time (%) = 0.267945 (3.51151)
Comm time (%) = 1.8156 (23.794)
Outpt time (%) = 0.418886 (5.48963)
Other time (%) = 3.91762 (51.3417)
Nlocal: 250 ave 502 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 12 ave 25 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 620.5 ave 1252 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2482
Ave neighs/atom = 2.482
Neighbor list builds = 1725
Dangerous builds = 0

89
examples/pour/log.pour.2d.12Feb07.linux.1
View File

@ -1,89 +0,0 @@
LAMMPS (12 Feb 2007)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary p fm p
newton off
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hertzian 2000.0 50.0 0.0 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity spherical 90.0 -90.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 100 dump.pour
run 25000
Memory usage per processor = 0.328064 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3310.8798 0 5000
7000 672 3505.2381 0 5000
8000 672 3325.8942 0 5000
9000 672 3165.2505 0 5000
10000 896 3170.2667 0 5000
11000 896 2944.0565 0 5000
12000 896 2862.9537 0 5000
13000 1000 2862.2101 0 5000
14000 1000 2638.5235 0 5000
15000 1000 2218.2739 0 5000
16000 1000 1583.5051 0 5000
17000 1000 963.53755 0 5000
18000 1000 666.8307 0 5000
19000 1000 339.73655 0 5000
20000 1000 100.52829 0 5000
21000 1000 56.112393 0 5000
22000 1000 47.013733 0 5000
23000 1000 32.615049 0 5000
24000 1000 25.853047 0 5000
25000 1000 17.216223 0 5000
Loop time of 22.8967 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 9.27836 (40.5226)
Neigh time (%) = 2.03788 (8.90029)
Comm time (%) = 0.293353 (1.2812)
Outpt time (%) = 1.06686 (4.65942)
Other time (%) = 10.2203 (44.6364)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 27 ave 27 max 27 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2441 ave 2441 max 2441 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2441
Ave neighs/atom = 2.441
Neighbor list builds = 1758
Dangerous builds = 0

305
examples/rigid/log.rigid.12Feb07.liberty.4
View File

@ -1,305 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.41814 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722842e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690664 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532812 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652437 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.02681437 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.058989 0 5269.4979 12.062708
9750 16738.013 0.1355011 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270524 0 5269.5237 11.395098
9900 16738.489 -0.00024984559 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 1.86143 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0128456 (0.690097)
Neigh time (%) = 0.0243435 (1.30779)
Comm time (%) = 1.21756 (65.4102)
Outpt time (%) = 0.102895 (5.52778)
Other time (%) = 0.503778 (27.0641)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

305
examples/rigid/log.rigid.12Feb07.linux.1
View File

@ -1,305 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.42781 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722836e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690665 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652435 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814369 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589887 0 5269.4979 12.062708
9750 16738.013 0.1355012 0 5269.5101 11.407246
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270518 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.851031 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.071532 (8.40533)
Neigh time (%) = 0.117486 (13.8051)
Comm time (%) = 0.108591 (12.7599)
Outpt time (%) = 0.133537 (15.6912)
Other time (%) = 0.419885 (49.3384)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 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
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997

