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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13470 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2015-05-15 19:27:25 +00:00
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commit 723da5079a
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187
examples/balance/log.balance.8Aug14.linux.1
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LAMMPS (6 Aug 2014)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp2.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Memory usage per processor = 2.47688 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -29.143179 -1.2407285 1 1
100 26.269576 -29.713313 7.9052334 1 1
200 26.368336 -29.809962 1.6412462 1 1
300 26.479082 -29.920083 2.3678653 1 1
400 26.522239 -29.965537 6.6787858 1 1
500 25.725591 -29.168034 0.67065285 1 1
600 26.247693 -29.692706 7.9887712 1 1
700 26.237368 -29.676926 1.5987214 1 1
800 25.889643 -29.431589 4.6160859 1 1
900 23.635295 -27.372963 9.029962 1 1
1000 22.571904 -25.87422 1.8936085 1 1
1100 17.493795 -21.447274 9.502619 1 1
1200 17.21446 -20.726965 6.3578919 1 1
1300 16.424349 -19.757477 3.9025111 1 1
1400 15.069397 -18.150758 1.7722934 1 1
1500 13.672356 -16.747025 1.6933566 1 1
1600 13.650116 -16.619621 1.8108274 1 1
1700 13.303273 -16.289865 2.1173395 1 1
1800 13.189157 -16.433469 2.3341581 1 1
1900 12.309945 -15.352036 1.8704209 1 1
2000 11.886083 -14.775509 1.1824078 1 1
2100 11.931751 -14.808576 1.4443891 1 1
2200 11.566481 -14.45758 1.6046615 1 1
2300 11.293867 -14.167575 1.2369896 1 1
2400 10.997115 -13.899448 1.2521445 1 1
2500 11.255796 -14.117915 1.2188878 1 1
2600 11.028483 -13.88919 1.5657507 1 1
2700 10.679604 -13.525615 1.3779438 1 1
2800 10.72712 -13.542346 1.3504776 1 1
2900 10.29658 -13.156005 1.106932 1 1
3000 10.507712 -13.322982 1.3247311 1 1
3100 10.122267 -12.967566 1.3119197 1 1
3200 10.229511 -13.117959 0.43205276 1 1
3300 10.060076 -12.888659 1.1560338 1 1
3400 9.7649382 -12.542068 0.92370961 1 1
3500 9.8964272 -12.682043 1.525181 1 1
3600 9.7979319 -12.560807 0.98538633 1 1
3700 9.70963 -12.495541 1.278903 1 1
3800 9.4498147 -12.222316 0.80075307 1 1
3900 9.4211837 -12.172137 1.0971798 1 1
4000 8.8503109 -11.608159 0.87029428 1 1
4100 8.6085875 -11.361707 1.3911713 1 1
4200 8.8902325 -11.630052 0.60327358 1 1
4300 8.4879323 -11.22464 1.2824462 1 1
4400 8.6186419 -11.343483 1.3623783 1 1
4500 8.4155172 -11.147487 0.95317261 1 1
4600 8.1545708 -10.858704 1.0953677 1 1
4700 8.1231214 -10.842342 1.1942102 1 1
4800 8.2260678 -10.954377 1.342099 1 1
4900 8.2952311 -11.024799 0.4455958 1 1
5000 8.0072889 -10.712778 0.71127126 1 1
5100 8.2219617 -10.915043 0.51559239 1 1
5200 7.7151473 -10.395064 1.0283055 1 1
5300 8.1825451 -10.865184 0.67096093 1 1
5400 7.9544966 -10.661831 0.71374926 1 1
5500 7.7101446 -10.395936 0.581946 1 1
5600 7.761341 -10.437733 0.66069516 1 1
5700 7.4740146 -10.124135 0.38720649 1 1
5800 7.4570464 -10.115214 0.76129075 1 1
5900 7.3194274 -9.9539434 0.62089731 1 1
6000 7.1529547 -9.9290591 0.72896317 1 1
6100 7.1283343 -9.791939 0.95687845 1 1
6200 7.4898886 -10.146467 0.21325379 1 1
6300 7.2100631 -9.8724448 0.81042212 1 1
6400 7.4530862 -10.103134 1.0443809 1 1
6500 7.0277811 -9.7063095 0.53556968 1 1
6600 7.1351634 -9.7994029 0.59850387 1 1
6700 7.0807165 -9.7179253 0.66643244 1 1
6800 6.8030877 -9.4712346 0.71547342 1 1
6900 7.0802569 -9.7346339 0.94027512 1 1
7000 7.2685023 -9.9258628 0.75699214 1 1
7100 7.132778 -9.7783121 0.57020576 1 1
7200 7.2325949 -9.8676608 0.42864948 1 1
7300 6.5677747 -9.2069508 0.4103209 1 1
7400 6.3548561 -9.0547336 0.45032884 1 1
7500 6.128051 -8.7180622 0.64151203 1 1
7600 6.50016 -9.0811666 0.60133349 1 1
7700 6.0862975 -8.6987945 0.90642662 1 1
7800 6.3102869 -8.9711312 0.49774937 1 1
7900 6.1864165 -8.7613287 0.80802361 1 1
8000 6.6159172 -9.2234603 0.75356041 1 1
8100 6.1988657 -8.8198487 1.2278013 1 1
8200 6.1999331 -8.7862435 0.38534909 1 1
8300 6.2322998 -8.8436377 0.67014742 1 1
8400 6.1398653 -8.7593363 0.50274405 1 1
8500 6.1016023 -8.6715455 0.48702156 1 1
8600 6.4623092 -9.0350879 1.1011124 1 1
8700 6.0495086 -8.620864 0.65510547 1 1
8800 6.3392655 -8.9135394 1.0279663 1 1
8900 6.2402245 -8.8039625 0.7529844 1 1
9000 6.1724079 -8.7362978 0.6190889 1 1
9100 5.9957105 -8.5921763 0.62658049 1 1
9200 6.1167415 -8.6695353 0.58604088 1 1
9300 6.1121824 -8.6694028 0.31879369 1 1
9400 6.2418468 -8.8086573 0.40396444 1 1
9500 6.5424895 -9.1451132 0.41864492 1 1
9600 5.8643961 -8.4388693 0.41628547 1 1
9700 6.074328 -8.670679 0.87230053 1 1
9800 5.8804295 -8.4395272 0.29416346 1 1
9900 6.4058053 -8.9768534 0.56448884 1 1
10000 5.9230309 -8.5277755 0.47271113 1 1
Loop time of 0.678693 on 1 procs for 10000 steps with 361 atoms
Pair time (%) = 0.295739 (43.5748)
Neigh time (%) = 0.245823 (36.22)
Comm time (%) = 0.00546813 (0.805685)
Outpt time (%) = 0.00218081 (0.321326)
Other time (%) = 0.129482 (19.0781)
Nlocal: 361 ave 361 max 361 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: 1154 ave 1154 max 1154 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1154
Ave neighs/atom = 3.19668
Neighbor list builds = 3617
Dangerous builds = 0

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LAMMPS (6 Aug 2014)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp2.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Memory usage per processor = 2.48839 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
1200 17.214459 -20.726966 6.3578912 1.0304709 1.0193906
1300 16.423958 -19.757225 3.9029256 1.1191136 1.0083102
1400 15.012852 -18.098102 1.7597439 1.0858726 1.0193906
1500 13.461764 -16.535123 1.4686056 1.0526316 1.0083102
1600 13.106004 -16.085302 1.8546143 1.0637119 1.0193906
1700 12.80425 -15.830311 2.2764849 1.0858726 1.0193906
1800 12.82407 -15.994641 1.8366224 1.0637119 1.0083102
1900 12.454854 -15.451 2.2749834 1.0637119 1.0083102
2000 12.540647 -15.443095 1.4020632 1.1191136 1.0193906
2100 12.361566 -15.280286 1.7129448 1.0747922 1.0193906
2200 11.824241 -14.796257 1.2138522 1.0415512 1.0083102
2300 11.877741 -14.718012 1.1220571 1.0193906 1.0083102
2400 11.823064 -14.661316 1.2173135 1.0193906 1.0193906
2500 11.31359 -14.142933 0.92120181 1.0858726 1.0083102
2600 11.136944 -13.863395 1.4010729 1.0304709 1.0083102
2700 11.485612 -14.156728 1.8796242 1.0304709 1.0083102
2800 10.802563 -13.545877 1.0103447 1.0193906 1.0083102
2900 10.49187 -13.191367 1.0883248 1.0193906 1.0083102
3000 10.726784 -13.439454 0.99457845 1.0304709 1.0083102
3100 10.833 -13.520035 1.0345491 1.0304709 1.0083102
3200 10.052065 -12.706149 1.2016906 1.0193906 1.0193906
3300 9.9376633 -12.553477 0.91315033 1.0304709 1.0193906
3400 9.5316521 -12.154267 0.9791642 1.0637119 1.0193906
3500 9.6314158 -12.185882 1.1997938 1.0747922 1.0193906
3600 9.2487441 -11.909318 0.93771128 1.0083102 1.0083102
3700 9.4444972 -12.140835 1.6232294 1.0193906 1.0083102
3800 9.353692 -11.920917 1.1822596 1.0304709 1.0193906
3900 9.2687352 -11.794137 0.6481396 1.0083102 1.0193906
4000 8.8475074 -11.393835 1.0247994 1.0637119 1.0083102
4100 9.1567354 -11.736016 1.2010452 1.0415512 1.0193906
4200 9.0194676 -11.573828 0.99535374 1.0526316 1.0083102
4300 8.8654567 -11.374826 0.85581635 1.0637119 1.0083102
4400 8.9511371 -11.522595 1.4445704 1.0415512 1.0083102
4500 8.3982268 -10.946911 0.67323953 1.0083102 1.0304709
4600 8.2170717 -10.7658 1.1416655 1.0304709 1.0193906
4700 8.8697214 -11.436313 1.1707753 1.0193906 1.0304709
4800 8.1095786 -10.63002 0.79286006 1.0304709 1.0193906
4900 7.9904032 -10.531516 1.2415325 1.0415512 1.0193906
5000 7.9563031 -10.474368 0.84032799 1.0193906 1.0083102
5100 7.8068812 -10.312667 0.97823478 1.1080332 1.0083102
5200 7.7388524 -10.230302 0.86534263 1.0415512 1.0083102