305
examples/rigid/log.rigid.poems.12Feb07.liberty.4
View File

@ -1,305 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.4946 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384276
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184718
1150 20849.582 206.01695 0 3680.9472 -0.86699164
1200 21815.003 45.317416 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064076
1300 20780.781 217.36505 0 3680.8286 6.0538621
1350 20558.972 254.3648 0 3680.8601 -3.6773984
1400 21485.029 99.812952 0 3680.6511 -16.185471
1450 21771.108 52.159597 0 3680.6775 -2.4756679
1500 21520.948 93.503946 0 3680.3286 2.1023577
1550 21351.418 121.68139 0 3680.2511 5.5159972
1600 20778.805 216.92173 0 3680.0559 15.089183
1650 21477.639 100.21821 0 3679.8247 -1.1045931
1700 18501.343 596.4785 0 3680.0357 -15.679631
1750 18563.643 587.3477 0 3681.2882 33.53217
1800 19110.189 494.82277 0 3679.8543 18.024037
1850 21364.196 119.23462 0 3679.9339 2.529149
1900 20146.64 322.14631 0 3679.9197 5.7311673
1950 20692.671 231.25338 0 3680.0319 4.2977687
2000 20943.903 189.11238 0 3679.7629 -22.645639
2050 19668.148 401.81475 0 3679.8394 3.6256063
2100 20280.572 299.73979 0 3679.8351 7.4809366
2150 19182.127 483.47805 0 3680.4992 22.615355
2200 21299.767 130.77158 0 3680.7327 4.7114063
2250 20487.762 266.50325 0 3681.1302 -8.6408345
2300 18655.048 571.92772 0 3681.1023 -5.266975
2350 21512.632 95.763771 0 3681.2025 -9.3526622
2400 21467.744 103.31997 0 3681.2773 -29.599491
2450 20097.033 332.78544 0 3682.291 35.886632
2500 20761.514 222.1498 0 3682.4021 -12.52654
2550 20410.179 280.57555 0 3682.272 -22.280218
2600 21469.95 103.95758 0 3682.2826 -10.039024
2650 20711.858 230.38535 0 3682.3616 5.3554349
2700 18584.052 585.19766 0 3682.5397 21.807604
2750 20511.368 263.53176 0 3682.0931 -4.7085799
2800 20592.991 249.9677 0 3682.1328 -6.5329985
2850 17078.939 835.43473 0 3681.9245 16.780854
2900 19704.624 397.94471 0 3682.0488 -0.87435077
2950 19282.968 468.43149 0 3682.2595 7.0271622
3000 20552.037 256.84085 0 3682.1804 -2.9282943
3050 20934.711 193.08576 0 3682.2043 3.8942358
3100 21703.768 64.8113 0 3682.106 0.063237279
3150 18722.82 561.7019 0 3682.172 -1.4520091
3200 18284.044 634.53317 0 3681.8739 6.3415584
3250 21255.255 139.48628 0 3682.0288 2.6455564
3300 20558.956 255.77083 0 3682.2636 -3.9152408
3350 20373.309 286.62048 0 3682.1719 4.5400971
3400 20618.175 245.81811 0 3682.1806 5.7100283
3450 19473.455 436.70128 0 3682.2771 11.870427
3500 18903.565 531.91776 0 3682.5119 -9.3476901
3550 21030.252 177.18619 0 3682.2282 -14.260278
3600 19942.611 357.98433 0 3681.7528 11.183792
3650 20388.541 283.86156 0 3681.9518 -8.2736257
3700 20724.985 226.58383 0 3680.748 -13.429981
3750 21586.121 84.456333 0 3682.1432 -2.7515188
3800 21478.159 102.70951 0 3682.4027 -2.5874121
3850 18107.437 665.11995 0 3683.0262 11.062091
3900 19602.682 415.48105 0 3682.5947 17.867347
3950 19208.319 480.73213 0 3682.1186 0.55405471
4000 20700.944 232.01332 0 3682.1706 4.2790356
4050 18241.028 641.65227 0 3681.8236 14.819974
4100 16330.098 961.03753 0 3682.7206 -8.1781858
4150 20507.949 263.34806 0 3681.3396 -5.2032219
4200 21620.592 79.051795 0 3682.4838 -11.796063
4250 20841.315 209.02052 0 3682.573 -5.781042
4300 21378.616 119.44038 0 3682.5431 -3.0055326
4350 21391.4 116.89963 0 3682.133 1.2620601
4400 20092.07 333.32793 0 3682.0062 11.429014
4450 19315.512 461.83055 0 3681.0825 1.3462703
4500 20839.628 208.21416 0 3681.4855 4.709479
4550 14522.388 1263.1063 0 3683.5043 -20.816537
4600 21284.581 134.21556 0 3681.6457 -4.8183612
4650 20126.198 327.1439 0 3681.5103 -5.5395838
4700 21764.236 54.44036 0 3681.813 3.4863656
4750 21095.836 165.90339 0 3681.876 6.1541649
4800 20619.747 245.94729 0 3682.5718 2.5595916
4850 20763.177 222.12286 0 3682.6523 -8.6266804
4900 20537.14 259.67462 0 3682.5313 -15.421035
4950 21422.584 112.253 0 3682.6837 -1.4727022
5000 16257.411 972.68578 0 3682.2542 2.3147962
5050 19857.171 373.56369 0 3683.0922 -15.300375
5100 15635.264 1076.6903 0 3682.5676 36.8946
5150 21553.911 90.645813 0 3682.9642 1.5400926
5200 21559.956 89.704166 0 3683.0302 2.0981184
5250 19117.968 496.85067 0 3683.1787 29.282193
5300 21330.342 127.91971 0 3682.9767 2.4699055
5350 21829.625 44.595903 0 3682.8667 -11.606558
5400 21789.041 51.183465 0 3682.6902 -3.8674971
5450 19143.18 491.7975 0 3682.3275 -0.6880826
5500 19773.011 386.55132 0 3682.0532 -0.39276859
5550 21170.746 153.72971 0 3682.1873 -0.039885143
5600 20634.546 243.05851 0 3682.1496 -10.510731
5650 18940.14 525.80138 0 3682.4913 -8.4026702
5700 18137.059 658.45807 0 3681.3012 1.8086854
5750 18402.492 614.81681 0 3681.8988 18.121726
5800 15725.316 1060.3153 0 3681.2013 32.3919
5850 21350.969 122.71085 0 3681.2057 1.6244497
5900 20596.373 248.09794 0 3680.8268 -10.287271
5950 19586.195 416.65918 0 3681.0251 7.1327258
6000 20566.394 252.63425 0 3680.3666 9.3309712
6050 18063.299 667.31886 0 3677.8687 -10.246241
6100 17305.121 797.2545 0 3681.4414 14.554146
6150 19696.433 395.50284 0 3678.2416 4.1990406
6200 20908.19 195.69314 0 3680.3915 -9.0297611
6250 20767.885 219.35847 0 3680.6727 -5.4239147
6300 20271.076 302.48547 0 3680.9981 7.5881011
6350 21510.748 96.348849 0 3681.4736 -0.28663642
6400 21731.982 60.504382 0 3682.5014 -3.5673143
6450 19495.709 434.28569 0 3683.5706 4.7979099
6500 18668.623 571.92754 0 3683.3647 1.5185672
6550 16004.711 1016.2903 0 3683.7422 8.1972253
6600 20629.015 244.44595 0 3682.615 3.8351386
6650 21647.055 75.493996 0 3683.3365 -0.10989704
6700 19793.226 384.41402 0 3683.2851 7.7597696
6750 20441.55 275.94512 0 3682.8702 3.6110747
6800 21623.66 79.350309 0 3683.2936 -6.3458991
6850 21644.786 75.922535 0 3683.3869 -22.166786
6900 18150.965 657.76117 0 3682.9219 -14.903565
6950 21192.162 150.83369 0 3682.8607 -7.6579085
7000 20481.657 268.91866 0 3682.5281 -10.728925
7050 19265.165 471.58584 0 3682.4467 -3.1547895
7100 20241.165 308.92052 0 3682.4479 10.770847
7150 20883.514 201.92495 0 3682.5106 12.276271
7200 20675.066 236.51208 0 3682.3564 4.0653811
7250 21464.099 105.01329 0 3682.3631 -4.2891409
7300 19279.539 469.63353 0 3682.89 19.415276
7350 20266.489 304.68631 0 3682.4344 -0.15439874
7400 18978.717 519.39579 0 3682.5153 19.185958
7450 20816.852 213.20924 0 3682.6845 18.435432
7500 20655.662 240.16805 0 3682.7785 -4.4996568
7550 19061.292 506.0418 0 3682.9238 -1.7545473
7600 20564.235 255.25251 0 3682.625 -5.3903401
7650 21273.693 137.41485 0 3683.0303 -6.9034645
7700 20999.106 183.2458 0 3683.0968 -5.9941062
7750 18886.194 534.2212 0 3681.9202 5.9891004
7800 20327.925 294.85306 0 3682.8405 -2.5902629
7850 19533.408 427.77688 0 3683.3448 -4.9977086
7900 20973.609 187.37509 0 3682.9765 0.11759117
7950 18164.635 654.02996 0 3681.4691 16.402128
8000 20938.276 193.48738 0 3683.2 -5.9311301
8050 20819.498 213.21616 0 3683.1324 1.3392987
8100 19553.561 424.27379 0 3683.2006 -2.5040641
8150 17524.659 759.26187 0 3680.0384 -37.279253
8200 21104.916 165.88837 0 3683.3744 -3.8952964
8250 19614.453 414.27984 0 3683.3553 -2.9352541
8300 13365.081 1457.0212 0 3684.5347 100.4608
8350 20920.925 197.0494 0 3683.8702 -11.661629
8400 19724.857 396.41163 0 3683.8878 0.74045509
8450 21751.144 58.967512 0 3684.1583 -4.095218
8500 21283.998 136.40954 0 3683.7425 -5.4781843
8550 19255.08 474.01022 0 3683.1903 0.61248835
8600 20786.099 219.06078 0 3683.4107 9.7864578
8650 20801.493 216.74923 0 3683.6647 7.1280503
8700 19893.433 368.11056 0 3683.6827 -9.5312543
8750 21072.739 171.47966 0 3683.6028 -17.222136
8800 18791.068 551.89466 0 3683.7394 -13.425301
8850 20323.723 296.58355 0 3683.8708 1.2544121
8900 19160.522 487.13728 0 3680.5575 7.5449432
8950 20247.9 309.46468 0 3684.1146 -11.397923
9000 20721.089 230.36979 0 3683.8846 11.354348
9050 21798.873 51.104409 0 3684.25 -9.645863
9100 21093.423 168.78605 0 3684.3565 -1.2127948
9150 20954.177 191.65626 0 3684.0191 0.61911701
9200 17054.376 842.546 0 3684.942 41.714389
9250 19253.515 475.58375 0 3684.5029 13.186069
9300 21681.124 71.036838 0 3684.5575 -4.139581
9350 21796.739 51.725799 0 3684.5157 -8.5902286
9400 21631.679 79.362722 0 3684.6425 -8.7541514
9450 18537.758 595.38459 0 3685.011 -6.2719267
9500 17152.352 824.77642 0 3683.5018 46.593524
9550 20928.938 196.82808 0 3684.9843 -1.5521829
9600 15991.62 1020.98 0 3686.25 -3.8314742
9650 19629.68 414.15513 0 3685.7685 32.867017
9700 20900.569 201.75492 0 3685.183 6.1694301
9750 17072.588 841.426 0 3686.8573 -4.0468499
9800 21939.049 29.032402 0 3685.5406 -9.1896877
9850 21261.674 141.7745 0 3685.3869 -13.02325
9900 19393.195 452.88226 0 3685.0814 1.4304574
9950 17226.824 814.05288 0 3685.1902 19.353254
10000 20630.15 245.97222 0 3684.3306 0.61583151
Loop time of 16.4503 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.123495 (0.750712)
Neigh time (%) = 0.0552313 (0.335746)
Comm time (%) = 1.68884 (10.2663)
Outpt time (%) = 0.101621 (0.617742)
Other time (%) = 14.4811 (88.0295)
Nlocal: 20.25 ave 74 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 42 ave 90 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 211.25 ave 769 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 845
Ave neighs/atom = 10.4321
Neighbor list builds = 991
Dangerous builds = 929