5300 7.5873452 -10.069396 0.99794051 1.0193906 1.0193906
5400 7.4358784 -9.9527014 0.56681844 1.0193906 1.0193906
5500 7.6351531 -10.16306 1.0215393 1.0193906 1.0193906
5600 7.5825632 -10.05578 0.0049597643 1.0747922 1.0083102
5700 7.4323696 -9.9296172 0.90262084 1.0415512 1.0083102
5800 7.3768195 -9.8640836 0.89878667 1.0526316 1.0083102
5900 7.5820041 -10.079465 0.89180801 1.0193906 1.0083102
6000 7.4984197 -9.9924314 1.3133848 1.0193906 1.0193906
6100 7.3538317 -9.8293516 0.61568908 1.0637119 1.0193906
6200 7.3956295 -9.879711 0.62701845 1.0083102 1.0193906
6300 7.5633073 -10.078339 0.83045361 1.0193906 1.0083102
6400 7.3924497 -9.8926214 0.83522981 1.0193906 1.0193906
6500 7.2630044 -9.7462226 0.82707877 1.0193906 1.0193906
6600 6.9637334 -9.4331344 0.79695817 1.0083102 1.0304709
6700 7.5364035 -10.035962 1.0313301 1.0193906 1.0193906
6800 7.1697754 -9.6443644 0.77560827 1.0193906 1.0193906
6900 7.0817457 -9.5627768 0.59893367 1.0526316 1.0083102
7000 6.962387 -9.434433 1.2062381 1.0193906 1.0083102
7100 7.2023907 -9.6906297 0.83672978 1.0193906 1.0083102
7200 7.0461626 -9.4944171 0.6740122 1.0304709 1.0083102
7300 7.252873 -9.7303632 1.0041373 1.0304709 1.0083102
7400 7.2817417 -9.7561883 0.54218799 1.0415512 1.0193906
7500 6.6874861 -9.1404021 0.9183405 1.0304709 1.0083102
7600 6.6881245 -9.1193275 0.70662744 1.0304709 1.0083102
7700 6.9387188 -9.3970952 0.67733499 1.0858726 1.0083102
7800 7.0104929 -9.4610166 0.93166644 1.0304709 1.0083102
7900 6.6379242 -9.0893551 0.64667101 1.0193906 1.0193906
8000 6.9831552 -9.44932 0.71823009 1.0304709 1.0083102
8100 6.7012088 -9.1404387 0.86249147 1.0415512 1.0083102
8200 6.8978584 -9.3575624 0.95208711 1.0193906 1.0083102
8300 6.942591 -9.4024015 1.093981 1.0083102 1.0083102
8400 6.6912062 -9.1548196 1.0664527 1.0304709 1.0083102
8500 6.8077391 -9.2488414 0.74303224 1.0526316 1.0193906
8600 6.7284715 -9.1530205 0.70099217 1.0304709 1.0193906
8700 6.7785633 -9.2329029 0.48827807 1.0193906 1.0083102
8800 6.6847397 -9.1338456 1.0121617 1.0637119 1.0083102
8900 6.7361401 -9.1871678 0.70823435 1.0193906 1.0083102
9000 6.6911248 -9.1397795 0.29822566 1.0304709 1.0193906
9100 6.4638324 -8.9014907 0.44788652 1.0415512 1.0193906
9200 6.6981866 -9.1988691 0.48356831 1.0415512 1.0193906
9300 6.3422849 -8.810212 0.61804669 1.0083102 1.0193906
9400 6.8761132 -9.3580644 0.65062175 1.0304709 1.0193906
9500 6.6819303 -9.1457164 0.59522216 1.0304709 1.0083102
9600 6.2744415 -8.7028417 0.55830174 1.0193906 1.0193906
9700 6.7103177 -9.1467044 0.32461574 1.0415512 1.0193906
9800 6.7992083 -9.2562723 1.0772631 1.0193906 1.0083102
9900 6.4176977 -8.8245968 0.78396354 1.0193906 1.0304709
10000 6.4572759 -8.8911667 0.68051121 1.0083102 1.0083102
Loop time of 0.348356 on 4 procs for 10000 steps with 361 atoms
Pair time (%) = 0.0763658 (21.9218)
Neigh time (%) = 0.066243 (19.0159)
Comm time (%) = 0.111105 (31.8942)
Outpt time (%) = 0.00226367 (0.649815)
Other time (%) = 0.0923778 (26.5182)
Nlocal: 90.25 ave 91 max 90 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 31.75 ave 36 max 29 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 271.25 ave 429 max 148 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 1085
Ave neighs/atom = 3.00554
Neighbor list builds = 3679
Dangerous builds = 0

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LAMMPS (20 Jan 2015)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds all all 1 1.0 1.5
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 5.0
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Memory usage per processor = 4.44159 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -2.2032569 3.1039469 1 1
100 27.623422 -6.228166 2.6542136 1 1
200 33.35302 -15.746749 3.2018248 1 1
300 39.17734 -24.1557 4.9116986 1 1
400 41.660701 -27.615203 8.6214672 1 1
500 37.155021 -24.097062 3.2656511 1 1
600 35.073269 -21.540753 2.3563146 1 1
700 36.834048 -22.263806 3.9446575 1 1
800 38.779544 -24.439636 5.2926515 1 1
900 37.764544 -24.918222 4.1067761 1 1
1000 39.214315 -25.607167 5.7436264 1 1
1100 34.711773 -22.939107 3.8075193 1 1
1200 32.350981 -21.801614 5.4992314 1 1
1300 31.087697 -19.400319 7.0568771 1 1
1400 30.305238 -17.852561 5.272329 1 1
1500 26.876554 -15.614136 1.7313695 1 1
1600 25.520319 -14.820378 1.1610394 1 1
1700 25.583866 -13.603046 1.1045813 1 1
1800 25.475452 -13.121538 2.0386901 1 1
1900 25.53171 -12.007373 2.1202605 1 1
2000 25.959412 -13.074754 1.8072299 1 1
2100 28.127374 -14.657159 1.2365137 1 1
2200 26.811943 -12.963554 2.0979841 1 1
2300 25.754468 -12.882263 1.9859074 1 1
2400 26.397386 -13.50675 1.8439925 1 1
2500 26.226779 -13.176545 2.0562487 1 1
2600 26.36113 -13.830312 2.7656768 1 1
2700 26.091842 -14.507808 3.5103247 1 1
2800 25.859086 -14.020446 1.774521 1 1
2900 21.897888 -13.158283 0.48699163 1 1
3000 20.406116 -11.204565 -0.5964511 1 1
3100 20.858327 -10.337012 0.11898702 1 1
3200 21.516837 -10.333517 0.2641953 1 1
3300 23.07237 -11.291785 1.2081954 1 1
3400 25.392241 -13.247098 0.7030958 1 1
3500 25.819429 -12.675177 2.033555 1 1
3600 25.037231 -12.366459 2.0793386 1 1
3700 23.944539 -11.027573 0.57647796 1 1
3800 22.676166 -10.405731 0.23488488 1 1
3900 21.075382 -9.4705914 0.032027373 1 1
4000 23.816723 -11.168738 0.7446704 1 1
4100 24.557566 -11.359442 1.4192388 1 1
4200 23.474589 -11.38847 1.2289527 1 1
4300 21.936191 -11.309198 -0.81923475 1 1
4400 21.802163 -10.399593 -0.298252 1 1
4500 22.192284 -10.539866 0.38230469 1 1
4600 23.651684 -10.740589 1.4685321 1 1
4700 23.1095 -11.95823 0.43469901 1 1
4800 22.671084 -11.201971 0.5766232 1 1
4900 22.115308 -11.036275 0.30521409 1 1
5000 21.965557 -10.441122 -0.59235266 1 1
5100 23.249361 -11.187019 0.33204798 1 1
5200 22.951101 -11.280229 0.29317484 1 1
5300 22.536559 -10.274024 0.57603522 1 1
5400 23.081711 -10.926673 -0.7206378 1 1
5500 24.110978 -12.081003 -0.49696138 1 1
5600 24.60867 -11.808475 1.9153035 1 1
5700 24.91524 -13.572414 0.23887774 1 1
5800 23.596848 -12.042942 0.53692521 1 1
5900 22.723517 -11.302192 1.1883397 1 1
6000 22.65384 -10.775043 1.008983 1 1
6100 22.795472 -10.948454 -0.11394295 1 1
6200 21.805601 -11.073296 -0.37848264 1 1
6300 23.531974 -12.3398 -0.31023717 1 1
6400 23.788692 -12.00087 1.0778684 1 1
6500 23.09771 -11.451539 0.58575792 1 1
6600 22.532906 -11.202202 -0.43541813 1 1
6700 23.154697 -10.329622 0.2217121 1 1
6800 22.523842 -9.8783418 0.14986428 1 1
6900 23.122939 -10.663183 -0.039039378 1 1
7000 24.608416 -10.970679 0.74360604 1 1
7100 24.166564 -11.487147 0.64387099 1 1
7200 23.686058 -10.715896 1.2925085 1 1
7300 21.736425 -10.352004 1.0764821 1 1
7400 21.756938 -10.074508 1.0701387 1 1
7500 22.323591 -11.203855 -0.36457356 1 1
7600 22.730259 -10.662609 0.73122128 1 1
7700 23.202667 -11.659299 0.7119523 1 1
7800 23.471274 -11.74546 0.84848437 1 1
7900 23.949693 -11.305441 1.1163795 1 1
8000 22.47431 -10.130036 -0.066154223 1 1
8100 21.305517 -9.523347 0.21062991 1 1
8200 22.14769 -10.939055 -0.33086967 1 1
8300 22.581082 -10.60462 0.56817072 1 1
8400 21.856655 -9.8759247 0.60046875 1 1
8500 22.971535 -10.126406 0.46814301 1 1
8600 21.888692 -10.223103 0.29953654 1 1
8700 21.93789 -9.7821619 0.51904139 1 1
8800 23.068366 -9.4753396 1.3557868 1 1
8900 21.011634 -9.5857411 -0.13494832 1 1
9000 23.266565 -10.310167 0.096937028 1 1
9100 24.112118 -11.204616 0.20521367 1 1
9200 24.11651 -11.994971 0.060396253 1 1
9300 22.453882 -11.015744 -0.33537139 1 1
9400 21.910618 -9.319849 0.74015472 1 1
9500 22.605739 -9.7058087 -0.054051974 1 1
9600 22.758713 -9.2000096 1.1199546 1 1
9700 22.547301 -11.348949 -0.84949978 1 1
9800 22.247969 -9.6757072 1.0696272 1 1
9900 22.906215 -11.062401 -0.54889231 1 1
10000 22.67397 -10.692979 0.57023228 1 1
Loop time of 1.70238 on 1 procs for 10000 steps with 361 atoms