305
examples/rigid/log.rigid.poems.12Feb07.linux.1
View File

@ -1,305 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 36 45
10 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
1 clusters, 9 bodies, 8 joints, 81 atoms
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.50473 Mbytes
Step Temp E_pair E_mol TotEng Press
0 217.7783 3430.3907 0 3466.6871 -2.7403788
50 13679.637 1404.2468 0 3684.1863 12.446066
100 16777.225 888.87665 0 3685.0808 -31.828677
150 19595.365 418.45042 0 3684.3446 40.709078
200 18524.188 596.47273 0 3683.8375 -0.8159371
250 21015.789 180.96521 0 3683.5967 -10.042469
300 20785.513 219.25314 0 3683.5053 2.6452719
350 21072.46 171.2554 0 3683.3321 7.0609024
400 19956.414 356.36381 0 3682.4328 19.320259
450 20724.42 227.73284 0 3681.8028 8.1259249
500 20152.578 322.71466 0 3681.4777 5.4929878
550 20017.022 345.29701 0 3681.4673 5.4661666
600 17897.743 698.72196 0 3681.6791 3.2854742
650 17297.758 796.60256 0 3679.5623 15.191113
700 18581.934 584.29715 0 3681.2861 5.1588289
750 21774.158 52.821062 0 3681.8474 -10.775664
800 21604.055 81.188546 0 3681.8644 -3.2045743
850 17821.483 711.53827 0 3681.7854 7.4384277
900 21033.292 175.98127 0 3681.5299 -16.345167
950 20968.166 186.59847 0 3681.2929 -2.330456
1000 20490.66 266.19375 0 3681.3037 11.787983
1050 20222.396 310.94072 0 3681.34 -8.3459539
1100 21321.687 127.61533 0 3681.2299 -1.2184717
1150 20849.582 206.01695 0 3680.9472 -0.86699156
1200 21815.003 45.317415 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064077
1300 20780.781 217.36506 0 3680.8286 6.053862
1350 20558.972 254.36481 0 3680.8601 -3.6773966
1400 21485.029 99.812935 0 3680.6511 -16.185472
1450 21771.107 52.159605 0 3680.6775 -2.4756675
1500 21520.948 93.503934 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.5159957
1600 20778.805 216.92176 0 3680.0559 15.089186
1650 21477.638 100.2183 0 3679.8247 -1.1045812
1700 18501.341 596.47889 0 3680.0357 -15.67966
1750 18563.642 587.34786 0 3681.2882 33.532195
1800 19110.187 494.82315 0 3679.8543 18.024044
1850 21364.193 119.2351 0 3679.9339 2.5291255
1900 20146.632 322.14766 0 3679.9197 5.7312569
1950 20692.671 231.25335 0 3680.0319 4.2977718
2000 20943.904 189.1123 0 3679.7629 -22.645328
2050 19668.094 401.82367 0 3679.8394 3.625351
2100 20280.495 299.75279 0 3679.8352 7.4808501
2150 19181.964 483.50484 0 3680.4989 22.618437
2200 21300.002 130.73207 0 3680.7324 4.7107204
2250 20487.278 266.58364 0 3681.13 -8.6436788
2300 18653.922 572.11506 0 3681.102 -5.2650803
2350 21513.162 95.675284 0 3681.2022 -9.358275
2400 21466.87 103.46516 0 3681.2768 -29.576898
2450 20098.852 332.48096 0 3682.2896 35.802574
2500 20763.224 221.86356 0 3682.401 -12.492465
2550 20425.308 278.04709 0 3682.265 -22.360414
2600 21467.742 104.32441 0 3682.2815 -10.062558
2650 20774.17 220.00066 0 3682.3623 5.2193436
2700 18569.233 587.73881 0 3682.6109 22.145192
2750 20654.466 239.78519 0 3682.1961 -6.9106068
2800 20814.792 213.06343 0 3682.1954 -6.9316614
2850 16353.471 956.9648 0 3682.5433 34.229058
2900 19519.089 429.00752 0 3682.189 8.7072031
2950 20171.665 320.18684 0 3682.1309 2.7223515
3000 20470.108 270.26106 0 3681.9457 -8.2674499
3050 20359.511 288.83368 0 3682.0856 -4.69092
3100 19856.099 372.69336 0 3682.0432 9.3653131
3150 20561.401 254.89391 0 3681.794 6.7807193
3200 18974.717 519.59328 0 3682.0462 14.028207
3250 17201.03 816.05668 0 3682.895 30.827229
3300 21032.748 176.57229 0 3682.0304 -8.8776478
3350 17299.203 798.82174 0 3682.0222 -6.5474977
3400 16871.128 870.67484 0 3682.5295 -23.235008
3450 19319.303 462.06051 0 3681.9443 -11.811901
3500 17860.126 705.48294 0 3682.1705 -15.992033
3550 21874.357 36.186306 0 3681.9124 -2.4098493
3600 21393.595 116.22067 0 3681.8199 -10.262929
3650 20544.718 257.71089 0 3681.8306 0.55484185
3700 20330.417 293.63761 0 3682.0404 16.661746
3750 21244.461 141.09081 0 3681.8343 4.9615754
3800 19958.592 355.64853 0 3682.0806 13.979713
3850 21497.423 98.927167 0 3681.8309 -6.621684
3900 21769.359 53.67612 0 3681.9026 -1.926207
3950 19975.772 352.52452 0 3681.8198 9.245817
4000 21113.483 163.03078 0 3681.9446 2.7569744
4050 19709.067 397.27579 0 3682.1202 -3.0811456
4100 21815.578 46.077634 0 3682.0073 -12.520188
4150 21642.428 74.997052 0 3682.0685 -1.1460009
4200 19928.01 360.19492 0 3681.53 8.857095
4250 17863.117 703.82283 0 3681.009 33.346649
4300 20382.848 284.9686 0 3682.1099 -7.0563493
4350 21589.546 83.691599 0 3681.9492 -6.3466935
4400 21561.341 88.259907 0 3681.8167 -0.05858595
4450 19016.303 512.39829 0 3681.7821 43.125503
4500 20065.798 337.40858 0 3681.7083 1.7677159
4550 19263.771 471.03594 0 3681.6644 -23.462523
4600 20845.688 207.74162 0 3682.023 0.16598388
4650 19646.643 407.84353 0 3682.2841 11.884842
4700 20692.329 233.43094 0 3682.1524 -14.265029
4750 17999.182 682.2895 0 3682.1531 -25.09426
4800 20585.117 251.43776 0 3682.2906 10.111397
4850 19368.488 453.98051 0 3682.0618 6.199069
4900 20416.868 279.66263 0 3682.474 7.5050136
4950 21376.045 119.55597 0 3682.2302 -9.6343892
5000 21346.337 124.42913 0 3682.1519 -3.6930357
5050 19787.72 384.70087 0 3682.6542 -5.855159
5100 20440.061 275.27592 0 3681.9528 1.7528745
5150 15625.189 1079.1543 0 3683.3525 19.539205
5200 20308.779 297.80498 0 3682.6014 8.9223119
5250 21044.849 175.43646 0 3682.9113 5.2785373
5300 20543.584 258.744 0 3682.6747 1.2007699
5350 21171.39 154.69163 0 3683.2566 -12.896011
5400 19626.405 409.45045 0 3680.518 16.150799
5450 20550.071 258.26489 0 3683.2766 -21.262685
5500 19104.84 499.01387 0 3683.1539 11.949545
5550 19559.267 422.41448 0 3682.2923 3.8829356
5600 20044.332 342.61709 0 3683.3391 -1.7700503
5650 21953.27 25.016694 0 3683.8951 -22.754979
5700 21639.986 77.352619 0 3684.017 -15.578393
5750 21144.414 159.81932 0 3683.8884 -9.0956708
5800 19267.59 472.68582 0 3683.9509 12.517057
5850 21221.184 146.53726 0 3683.4012 -0.35975116
5900 21141.226 159.83342 0 3683.371 0.79471018
5950 20417.806 280.84037 0 3683.808 -4.380384
6000 15946.467 1025.7528 0 3683.4973 -2.9233738
6050 20307.785 299.10545 0 3683.7362 -7.6865743
6100 18110.389 663.98174 0 3682.3799 4.1591862
6150 19958.364 357.9562 0 3684.3502 0.64161306
6200 18283.091 637.04273 0 3684.2246 1.3409324
6250 17081.956 837.9693 0 3684.962 -6.7113704
6300 21382.883 120.98513 0 3684.7989 -13.987822
6350 19952.702 359.01391 0 3684.4642 6.3550454
6400 20832.557 212.50673 0 3684.5995 -1.5787609
6450 18646.002 577.10671 0 3684.7738 7.7299342
6500 18261.033 641.30218 0 3684.8076 17.386854
6550 18426.877 613.53329 0 3684.6794 -3.3462219
6600 20349.993 293.18762 0 3684.8531 -12.422327
6650 21112.2 166.06059 0 3684.7606 -6.7451773
6700 20046.245 343.52129 0 3684.5621 -4.0057021
6750 20834.1 212.52233 0 3684.8724 -1.5556583
6800 21150.619 159.68754 0 3684.7908 -1.5850612
6850 20008.249 350.12255 0 3684.8308 6.4872768
6900 18654.888 575.51473 0 3684.6627 -17.992304
6950 19708.289 400.17932 0 3684.8942 7.0106327
7000 20437.426 278.17876 0 3684.4164 6.2019137
7050 19604.082 416.96446 0 3684.3114 -3.924055
7100 18301.87 633.03111 0 3683.3428 19.029745
7150 18558.782 591.49191 0 3684.6222 25.690348
7200 16746.788 894.4891 0 3685.6204 9.3897347
7250 19956.035 358.65844 0 3684.6642 2.9307876
7300 21612.74 82.596669 0 3684.7199 -6.0761772
7350 21082.361 170.97104 0 3684.6979 -1.6531911
7400 21447.623 110.03038 0 3684.6342 -9.6680921
7450 21815.262 48.645261 0 3684.5222 -2.4194461
7500 21586.807 86.513539 0 3684.3147 0.80475725
7550 21432.021 112.08344 0 3684.087 3.7213279
7600 18765.76 557.30844 0 3684.9351 25.566982
7650 19237.591 477.51887 0 3683.784 -0.93181342
7700 20058.61 340.75274 0 3683.8544 4.1984966
7750 21689.282 69.4903 0 3684.3707 -8.0484797
7800 21149.046 159.71259 0 3684.5537 7.1881243
7850 19334.412 461.23349 0 3683.6355 14.066324
7900 21263.983 140.83705 0 3684.8343 -14.739146
7950 20871.691 206.2356 0 3684.8508 -11.575259
8000 18916.496 531.93786 0 3684.6872 -20.395653
8050 20703.238 233.97858 0 3684.5183 4.2191304
8100 19544.399 426.74441 0 3684.1442 15.563275
8150 17578.916 755.02603 0 3684.8454 23.23474
8200 18121.828 663.35414 0 3683.6588 -23.277149
8250 19000.859 515.63274 0 3682.4425 8.1499185
8300 16312.856 965.20527 0 3684.0147 69.340264
8350 17908.285 699.50533 0 3684.2195 -13.64631
8400 19971.59 355.22033 0 3683.8187 6.2163041
8450 13617.129 1415.4014 0 3684.9229 -9.1829017
8500 20374.985 288.34097 0 3684.1719 1.0194401
8550 21452.212 108.96717 0 3684.3359 -8.0882838
8600 17196.613 818.7652 0 3684.8674 -2.1874477
8650 21510.389 99.326067 0 3684.3909 -3.5449392
8700 21446.623 109.76972 0 3684.2068 -0.76115037
8750 20700.162 234.50311 0 3684.5301 2.0551713
8800 21686.769 69.759974 0 3684.2215 -3.6322891
8850 20892.916 201.69594 0 3683.8486 0.57163157
8900 18095.714 668.44418 0 3684.3965 19.055292
8950 21325.044 129.56368 0 3683.7377 2.2916549
9000 20739.771 227.15562 0 3683.7842 -6.4759144
9050 20683.885 235.94003 0 3683.2543 1.8163478
9100 21432.386 111.08386 0 3683.1483 -9.5573949
9150 21686.43 69.315468 0 3683.7205 2.1854565
9200 16916.728 864.20897 0 3683.6636 7.2632357
9250 20122.374 329.80422 0 3683.5332 6.2589988
9300 20621.693 246.58967 0 3683.5386 -20.210043
9350 20343.792 292.92921 0 3683.5612 0.47974589
9400 20334.062 294.47957 0 3683.4899 -5.5269222
9450 20971.669 188.26826 0 3683.5464 1.5825497
9500 20948.938 191.99574 0 3683.4855 1.7294775
9550 21557.149 90.697719 0 3683.5559 4.5248095
9600 21121.109 162.83027 0 3683.0151 -3.8673505
9650 21306.551 132.27859 0 3683.3704 -0.05028404
9700 21064.24 172.82072 0 3683.5273 1.7248916
9750 18962.129 523.71798 0 3684.0729 17.93568
9800 21192.894 151.77036 0 3683.9193 -0.2514556
9850 20585.229 252.91402 0 3683.7855 9.2033197
9900 21584.165 86.429361 0 3683.7902 -5.4686156
9950 21190.652 151.98402 0 3683.7593 -3.5815764
10000 20061.072 340.24042 0 3683.7525 -2.2008049
Loop time of 25.7955 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.950715 (3.68559)
Neigh time (%) = 0.339646 (1.31669)
Comm time (%) = 0.113344 (0.439395)
Outpt time (%) = 0.168425 (0.652924)
Other time (%) = 24.2234 (93.9054)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 60 ave 60 max 60 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 721 ave 721 max 721 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 721
Ave neighs/atom = 8.90123
Neighbor list builds = 989
Dangerous builds = 911