Pair time (%) = 0.492921 (28.9548)
Bond time (%) = 0.2415 (14.1861)
Neigh time (%) = 0.832589 (48.9074)
Comm time (%) = 0.0141609 (0.831829)
Outpt time (%) = 0.00105119 (0.0617482)
Other time (%) = 0.120155 (7.05806)
Nlocal: 361 ave 361 max 361 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: 2706 ave 2706 max 2706 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2706
Ave neighs/atom = 7.49584
Ave special neighs/atom = 5.61773
Neighbor list builds = 4877
Dangerous builds = 0

203
examples/balance/log.balance.bond.fast.21Jan15.linux.4
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@ -1,203 +0,0 @@
LAMMPS (20 Jan 2015)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds all all 1 1.0 1.5
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 5.0
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Memory usage per processor = 4.49417 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
400 41.660701 -27.615203 8.6214674 1.3518006 1.0083102
500 37.155014 -24.097047 3.2656265 1.3296399 1.0193906
600 35.067719 -21.53529 2.3617122 1.3296399 1.0083102
700 36.797606 -22.272819 4.1085032 1.3739612 1.0083102
800 38.930342 -24.864401 4.7625466 1.3296399 1.0083102
900 38.730963 -25.045492 3.5573709 1.3961219 1.0193906
1000 38.984871 -26.014244 5.5553204 1.3074792 1.0083102
1100 35.866405 -24.460824 4.4136958 1.1745152 1.0304709
1200 31.856499 -21.327208 4.8683292 1.2299169 1.0083102
1300 30.644325 -20.323116 7.9280951 1.1412742 1.0193906
1400 31.741624 -21.112623 4.3143446 1.0969529 1.0083102
1500 27.833154 -16.776664 1.2660178 1.1301939 1.0193906
1600 26.34891 -15.593189 0.058681042 1.1191136 1.0193906
1700 24.885178 -14.001838 1.3274486 1.1080332 1.0193906
1800 26.427047 -14.569617 0.72975905 1.1301939 1.0304709
1900 25.381784 -13.64581 0.81944943 1.1301939 1.0193906
2000 25.723386 -13.333268 1.4334528 1.1301939 1.0193906
2100 26.606752 -13.0949 1.2989863 1.1634349 1.0083102
2200 26.509512 -13.387688 1.1167579 1.1523546 1.0193906
2300 25.639992 -13.179846 2.2501322 1.1745152 1.0083102
2400 26.150503 -13.491713 0.76868673 1.2188366 1.0083102
2500 25.972499 -12.063864 0.34516973 1.1412742 1.0083102
2600 25.486036 -12.940458 0.76199757 1.1412742 1.0193906
2700 26.230132 -13.652341 1.7338723 1.1745152 1.0304709
2800 25.772724 -14.463605 2.8585269 1.0969529 1.0083102
2900 25.103016 -13.919596 2.2930476 1.0083102 1.0193906
3000 24.01254 -12.717424 0.47774495 1.0304709 1.0193906
3100 20.736549 -10.890076 -0.98873052 1.1191136 1.0193906
3200 19.941553 -10.018251 -0.99096631 1.0969529 1.0083102
3300 21.873239 -10.239556 -0.3143815 1.0747922 1.0193906
3400 22.862231 -9.8339225 0.26144526 1.0858726 1.0083102
3500 25.147981 -10.880207 1.4798766 1.1080332 1.0193906
3600 25.180896 -11.622133 0.77173223 1.0747922 1.0083102
3700 23.556788 -11.299634 0.55954881 1.0858726 1.0083102
3800 22.493407 -10.659886 0.11815461 1.0747922 1.0083102
3900 21.039439 -10.814837 -1.1505917 1.0969529 1.0083102
4000 21.595234 -9.5907841 -0.18492957 1.0526316 1.0083102
4100 22.241581 -10.021155 -0.45382989 1.0526316 1.0193906
4200 22.580958 -9.424629 1.2640842 1.0858726 1.0083102
4300 23.254321 -10.231677 1.4385745 1.0747922 1.0083102
4400 22.155518 -10.378937 -0.25935415 1.0858726 1.0083102
4500 21.786702 -9.9697581 -0.38862549 1.1634349 1.0193906
4600 21.483407 -9.8450983 0.1027055 1.0858726 1.0083102
4700 22.049222 -10.118926 0.042422718 1.0747922 1.0083102
4800 22.278153 -10.189539 -0.16842442 1.1191136 1.0193906
4900 23.783566 -10.754126 0.25570457 1.0637119 1.0193906
5000 22.996999 -10.035746 2.0164077 1.0526316 1.0083102
5100 22.291983 -10.132069 -0.59577654 1.0858726 1.0083102
5200 21.988363 -9.4430094 0.59736801 1.1191136 1.0193906
5300 20.725686 -9.6416497 -0.23784458 1.0969529 1.0083102
5400 23.294636 -9.85156 0.86168288 1.0747922 1.0083102
5500 22.426116 -10.090518 0.43379868 1.0526316 1.0193906
5600 24.100731 -10.615051 0.21676601 1.1080332 1.0083102
5700 22.767374 -10.461632 0.50164522 1.0858726 1.0193906
5800 21.665039 -9.4705485 0.10158023 1.1080332 1.0193906
5900 23.754335 -9.8103385 0.82641206 1.0637119 1.0083102
6000 23.764263 -10.822225 0.0086706095 1.0637119 1.0193906
6100 23.061093 -10.66149 0.64615841 1.0858726 1.0193906
6200 23.231721 -11.326359 0.97854607 1.0526316 1.0193906
6300 22.063301 -10.866822 0.57761463 1.0304709 1.0083102
6400 21.893824 -9.9403304 1.3271195 1.0304709 1.0083102
6500 21.819506 -10.378298 -0.13622266 1.0858726 1.0083102
6600 23.585267 -10.859164 1.2332959 1.0415512 1.0083102
6700 23.929532 -11.205031 0.14390049 1.0415512 1.0193906
6800 22.94314 -11.233426 0.32383955 1.1301939 1.0083102
6900 23.734174 -10.111417 0.21771857 1.0415512 1.0083102
7000 22.628793 -9.9941906 -0.92631583 1.0747922 1.0083102
7100 21.490557 -8.6579625 -0.07159052 1.0526316 1.0193906
7200 21.927094 -9.528413 -0.3508067 1.0193906 1.0083102
7300 21.943432 -9.9866332 0.3033917 1.0415512 1.0193906
7400 24.43301 -10.32538 1.0510565 1.0415512 1.0193906
7500 23.463108 -10.582478 -0.22352118 1.1191136 1.0193906
7600 21.46269 -9.216786 -0.33836008 1.0747922 1.0083102
7700 21.319723 -9.2120009 -0.59833641 1.1301939 1.0083102
7800 22.097084 -10.093375 -0.87261682 1.0526316 1.0304709
7900 23.186493 -9.8320314 -0.021894508 1.0858726 1.0083102
8000 24.449738 -10.441875 1.3850788 1.1412742 1.0193906
8100 22.766547 -10.411191 0.24146571 1.0747922 1.0083102
8200 21.630901 -9.8179811 -0.53917965 1.0304709 1.0083102
8300 22.453992 -9.1084537 0.57116298 1.0747922 1.0083102
8400 22.199214 -9.4209101 0.070865332 1.1301939 1.0083102
8500 22.198633 -9.4525954 0.34217625 1.1191136 1.0083102
8600 23.984248 -11.161067 0.51361855 1.0637119 1.0083102
8700 24.263363 -11.839759 0.13644863 1.0747922 1.0193906
8800 23.289118 -9.8009851 0.91489484 1.0526316 1.0304709
8900 24.143641 -10.312225 0.081112692 1.0415512 1.0083102
9000 23.111923 -10.40996 -0.47374519 1.0637119 1.0083102
9100 21.863926 -10.475378 0.062392283 1.0747922 1.0193906
9200 23.441607 -10.205203 0.49831793 1.1412742 1.0193906
9300 22.795416 -10.01578 0.099598266 1.0193906 1.0083102
9400 23.540787 -10.811556 0.19109305 1.0747922 1.0193906
9500 22.438597 -10.140651 0.52944782 1.0304709 1.0193906
9600 23.513188 -10.956581 1.474452 1.0969529 1.0083102
9700 22.958673 -11.158105 -0.061358964 1.1523546 1.0193906
9800 22.989978 -10.461202 -0.11504011 1.0637119 1.0083102
9900 22.321529 -9.4743506 -0.46174667 1.0969529 1.0083102
10000 21.559071 -9.3390062 -0.24571278 1.0969529 1.0083102
Loop time of 0.721486 on 4 procs for 10000 steps with 361 atoms
Pair time (%) = 0.133076 (18.4448)
Bond time (%) = 0.0595608 (8.25529)
Neigh time (%) = 0.27641 (38.3112)
Comm time (%) = 0.142561 (19.7593)
Outpt time (%) = 0.0016793 (0.232756)
Other time (%) = 0.108199 (14.9967)
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 121.5 ave 131 max 107 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 602.75 ave 680 max 538 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 2411
Ave neighs/atom = 6.67867
Ave special neighs/atom = 5.61773
Neighbor list builds = 4865
Dangerous builds = 0

502
examples/balance/log.balance.bond.slow.21Jan15.linux.1
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@ -1,502 +0,0 @@
LAMMPS (20 Jan 2015)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds all all 1 1.0 1.5
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Memory usage per processor = 6.31529 Mbytes
Step Temp E_pair Press 10[3] 10
0 0.57437856 0 0.26099453 1 1
100 0.29756515 0 0.10149401 1 1
200 0.35394813 0 0.075159099 1 1
300 0.39245849 0 0.033002384 1 1
400 0.34078347 0 -0.020825841 1 1
500 0.35201095 0 -0.062637506 1 1
600 0.34014717 0 -0.11122965 1 1
700 0.3323524 0 -0.11598015 1 1
800 0.35116047 0 -0.096162395 1 1
900 0.35695352 0 -0.01385176 1 1