306
examples/rigid/log.rigid.poems2.12Feb07.liberty.4
View File

@ -1,306 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 2 by 2 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.83868 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -49.218825
50 12167.633 1505.5478 0 3758.8133 33.574274
100 17556.978 512.66277 0 3763.9549 7.6047451
150 19579.586 138.04942 0 3763.8987 -16.463506
200 19757.51 105.30542 0 3764.1036 7.5942941
250 18218.374 390.10747 0 3763.8804 19.672945
300 19383.039 174.40688 0 3763.8586 10.032093
350 20125.986 36.972611 0 3764.0071 6.0125969
400 18888.816 266.10975 0 3764.0386 8.3046039
450 19307.656 188.2511 0 3763.743 7.8887976
500 16331.197 738.56392 0 3762.8597 13.456852
550 19318.722 186.16172 0 3763.7027 8.2282227
600 19455.268 161.20621 0 3764.0336 7.7732896
650 18487.011 340.03216 0 3763.5528 3.9255991
700 17321.201 556.32471 0 3763.9545 -6.4011523
750 18979.187 249.04389 0 3763.7082 2.1939314
800 19342.456 181.85552 0 3763.7918 12.876517
850 19070.641 232.19342 0 3763.7936 8.2159078
900 19478.873 156.65987 0 3763.8586 7.4568244
950 19912.415 76.437437 0 3763.9216 5.8486682
1000 16003.749 802.39753 0 3766.0548 55.191187
1050 19859.583 86.64176 0 3764.3424 8.7977394
1100 19229.575 203.61488 0 3764.6473 -4.0979799
1150 18821.6 279.15861 0 3764.64 1.5304912
1200 19392.695 173.59744 0 3764.8373 10.841959
1250 16459.624 717.32104 0 3765.3995 40.93
1300 19343.863 182.59043 0 3764.7874 9.4801222
1350 20019.643 57.503573 0 3764.8448 8.041765
1400 18549.582 329.31436 0 3764.4221 13.151345
1450 15163.926 957.47583 0 3765.6103 -7.3048398
1500 19223.688 204.15164 0 3764.0939 6.5539049
1550 18147.996 404.12675 0 3764.8668 13.092195
1600 18615.043 317.42462 0 3764.6548 5.9101585
1650 20120.654 38.887963 0 3764.935 0.38926372
1700 19450.904 162.98318 0 3765.0025 7.9275461
1750 19374.634 177.37922 0 3765.2744 8.7907106
1800 19424.403 167.93984 0 3765.0514 5.6664259
1850 17936.476 442.80024 0 3764.3699 14.101091
1900 19982.598 64.405734 0 3764.8868 3.8454902
1950 16216.207 761.84618 0 3764.8475 19.873084
2000 18584.309 322.14125 0 3763.6799 12.138411
2050 20107.968 41.025323 0 3764.723 5.3931463
2100 20002.381 60.584283 0 3764.7288 0.25773654
2150 16949.202 626.70007 0 3765.4412 12.954412
2200 20010.949 58.809053 0 3764.5403 -1.2239084
2250 18982.71 247.01257 0 3762.3292 8.977934
2300 18401.513 354.84007 0 3762.5277 7.0021344
2350 19390.418 172.96117 0 3763.7793 1.8207539
2400 16084.09 785.7786 0 3764.3137 -12.437816
2450 18871.606 268.52952 0 3763.2713 14.613895
2500 19686.081 117.99211 0 3763.5626 8.3329722
2550 18875.819 267.86112 0 3763.3831 -0.48856518
2600 17010.705 613.30983 0 3763.4405 11.630319
2650 18797.741 282.8114 0 3763.8745 8.1020989
2700 19726.505 110.11368 0 3763.1701 6.5575356
2750 19436.803 164.0424 0 3763.4504 6.8766681
2800 18357.485 362.53565 0 3762.0699 29.446982
2850 19004.145 243.73317 0 3763.0192 8.1423479
2900 20108.185 39.496053 0 3763.234 4.5848354
2950 15919.562 814.90854 0 3762.9756 23.062229
3000 17654.881 493.61172 0 3763.0342 5.545646
3050 18711.769 298.14871 0 3763.2911 7.243461
3100 16038.72 793.07314 0 3763.2064 14.346203
3150 19925.087 73.363563 0 3763.1945 6.1598038
3200 19305.94 187.89701 0 3763.0711 13.363938
3250 19779.251 100.11507 0 3762.9394 -4.2931123
3300 17922.539 444.12789 0 3763.1166 11.814226
3350 18967.646 250.37413 0 3762.9011 10.599374
3400 16940.148 625.60864 0 3762.673 27.487664
3450 19284.152 191.53891 0 3762.6781 7.1971328
3500 19321.512 184.58448 0 3762.6423 7.1507645
3550 19631.049 126.97845 0 3762.358 6.6703895
3600 18494.976 337.74154 0 3762.7371 5.2298746
3650 19117.634 222.45812 0 3762.7607 5.5119957
3700 19400.367 170.05551 0 3762.716 5.1505902
3750 19912.752 75.322358 0 3762.869 4.9003403
3800 18564.109 325.06781 0 3762.8658 14.09429
3850 19846.304 87.655562 0 3762.8971 9.0642301
3900 19476.444 156.1165 0 3762.8653 -2.9763615
3950 19647.738 124.43854 0 3762.9085 6.1008067
4000 18123.616 406.3511 0 3762.5762 12.300492
4050 16574.617 693.99841 0 3763.372 8.1837692
4100 18946.287 254.50552 0 3763.0773 10.419471
4150 18466.555 343.35133 0 3763.0837 1.7173061
4200 19477.739 156.04727 0 3763.0359 9.9334234
4250 19680.9 118.38024 0 3762.9913 6.7698432
4300 18320.329 369.90558 0 3762.5591 2.8725905
4350 18767.214 286.789 0 3762.199 10.607372
4400 16894.629 634.49312 0 3763.1281 11.825821
4450 17915.848 444.62515 0 3762.3748 5.59808
4500 19487.927 154.02671 0 3762.9021 4.5536547
4550 19880.496 81.301302 0 3762.8746 9.5930235
4600 19872.228 82.669863 0 3762.7122 6.7573135
4650 15769.89 843.11924 0 3763.4693 15.845442
4700 19720.045 110.85283 0 3762.7129 6.1293004
4750 19764.607 102.5192 0 3762.6317 8.94455
4800 17562.467 510.78691 0 3763.0956 13.972896
4850 19463.538 158.32481 0 3762.6836 1.0093239
4900 17932.952 441.75053 0 3762.6675 12.701684
4950 19084.979 228.62301 0 3762.8785 11.759924
5000 19472.38 156.9411 0 3762.9375 11.220659
5050 19453.908 160.3778 0 3762.9533 12.301143
5100 19521.287 147.96055 0 3763.0137 12.392696
5150 18128.471 405.81521 0 3762.9394 11.945434
5200 17049.524 605.73212 0 3763.0514 -0.12699639
5250 19645.014 125.0255 0 3762.991 -0.52279382
5300 18281.054 377.45844 0 3762.8388 20.11439
5350 19457.083 159.77948 0 3762.9429 6.3853596
5400 18431.165 349.7041 0 3762.8827 4.871088
5450 19431.127 164.51144 0 3762.8682 -3.2111996
5500 19538.523 144.42775 0 3762.6727 4.5926045
5550 16105.678 780.35525 0 3762.8882 54.598614
5600 20038.616 51.570638 0 3762.4254 4.5474063
5650 19774.413 100.34213 0 3762.2704 0.78153427
5700 19210.59 204.66324 0 3762.18 5.4298437
5750 19146.331 216.47595 0 3762.0928 7.0574791
5800 19058.521 232.88706 0 3762.2428 5.1938614
5850 19195.04 207.81355 0 3762.4506 -3.7719233
5900 18304.113 372.73776 0 3762.3882 -0.65463254
5950 19936.776 70.443763 0 3762.4393 9.3331421
6000 19413.016 167.50961 0 3762.5125 9.6998807
6050 19169.847 212.36264 0 3762.3343 13.97952
6100 19873.513 82.452317 0 3762.7325 7.797884
6150 18911.794 260.42784 0 3762.6119 3.8761488
6200 19153.7 215.69884 0 3762.6802 2.9164092
6250 18802.916 280.37164 0 3762.3932 9.5188585
6300 19385.046 172.8566 0 3762.6799 9.6703687
6350 20042.403 51.159768 0 3762.7159 7.6850802
6400 17671.74 490.05042 0 3762.5948 14.096008
6450 18092.22 412.77197 0 3763.1832 0.82294201
6500 19953.711 67.838094 0 3762.9698 8.1400023
6550 19818.338 92.883562 0 3762.9461 8.055057
6600 19323.833 183.93088 0 3762.4184 5.2727635
6650 18642.816 310.35894 0 3762.7323 19.352453
6700 16246.778 753.95834 0 3762.6209 24.682771
6750 19362.672 176.94037 0 3762.6204 4.5345155
6800 18813.849 278.64468 0 3762.6908 9.7383715
6850 19386.278 172.79274 0 3762.8443 -2.8239186
6900 19206.609 206.02588 0 3762.8054 8.1264361
6950 18068.847 416.85422 0 3762.9369 2.3525156
7000 18369.805 360.43314 0 3762.249 13.728295
7050 18426.189 350.61688 0 3762.8741 14.517035
7100 17656.982 492.79834 0 3762.6098 11.126444
7150 18141.722 402.98387 0 3762.562 14.510638
7200 18621.905 313.92925 0 3762.4301 1.4234708
7250 18374.083 360.03493 0 3762.6429 -3.8128826
7300 18040.277 421.82567 0 3762.6177 2.7635663
7350 19146.198 217.01003 0 3762.6023 11.264741
7400 18826.989 276.1892 0 3762.6686 12.390664
7450 16067.243 787.1796 0 3762.5949 14.180712
7500 18419.546 351.11771 0 3762.1448 12.922148
7550 18446.346 346.8971 0 3762.8871 15.016254
7600 18944.672 254.13521 0 3762.4077 10.235074
7650 18736.984 292.8881 0 3762.7 -8.4530721
7700 18741.654 291.39068 0 3762.0673 3.2144304
7750 18220.361 388.04072 0 3762.1816 15.132777
7800 19348.223 178.96147 0 3761.9658 4.4894323
7850 19401.949 169.04328 0 3761.9968 4.9313127
7900 18577.957 321.63399 0 3761.9965 10.7403
7950 17739.892 476.69976 0 3761.865 15.786414
8000 17512.557 519.37266 0 3762.4387 8.4816398
8050 19168.123 212.38445 0 3762.0369 1.9313036
8100 17916.044 443.46573 0 3761.2517 1.5416538
8150 18601.23 316.95165 0 3761.6238 10.656943
8200 17791.805 467.15931 0 3761.9381 2.2002016
8250 18321.607 369.09405 0 3761.9843 5.815164
8300 17334.957 552.06316 0 3762.2404 9.7175531
8350 17207.467 575.31923 0 3761.8872 5.6916957
8400 18225.217 387.22593 0 3762.2662 13.185636
8450 19004.047 243.03694 0 3762.3048 13.419491
8500 18952.876 252.61597 0 3762.4078 2.0529233
8550 19127.437 220.08856 0 3762.2066 -3.9009433
8600 19542.154 143.35104 0 3762.2684 9.2825505
8650 19294.525 189.17898 0 3762.2392 15.659987
8700 18832.532 274.05387 0 3761.5598 6.8307945
8750 18591.931 318.93488 0 3761.885 13.12084
8800 18576.38 322.04174 0 3762.1121 1.3006059
8850 19922.086 72.972833 0 3762.248 7.446691
8900 18892.839 263.55803 0 3762.2319 12.740409
8950 16486.736 708.70288 0 3761.8022 33.657286
9000 18628.335 312.81773 0 3762.5094 11.180187
9050 19286.823 190.4938 0 3762.1278 3.690949
9100 18973.378 247.96414 0 3761.5526 12.70188
9150 17256.927 566.17648 0 3761.9038 13.94458
9200 18507.288 334.66416 0 3761.9398 8.7036327
9250 18961.534 250.42427 0 3761.8194 2.441337
9300 19206.115 205.203 0 3761.8911 7.4983103
9350 19401.191 168.92055 0 3761.7336 4.4522417
9400 18069.392 415.54646 0 3761.7301 9.7253906
9450 18828.428 274.89551 0 3761.6415 12.99464
9500 18295.323 373.66825 0 3761.691 4.0189559
9550 17709.338 482.22946 0 3761.7365 -0.16619916
9600 19512.39 148.31281 0 3761.7184 6.188777
9650 19742.351 105.74048 0 3761.7315 8.5310602
9700 19892.658 77.898869 0 3761.7245 9.4480252
9750 19035.044 236.65131 0 3761.6595 8.943227
9800 17443.415 531.71826 0 3761.9802 20.612812
9850 19545.912 141.99994 0 3761.6133 5.9979112
9900 19542.173 142.22929 0 3761.1503 7.6623836
9950 19794.356 96.034607 0 3761.6561 2.4218049
10000 19058.563 232.34496 0 3761.7085 -1.2298428
Loop time of 17.5626 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0920856 (0.524327)
Neigh time (%) = 0.0420477 (0.239415)
Comm time (%) = 1.61713 (9.20777)
Outpt time (%) = 0.101673 (0.578917)
Other time (%) = 15.7097 (89.4496)
Nlocal: 20.25 ave 42 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 20.5 ave 37 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 164.25 ave 401 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 657
Ave neighs/atom = 8.11111
Neighbor list builds = 991
Dangerous builds = 930