1000 0.36986539 0 0.056772858 1 1
1100 0.34584644 0 0.084941323 1 1
1200 0.31921435 0 0.10545078 1 1
1300 0.32952819 0 0.124902 1 1
1400 0.34497365 0 0.12662081 1 1
1500 0.33429243 0 0.096230972 1 1
1600 0.33765387 0 0.025800542 1 1
1700 0.35134464 0 -0.04422593 1 1
1800 0.35003859 0 -0.096745576 1 1
1900 0.33839618 0 -0.095465943 1 1
2000 0.33732078 0 -0.094652802 1 1
2100 0.34552238 0 -0.076729261 1 1
2200 0.34893142 0 -0.036853228 1 1
2300 0.35379341 0 0.021124847 1 1
2400 0.34829744 0 0.09230184 1 1
2500 0.33038141 0 0.1399855 1 1
2600 0.30983019 0 0.12754742 1 1
2700 0.32992561 0 0.10485138 1 1
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3800 0.30891825 0 0.10605673 1 1
3900 0.33847951 0 0.13956139 1 1
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4800 0.35198515 0 -0.020901044 1 1
4900 0.35187284 0 0.043645941 1 1
5000 0.34887336 0 0.095698609 1 1
5100 0.30308163 0 0.11649328 1 1
5200 0.32401285 0 0.12072411 1 1
5300 0.33025072 0 0.10933161 1 1
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5800 0.30939887 0 -0.12356656 1 1
5900 0.32315628 0 -0.11338676 1 1
6000 0.34117485 0 -0.066198961 1 1
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6200 0.35130653 0 0.027660468 1 1
6300 0.35398766 0 0.087221238 1 1
6400 0.30963379 0 0.11990957 1 1
6500 0.3174541 0 0.14103528 1 1
6600 0.31989791 0 0.11575506 1 1
6700 0.33811477 0 0.060747353 1 1
6800 0.3424043 0 0.010357152 1 1
6900 0.34804319 0 -0.042621786 1 1
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7700 0.33093497 0 0.11924405 1 1
7800 0.31435814 0 0.12701724 1 1
7900 0.33132217 0 0.10793075 1 1
8000 0.33451798 0 0.077993125 1 1
8100 0.35188371 0 0.019929977 1 1
8200 0.33645742 0 -0.039302079 1 1
8300 0.3415632 0 -0.098067982 1 1
8400 0.30619282 0 -0.12952879 1 1
8500 0.34446484 0 -0.098084709 1 1
8600 0.33761673 0 -0.07069818 1 1
8700 0.34495452 0 -0.022458056 1 1
8800 0.33502983 0 0.027742411 1 1
8900 0.35418591 0 0.092390134 1 1
9000 0.31648387 0 0.12467398 1 1
9100 0.33994825 0 0.14460327 1 1
9200 0.33822571 0 0.11273284 1 1
9300 0.33260773 0 0.060063671 1 1
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9700 0.32088235 0 -0.12027075 1 1
9800 0.3320823 0 -0.11602794 1 1
9900 0.33916442 0 -0.080281044 1 1
10000 0.34852268 0 -0.01000914 1 1
10100 0.32955942 0 0.04258493 1 1
10200 0.34487898 0 0.086971308 1 1
10300 0.32325593 0 0.11558149 1 1
10400 0.30927871 0 0.12239437 1 1
10500 0.33176799 0 0.12285937 1 1
10600 0.35120027 0 0.084897432 1 1
10700 0.33129697 0 0.0053089279 1 1
10800 0.36028769 0 -0.04280715 1 1
10900 0.35552287 0 -0.084955999 1 1
11000 0.3406024 0 -0.096554577 1 1
11100 0.33041202 0 -0.10703492 1 1
11200 0.32442686 0 -0.084328121 1 1
11300 0.35952468 0 -0.020191965 1 1
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11700 0.33555094 0 0.12738686 1 1
11800 0.3458647 0 0.10963398 1 1
11900 0.33836678 0 0.067253864 1 1
12000 0.34853314 0 0.03201448 1 1
12100 0.34600048 0 -0.034833402 1 1
12200 0.33145631 0 -0.09865675 1 1
12300 0.32848884 0 -0.1248489 1 1
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12500 0.32622305 0 -0.061634993 1 1
12600 0.36213537 0 -0.0090593315 1 1
12700 0.34673866 0 0.036734645 1 1
12800 0.34606618 0 0.086267678 1 1
12900 0.34271431 0 0.12415522 1 1
13000 0.31993287 0 0.13879926 1 1
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13900 0.35209713 0 -0.018851408 1 1
14000 0.35702629 0 0.061046366 1 1
14100 0.33234093 0 0.094086465 1 1
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14600 0.34823843 0 0.024605569 1 1
14700 0.35298973 0 -0.040418888 1 1
14800 0.33679845 0 -0.10067728 1 1
14900 0.32790966 0 -0.10925568 1 1
15000 0.34208495 0 -0.09568004 1 1
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15200 0.35328398 0 -0.020236536 1 1
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15700 0.33681572 0 0.098607746 1 1