306
examples/rigid/log.rigid.poems2.12Feb07.linux.1
View File

@ -1,306 +0,0 @@
LAMMPS (12 Feb 2007)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
1 by 1 by 1 processor grid
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
#group clump1 id <> 1 9
#group clump2 id <> 10 18
#group clump3 id <> 19 27
#group clump4 id <> 28 36
#group clump5 id <> 37 45
#group clump6 id <> 46 54
#group clump7 id <> 55 63
#group clump8 id <> 64 72
#group clump9 id <> 73 81
#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 9 18
10 atoms in group clump2
group clump3 id <> 18 27
10 atoms in group clump3
group clump4 id <> 27 36
10 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 45 54
10 atoms in group clump6
group clump7 id <> 54 63
10 atoms in group clump7
group clump8 id <> 63 72
10 atoms in group clump8
group clump9 id <> 72 81
10 atoms in group clump9
fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
dump 1 all atom 50 dump.rigid
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.85083 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -49.218825
50 12167.633 1505.5478 0 3758.8133 33.574274
100 17556.978 512.66277 0 3763.9549 7.6047451
150 19579.586 138.04942 0 3763.8987 -16.463506
200 19757.51 105.30542 0 3764.1036 7.5942941
250 18218.374 390.10747 0 3763.8804 19.672945
300 19383.039 174.40688 0 3763.8586 10.032093
350 20125.986 36.972611 0 3764.0071 6.0125969
400 18888.816 266.10975 0 3764.0386 8.3046039
450 19307.656 188.2511 0 3763.743 7.8887976
500 16331.197 738.56392 0 3762.8597 13.456852
550 19318.722 186.16172 0 3763.7027 8.2282227
600 19455.268 161.20621 0 3764.0336 7.7732896
650 18487.011 340.03216 0 3763.5528 3.9255991
700 17321.201 556.32471 0 3763.9545 -6.4011523
750 18979.187 249.04389 0 3763.7082 2.1939314
800 19342.456 181.85552 0 3763.7918 12.876517
850 19070.641 232.19342 0 3763.7936 8.2159078
900 19478.873 156.65987 0 3763.8586 7.4568244
950 19912.415 76.437437 0 3763.9216 5.8486682
1000 16003.749 802.39753 0 3766.0548 55.191187
1050 19859.583 86.64176 0 3764.3424 8.7977394
1100 19229.575 203.61488 0 3764.6473 -4.0979799
1150 18821.6 279.15861 0 3764.64 1.5304912
1200 19392.695 173.59744 0 3764.8373 10.841959
1250 16459.624 717.32104 0 3765.3995 40.93
1300 19343.863 182.59043 0 3764.7874 9.4801222
1350 20019.643 57.503573 0 3764.8448 8.041765
1400 18549.582 329.31436 0 3764.4221 13.151345
1450 15163.926 957.47582 0 3765.6103 -7.3048396
1500 19223.689 204.15156 0 3764.0939 6.5539037
1550 18147.996 404.12674 0 3764.8668 13.092194
1600 18615.043 317.42458 0 3764.6548 5.910153
1650 20120.654 38.887996 0 3764.935 0.38927147
1700 19450.903 162.98348 0 3765.0025 7.9275404
1750 19374.636 177.37893 0 3765.2744 8.7907115
1800 19424.402 167.93995 0 3765.0514 5.6664351
1850 17936.625 442.77274 0 3764.3699 14.100683
1900 19982.599 64.405428 0 3764.8868 3.845421
1950 16216.44 761.80238 0 3764.8469 19.871956
2000 18584.234 322.15493 0 3763.6798 12.138618
2050 20107.969 41.025039 0 3764.723 5.3930845
2100 20002.411 60.57861 0 3764.7288 0.25780472
2150 16948.844 626.76647 0 3765.4413 12.955652
2200 20010.946 58.809564 0 3764.5403 -1.2241058
2250 18982.703 247.01388 0 3762.3292 8.9782072
2300 18401.642 354.81637 0 3762.5279 7.00181
2350 19390.361 172.97181 0 3763.7793 1.8204299
2400 16086.125 785.40108 0 3764.3132 -12.43145
2450 18872.351 268.39211 0 3763.2718 14.60112
2500 19684.688 118.25055 0 3763.5632 8.3452435
2550 18878.925 267.2853 0 3763.3825 -0.4776104
2600 17005.407 614.29162 0 3763.441 11.648752
2650 18827.389 277.31059 0 3763.8641 8.0646841
2700 19715.461 112.12451 0 3763.1358 6.611501
2750 19319.449 185.79269 0 3763.4684 7.0469373
2800 18120.942 406.44184 0 3762.1719 34.017493
2850 19401.627 170.17075 0 3763.0647 6.6156058
2900 20106.157 39.874788 0 3763.2371 3.9356029
2950 16814.814 649.4335 0 3763.288 19.866275
3000 16200.577 761.45184 0 3761.5588 24.481639
3050 18396.676 356.11264 0 3762.9044 11.886991
3100 17582.958 506.67523 0 3762.7786 -8.4420604
3150 18362.109 362.43838 0 3762.8289 20.848538
3200 17008.785 613.88943 0 3763.6645 17.861071
3250 19614.194 130.81389 0 3763.072 6.9309301
3300 18995.955 245.31261 0 3763.0821 -3.0930246
3350 18215.815 389.87474 0 3763.1737 7.0361215
3400 18068.71 417.08655 0 3763.144 9.961669
3450 19352.914 179.0126 0 3762.8855 13.271847
3500 18738.818 292.55665 0 3762.7082 8.7182296
3550 19469.912 157.36508 0 3762.9044 9.8811856
3600 18431.706 349.41269 0 3762.6916 9.8972814
3650 18819.962 277.76095 0 3762.9392 10.602006
3700 19813.675 93.945731 0 3763.1449 5.3804999
3750 18075.078 415.77801 0 3763.0146 6.6699336
3800 19422.14 166.53886 0 3763.2315 6.5699764
3850 18013.209 427.44475 0 3763.2243 0.47129141
3900 19193.889 208.87526 0 3763.2991 2.2645534
3950 16568.188 695.64549 0 3763.8284 18.270973
4000 17993.623 430.51008 0 3762.6626 10.839154
4050 19625.511 128.63837 0 3762.9922 5.7391383
4100 19069.298 231.35736 0 3762.7088 6.8146572
4150 18033.877 424.02231 0 3763.6292 2.7693427
4200 19950.626 68.482279 0 3763.0426 9.5547662
4250 18786.19 284.10677 0 3763.0309 14.089513
4300 19526.067 146.81821 0 3762.7565 3.5904061
4350 16343.335 736.72783 0 3763.2714 39.410491
4400 18759.668 288.81939 0 3762.8319 12.975401
4450 18633.251 312.20135 0 3762.8033 10.199762
4500 18079.31 414.80535 0 3762.8256 7.6705765
4550 18288.498 376.11039 0 3762.8693 12.253044
4600 18315.887 371.16083 0 3762.9918 5.0242317
4650 18901.901 262.59396 0 3762.9459 2.7293238
4700 19311.704 186.85051 0 3763.092 4.5926473
4750 19426.54 165.69302 0 3763.2005 -1.3847183
4800 18347.933 365.43611 0 3763.2015 7.9755076
4850 19952.067 68.477491 0 3763.3047 8.9724781
4900 19224.549 203.14962 0 3763.2513 8.0785966
4950 19857.322 85.89601 0 3763.1779 6.7304247
5000 19592.925 134.86246 0 3763.182 7.6141401
5050 19472.16 157.37877 0 3763.3343 9.2091755
5100 19814.831 93.787624 0 3763.2008 11.330509
5150 18211.407 390.82193 0 3763.3047 13.81542
5200 18828.994 276.3271 0 3763.1778 11.34844
5250 20121.332 37.261735 0 3763.4344 6.7338019
5300 17755.337 475.75071 0 3763.7761 14.167064
5350 20033.05 53.761483 0 3763.5855 5.3749453
5400 19332.059 183.54479 0 3763.5557 7.4674926
5450 19964.421 66.56191 0 3763.677 6.1167743
5500 19838.257 89.969443 0 3763.7207 3.3591427
5550 19202.804 207.40212 0 3763.4769 16.351587
5600 19855.825 86.760789 0 3763.7654 8.0189044
5650 19060.478 234.22396 0 3763.9421 6.1572157
5700 20124.587 37.161564 0 3763.937 7.5696918
5750 19304.489 189.01672 0 3763.9221 5.7150756
5800 18516.206 335.07659 0 3764.0036 3.5806069
5850 18093.127 413.01533 0 3763.5945 7.8629917
5900 17303.637 559.08088 0 3763.458 2.7072615
5950 19818.733 93.796285 0 3763.932 8.9805512
6000 18162.182 400.57864 0 3763.9457 13.263234
6050 18439.177 349.30792 0 3763.9703 6.4756606
6100 18899.456 263.84185 0 3763.741 10.898781
6150 17317.004 556.71789 0 3763.5704 11.704857
6200 18991.81 246.89696 0 3763.8989 3.2286864
6250 19868.798 84.388048 0 3763.795 5.9103508
6300 18989.135 247.26992 0 3763.7763 18.604444
6350 15978.578 804.89 0 3763.8858 12.169877
6400 18967.47 251.22915 0 3763.7236 6.8735765
6450 19294.369 190.87058 0 3763.9019 -1.5455507
6500 19826.451 92.014872 0 3763.5798 7.2553554
6550 17480.845 526.28717 0 3763.4807 5.5505499
6600 17806.087 465.8384 0 3763.262 26.481782
6650 17942.192 439.48981 0 3762.118 11.35985
6700 16468.094 712.95472 0 3762.6018 14.069858
6750 19305.119 188.34815 0 3763.3703 7.052136
6800 19988.201 62.004452 0 3763.5231 6.5334797
6850 20193.079 24.117041 0 3763.5761 3.4827497
6900 20011.596 57.729546 0 3763.5806 3.4890214
6950 18419.577 352.48285 0 3763.5157 0.47973678
7000 19178.531 212.01179 0 3763.5917 8.9488095
7050 18754.875 289.8693 0 3762.9942 15.271004
7100 19179.381 211.26035 0 3762.9975 7.7065367
7150 18221.392 388.75188 0 3763.0837 -5.5870803
7200 19508.765 150.73861 0 3763.4729 0.86924221
7250 16779.268 656.19712 0 3763.4689 9.6537749
7300 19184.405 210.6069 0 3763.2744 1.3949529
7350 17914.948 445.90458 0 3763.4876 8.5105795
7400 14040.559 1164.2709 0 3764.3744 -18.733631
7450 17680.643 489.04226 0 3763.2354 7.7465943
7500 15575.048 879.11471 0 3763.3829 11.73774
7550 16738.339 663.36831 0 3763.0607 19.071113
7600 18927.126 258.2804 0 3763.3038 8.7575196
7650 17033.929 610.18818 0 3764.6195 20.103976
7700 17800.589 463.84003 0 3760.2454 -0.58664763
7750 18337.643 367.47891 0 3763.3388 3.0646364
7800 20102.521 40.465427 0 3763.1544 5.890522
7850 18854.307 271.72975 0 3763.2681 21.40115
7900 18769.869 287.08151 0 3762.9832 13.873827
7950 19530.556 146.69214 0 3763.4618 6.9677806
8000 17967.757 436.48149 0 3763.8439 -8.7686357
8050 19995.451 60.489084 0 3763.3503 -0.16755556
8100 17668.554 491.39156 0 3763.346 5.2085894
8150 17041.937 607.0112 0 3762.9255 32.910713
8200 19634.282 127.02828 0 3763.0064 10.156284
8250 19464.43 158.26891 0 3762.7929 4.6092644
8300 18262.088 380.75171 0 3762.6199 -2.8465886
8350 19154.678 214.95549 0 3762.118 7.9411401
8400 18631.904 312.04844 0 3762.4011 8.5365875
8450 17326.79 552.9849 0 3761.6497 5.5282777
8500 18262.986 380.59746 0 3762.6319 4.5328455
8550 16355.636 733.37813 0 3762.1995 -0.081116392
8600 17652.805 494.50385 0 3763.5419 7.9532832
8650 16589.75 690.94159 0 3763.1175 5.9389722
8700 18767.632 287.52175 0 3763.0091 8.5339813
8750 19530.676 145.40209 0 3762.194 13.700999
8800 16209.935 760.89243 0 3762.7323 -3.8758006
8850 19909.854 75.790768 0 3762.8008 7.227949
8900 19162.868 213.40033 0 3762.0797 13.090144
8950 17996.377 429.38719 0 3762.0496 11.184399
9000 17366.686 545.41384 0 3761.4667 1.1354401
9050 16976.454 618.54424 0 3762.332 2.9998911
9100 19419.965 166.18943 0 3762.4793 9.2514375
9150 17900.022 448.30981 0 3763.1287 1.7569818
9200 18662.637 306.89813 0 3762.942 9.9910386
9250 19806.478 95.487105 0 3763.3534 1.7132635
9300 19065.731 233.31844 0 3764.0093 5.8910882
9350 15347.66 921.21669 0 3763.3759 8.8446349
9400 18056.449 416.32084 0 3760.1078 19.958532
9450 19104.743 225.75045 0 3763.6658 6.8595588
9500 18193.488 394.55096 0 3763.7154 5.7859475
9550 17005.07 614.383 0 3763.4701 26.389911
9600 18956.557 253.26137 0 3763.7349 9.313651
9650 18278.345 379.38464 0 3764.2634 -5.9106259
9700 19791.354 98.864736 0 3763.9303 7.4991305
9750 19840.264 89.82519 0 3763.9482 3.3775783
9800 19120.304 222.91513 0 3763.7122 -2.4237742
9850 15643.719 866.53246 0 3763.5175 4.7456523
9900 16998.456 616.53609 0 3764.3983 -1.5467682
9950 19670.981 121.07532 0 3763.8496 8.7750881
10000 16544.589 699.98952 0 3763.8022 -7.723777
Loop time of 26.9527 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.688746 (2.55539)
Neigh time (%) = 0.27122 (1.00628)
Comm time (%) = 0.133495 (0.495294)
Outpt time (%) = 0.140981 (0.523068)
Other time (%) = 25.7183 (95.42)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 528 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 528
Ave neighs/atom = 6.51852
Neighbor list builds = 993
Dangerous builds = 946

159
examples/shear/log.shear.12Feb07.liberty.4
View File

@ -1,159 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style eam
pair_coeff * * niu3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.68686 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346
50 300 -8239.0761 0 -8185.446 13404.703 19669.87
75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549
100 300 -8250.5856 0 -8196.9555 6735.754 19818.526
Loop time of 0.213186 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.175801 (82.4637)
Neigh time (%) = 0.00498581 (2.33871)
Comm time (%) = 0.0236108 (11.0752)
Outpt time (%) = 0.000816882 (0.383177)
Other time (%) = 0.00797158 (3.73926)
Nlocal: 478 ave 490 max 468 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1033.75 ave 1043 max 1021 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 11508.8 ave 12218 max 10874 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 46035
Ave neighs/atom = 24.0769
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.70559 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
100 297.48776 -8255.7637 0 -8220.3225 1519.5936 19869.252
200 300 -8259.5191 0 -8223.7786 407.14026 19843.233
300 306.85093 -8252.9546 0 -8216.3979 -1452.8459 19987.791
400 303.87074 -8246.296 0 -8210.0945 1276.3308 20128.061
500 299.00581 -8241.6473 0 -8206.0253 943.44685 20226.281
600 300 -8228.0773 0 -8192.3369 3740.0009 20307.41
700 302.55478 -8222.4773 0 -8186.4325 6034.1752 20412.441
800 291.55934 -8208.4477 0 -8173.7129 9870.4071 20534.96
900 300.04405 -8197.8106 0 -8162.0649 11858.874 20635.988
1000 303.4363 -8185.1721 0 -8149.0223 15860.089 20755.666
1100 300 -8172.7372 0 -8136.9967 19064.863 20868.017
1200 300 -8163.6948 0 -8127.9543 20503.74 20997.464
1300 300 -8157.774 0 -8122.0336 19017.48 21108.594
1400 301.23169 -8148.1245 0 -8112.2373 19838.433 21245.369
1500 300 -8137.0376 0 -8101.2972 19618.234 21361.383
1600 300 -8129.5673 0 -8093.8269 17832.316 21493.274
1700 300 -8131.9086 0 -8096.1682 15651.56 21609.288
1800 300 -8154.2629 0 -8118.5225 9602.8973 21725.302
1900 300 -8166.6747 0 -8130.9342 7079.4166 21855.971
2000 297.56913 -8164.1963 0 -8128.7455 6008.7168 21970.765
2100 307.18117 -8162.4989 0 -8125.903 5339.1594 22100.212
2200 307.91443 -8165.8526 0 -8129.1693 4903.917 22218.669
2300 307.29809 -8166.6561 0 -8130.0463 4057.1866 22343.232
2400 306.14212 -8165.725 0 -8129.2529 4381.5236 22462.91
2500 306.62123 -8166.8443 0 -8130.3151 2924.8251 22583.809
2600 300 -8166.6003 0 -8130.8598 2179.9998 22701.045
2700 309.89171 -8168.2224 0 -8131.3035 3044.4626 22836.599
2800 305.74412 -8166.2652 0 -8129.8404 1099.7498 22952.613
2900 301.2671 -8170.7739 0 -8134.8825 -2699.4417 23073.512
3000 300 -8171.8299 0 -8136.0895 -3656.4591 23189.527
Loop time of 8.00391 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 5.24986 (65.5912)
Neigh time (%) = 0.275418 (3.44104)
Comm time (%) = 0.891668 (11.1404)
Outpt time (%) = 0.975094 (12.1827)
Other time (%) = 0.611869 (7.64463)
Nlocal: 478 ave 508 max 449 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1006.75 ave 1064 max 959 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 11284 ave 12171 max 10415 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 45136
Ave neighs/atom = 23.6067
Neighbor list builds = 216
Dangerous builds = 0

159
examples/shear/log.shear.12Feb07.linux.1
View File

@ -1,159 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style eam
pair_coeff * * niu3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.92854 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346
25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346
50 300 -8237.7876 0 -8184.1576 13746.642 19678.792
75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233
100 300 -8245.8191 0 -8192.189 9038.4055 19770.872
Loop time of 1.256 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 1.16738 (92.9443)
Neigh time (%) = 0.03633 (2.89252)
Comm time (%) = 0.012652 (1.00733)
Outpt time (%) = 0.002018 (0.160669)
Other time (%) = 0.03762 (2.99523)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2122 ave 2122 max 2122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45975 ave 45975 max 45975 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45975
Ave neighs/atom = 24.0455
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 2.00339 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
100 300 -8263.5777 0 -8227.8373 2795.3643 19788.083
200 295.48797 -8257.8787 0 -8222.6759 2179.0845 19913.732
300 292.48667 -8250.5584 0 -8215.7131 2.9847512 20043.736
400 304.93883 -8245.9033 0 -8209.5745 179.50544 20125.384
500 294.27283 -8241.2854 0 -8206.2272 829.41012 20145.713
600 302.25208 -8230.3821 0 -8194.3734 4273.5024 20285.46
700 300 -8223.3443 0 -8187.6038 6565.4269 20406.893
800 303.62781 -8211.0391 0 -8174.8665 8116.0638 20515.088
900 297.87427 -8197.7869 0 -8162.2997 10317.159 20621.333
1000 300 -8181.081 0 -8145.3406 13621.801 20748.339
1100 307.26338 -8166.9162 0 -8130.3105 17420.976 20877.786
1200 300.29796 -8153.8084 0 -8118.0325 20385.904 20986.474
1300 300 -8147.0071 0 -8111.2667 21178.857 21115.921
1400 300 -8137.1276 0 -8101.3872 21423.889 21246.59
1500 308.75316 -8131.6139 0 -8094.8306 20067.792 21365.047
1600 300 -8133.2906 0 -8097.5501 16682.824 21477.398
1700 308.52741 -8149.3473 0 -8112.5909 11697.908 21599.518
1800 300 -8152.6978 0 -8116.9573 9550.2281 21737.514
1900 308.57591 -8146.2494 0 -8109.4873 9662.4382 21859.635
2000 308.26812 -8146.4139 0 -8109.6884 9661.2057 21976.871
2100 302.17107 -8146.0627 0 -8110.0636 8521.2058 22094.106
2200 305.08447 -8151.7703 0 -8115.4241 4427.9711 22218.669
2300 300 -8166.2097 0 -8130.4693 -1334.8828 22346.896
2400 304.42128 -8165.4861 0 -8129.219 -931.52307 22464.131
2500 291.59698 -8160.1078 0 -8125.3684 2248.0287 22592.358
2600 304.33702 -8161.3244 0 -8125.0673 3566.8213 22704.709
2700 308.4539 -8163.6628 0 -8126.9152 1887.5801 22825.608
2800 309.42404 -8163.7723 0 -8126.9092 -395.06508 22946.507
2900 307.81471 -8165.3682 0 -8128.6967 -3460.652 23077.176
3000 299.7731 -8165.3688 0 -8129.6554 -5437.2745 23191.969
Loop time of 41.2714 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 34.9492 (84.6813)
Neigh time (%) = 1.98951 (4.82056)
Comm time (%) = 0.404728 (0.98065)
Outpt time (%) = 2.83924 (6.87944)
Other time (%) = 1.08875 (2.63802)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2089 ave 2089 max 2089 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45088 ave 45088 max 45088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45088
Ave neighs/atom = 23.5816
Neighbor list builds = 216
Dangerous builds = 0

160
examples/shear/log.shear.void.12Feb07.liberty.4
View File

@ -1,160 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style eam
pair_coeff * * niu3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.67464 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582
50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062
75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777
100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395
Loop time of 0.183477 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.149475 (81.468)
Neigh time (%) = 0.00532675 (2.90322)
Comm time (%) = 0.0207931 (11.3328)
Outpt time (%) = 0.000882387 (0.480925)
Other time (%) = 0.00699979 (3.81507)
Nlocal: 427 ave 435 max 419 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 780.25 ave 792 max 769 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 9878.75 ave 10203 max 9534 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 39515
Ave neighs/atom = 23.1352
Neighbor list builds = 5
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.69123 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
100 307.23986 -7307.219 0 -7276.0171 -5006.3499 19862.724
200 300 -7309.7515 0 -7279.2849 -9319.6187 19862.401
300 298.46847 -7303.3937 0 -7273.0826 -9727.416 20012.256
400 298.27255 -7299.2458 0 -7268.9546 -7916.7896 20056.15
500 297.5947 -7299.7495 0 -7269.5271 -6499.9287 20136.515
600 299.11571 -7294.7189 0 -7264.342 -4738.4592 20278.808
700 299.12204 -7285.1912 0 -7254.8138 -1900.5818 20396.287
800 300 -7279.6074 0 -7249.1408 -601.56409 20516.31
900 300 -7272.2062 0 -7241.7396 372.01695 20624.997
1000 297.17814 -7265.7734 0 -7235.5934 -1620.5152 20750.781
1100 300 -7257.7175 0 -7227.2509 -1422.3295 20870.459
1200 300 -7254.9538 0 -7224.4872 -2924.6246 20990.137
1300 300 -7257.9757 0 -7227.5091 -4069.1414 21123.248
1400 300 -7265.0693 0 -7234.6027 -6549.1146 21249.033
1500 305.40659 -7268.4 0 -7237.3844 -9980.0284 21360.162
1600 307.73328 -7272.8967 0 -7241.6447 -12845.156 21479.84
1700 308.89481 -7272.8308 0 -7241.4609 -14742.73 21599.518
1800 301.22537 -7272.7599 0 -7242.1688 -15363.965 21736.293
1900 294.08915 -7269.2219 0 -7239.3555 -17918.885 21854.75
2000 300 -7267.3723 0 -7236.9057 -22110.158 21970.765
2100 303.71749 -7266.6269 0 -7235.7828 -24452.593 22103.876
2200 305.09813 -7260.5568 0 -7229.5724 -22990.432 22219.89
2300 302.38637 -7258.8153 0 -7228.1063 -21646.154 22335.905
2400 305.66165 -7262.3039 0 -7231.2623 -21131.332 22458.025
2500 298.90421 -7257.9905 0 -7227.6352 -21269.206 22592.358
2600 300.16888 -7256.8469 0 -7226.3631 -23698.687 22699.824
2700 296.33302 -7251.3734 0 -7221.2792 -26655.74 22826.829
2800 296.22091 -7248.3427 0 -7218.2599 -30008.453 22947.728
2900 301.32756 -7250.3222 0 -7219.7207 -28370.97 23080.84
3000 300 -7252.9148 0 -7222.4482 -28938.171 23201.739
Loop time of 6.9145 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 4.49671 (65.033)
Neigh time (%) = 0.231831 (3.35283)
Comm time (%) = 0.760524 (10.999)
Outpt time (%) = 0.882937 (12.7693)
Other time (%) = 0.5425 (7.84583)
Nlocal: 427 ave 441 max 415 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 784 ave 845 max 718 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 9597.25 ave 10151 max 9269 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 38389
Ave neighs/atom = 22.476
Neighbor list builds = 211
Dangerous builds = 0

160
examples/shear/log.shear.void.12Feb07.linux.1
View File

@ -1,160 +0,0 @@
LAMMPS (12 Feb 2007)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1
Created 1912 atoms
pair_style eam
pair_coeff * * niu3.eam
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set lower atom 2
264 settings made
set upper atom 3
264 settings made
# void
region void cylinder z 8 3.535534 2.5 INF INF
delete_atoms region void
Deleted 204 atoms, new total = 1708
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
timestep 0.001
run 100
Memory usage per processor = 1.91124 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346
25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346
50 300 -7292.2273 0 -7246.508 7558.4629 19680.84
75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503
100 300 -7297.4174 0 -7251.698 1627.881 19767.928
Loop time of 1.075 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 1.00034 (93.0552)
Neigh time (%) = 0.032266 (3.00149)
Comm time (%) = 0.011465 (1.06651)
Outpt time (%) = 0.001237 (0.11507)
Other time (%) = 0.029688 (2.76168)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1898 ave 1898 max 1898 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39444 ave 39444 max 39444 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39444
Ave neighs/atom = 23.0937
Neighbor list builds = 4
Dangerous builds = 0
# shear
velocity upper set 1.0 0 0
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
unfix 3
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new2d
dump 1 all atom 10 dump.shear
thermo 100
thermo_modify temp new2d
reset_timestep 0
run 3000
Memory usage per processor = 1.97639 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
100 300 -7311.9184 0 -7281.4518 -5944.573 19791.679
200 298.46333 -7306.5409 0 -7276.2304 -6669.0732 19903.341
300 298.05646 -7303.4774 0 -7273.2081 -10334.9 20033.654
400 297.71277 -7298.5998 0 -7268.3655 -7644.8753 20112.791
500 300 -7301.3145 0 -7270.8479 -6327.722 20143.842
600 306.29328 -7291.192 0 -7260.0863 -1482.3063 20281.66
700 308.44794 -7289.4349 0 -7258.1103 -3026.5046 20394.034
800 300 -7282.5733 0 -7252.1067 -3555.2034 20513.867
900 300 -7273.9966 0 -7243.53 -1850.9526 20622.554
1000 300 -7266.6095 0 -7236.1429 -1119.6046 20741.011
1100 301.26482 -7261.9024 0 -7231.3073 -1647.8612 20874.123
1200 299.17066 -7259.2281 0 -7228.8457 -1938.4437 20998.686
1300 300 -7263.9553 0 -7233.4887 -3376.9235 21112.258
1400 300 -7270.1139 0 -7239.6473 -5846.3511 21249.033
1500 307.98903 -7273.6991 0 -7242.4211 -6121.5944 21366.268
1600 300 -7278.9972 0 -7248.5306 -9389.2139 21484.725
1700 300 -7279.8403 0 -7249.3737 -14440.631 21615.394
1800 309.55921 -7284.1875 0 -7252.7501 -14795.954 21727.745
1900 299.29406 -7282.5749 0 -7252.18 -15392.232 21848.644
2000 299.964 -7271.7156 0 -7241.2526 -19451.05 21968.322
2100 308.54552 -7272.2334 0 -7240.8989 -23685.178 22100.212
2200 308.49102 -7271.1314 0 -7239.8025 -20630.136 22219.89
2300 290.31543 -7268.9828 0 -7239.4997 -19028.307 22342.011
2400 299.15433 -7259.7686 0 -7229.3878 -14272.769 22459.246
2500 299.15088 -7260.7963 0 -7230.4159 -14923.448 22576.482
2600 301.27999 -7258.5805 0 -7227.9839 -15706.203 22702.266
2700 307.83121 -7254.9828 0 -7223.7209 -19761.07 22830.493
2800 300 -7254.6086 0 -7224.142 -23849.892 22944.065
2900 303.23126 -7256.0886 0 -7225.2938 -23451.705 23080.84
3000 290.86402 -7255.5292 0 -7225.9904 -20678.136 23202.96
Loop time of 35.8098 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 30.3044 (84.6259)
Neigh time (%) = 1.63803 (4.57426)
Comm time (%) = 0.359993 (1.00529)
Outpt time (%) = 2.61713 (7.30842)
Other time (%) = 0.890292 (2.48617)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1882 ave 1882 max 1882 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38801 ave 38801 max 38801 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38801
Ave neighs/atom = 22.7172
Neighbor list builds = 205
Dangerous builds = 0