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15900 0.34289757 0 0.013849092 1 1
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16700 0.34336905 0 0.077996627 1 1
16800 0.33277414 0 0.11053634 1 1
16900 0.32183338 0 0.11680626 1 1
17000 0.34044352 0 0.10806555 1 1
17100 0.32967873 0 0.067759786 1 1
17200 0.36172278 0 -0.0048631904 1 1
17300 0.35619435 0 -0.04215545 1 1
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17500 0.33193585 0 -0.098831315 1 1
17600 0.3544756 0 -0.085660403 1 1
17700 0.34505209 0 -0.069640515 1 1
17800 0.36291124 0 -0.0063088133 1 1
17900 0.34255705 0 0.046794555 1 1
18000 0.34163238 0 0.11767705 1 1
18100 0.3466445 0 0.1351712 1 1
18200 0.33037668 0 0.12703659 1 1
18300 0.33677404 0 0.10956306 1 1
18400 0.34978954 0 0.087193072 1 1
18500 0.33354363 0 0.051095814 1 1
18600 0.34651729 0 0.0056245561 1 1
18700 0.32622232 0 -0.047319269 1 1
18800 0.32978847 0 -0.054929416 1 1
18900 0.34192451 0 -0.037252471 1 1
19000 0.34061294 0 -0.001167235 1 1
19100 0.34194478 0 0.016945224 1 1
19200 0.33321765 0 0.050665354 1 1
19300 0.33197783 0 0.080470585 1 1
19400 0.33284715 0 0.12423599 1 1
19500 0.33867856 0 0.12689524 1 1
19600 0.36092786 0 0.11417704 1 1
19700 0.34270183 0 0.069038291 1 1
19800 0.34880695 0 0.042483681 1 1
19900 0.33903644 0 0.034788638 1 1
20000 0.32590125 0 0.011383785 1 1
20100 0.30358859 0 0.0030743554 1 1
20200 0.31830224 0 0.017637826 1 1
20300 0.34195438 0 0.072811099 1 1
20400 0.31249563 0 0.10063541 1 1
20500 0.31544938 0 0.1405794 1 1
20600 0.30071644 0 0.12763486 1 1
20700 0.2890265 0 0.1136651 1 1
20800 0.28962296 0 0.094481978 1 1
20900 0.29447212 0 0.0967165 1 1
21000 0.31159961 0 0.067307231 1 1
21100 0.30490648 0 0.017689358 1 1
21200 0.30687262 0 -0.016055512 1 1
21300 0.30083286 0 -0.0014988997 1 1
21400 0.32070426 0 0.015960302 1 1
21500 0.31439311 0 0.038170385 1 1
21600 0.32617832 0 0.043263788 1 1
21700 0.35151793 0 0.066302727 1 1
21800 0.35912885 0 0.070099103 1 1
21900 0.32451958 0 0.068935768 1 1
22000 0.35219298 0 0.067161227 1 1
22100 0.34857705 0 0.032731746 1 1
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22300 0.34766017 0 -0.0027090483 1 1
22400 0.33426062 0 -0.023196063 1 1
22500 0.34174625 0 -0.025019717 1 1
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22700 0.3362653 0 -0.035815733 1 1
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22900 0.33813085 0 0.0077527467 1 1
23000 0.33339981 0 0.028340744 1 1
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23200 0.33074548 0 0.032378405 1 1
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23800 0.31781354 0 -0.012908449 1 1
23900 0.32405513 0 -0.015018071 1 1
24000 0.33549728 0 -0.012812915 1 1
24100 0.31368736 0 -0.020818372 1 1
24200 0.33533836 0 0.0056121057 1 1
24300 0.32530627 0 0.018183931 1 1
24400 0.31930662 0 0.027446878 1 1
24500 0.33540302 0 0.040307455 1 1
24600 0.34020431 0 0.027403921 1 1
24700 0.3291814 0 0.01204865 1 1
24800 0.31552604 0 0.019654111 1 1
24900 0.34727253 0 0.01670543 1 1
25000 0.35120105 0 0.0038617562 1 1
25100 0.32706871 0 -0.021196623 1 1
25200 0.32915282 0 -0.017146508 1 1
25300 0.32577518 0 -0.01312495 1 1
25400 0.33286855 0 0.0014726193 1 1
25500 0.33002601 0 0.0080974022 1 1
25600 0.34127655 0 0.014296091 1 1
25700 0.34048065 0 0.022513032 1 1
25800 0.33029079 0 0.038733531 1 1
25900 0.33031324 0 0.026156982 1 1
26000 0.32967371 0 0.028727383 1 1
26100 0.33775718 0 0.015607478 1 1
26200 0.35097144 0 0.012291703 1 1
26300 0.34303792 0 0.00094823191 1 1
26400 0.33632665 0 -0.0026904889 1 1
26500 0.33580127 0 -0.0074168555 1 1
26600 0.33063188 0 -0.020378601 1 1
26700 0.33581846 0 -0.00084397268 1 1
26800 0.32998532 0 0.015932208 1 1
26900 0.33825444 0 0.010428603 1 1
27000 0.32081518 0 0.019818223 1 1
27100 0.31448098 0 0.020093416 1 1
27200 0.32643684 0 0.021934917 1 1
27300 0.33289466 0 0.023713072 1 1
27400 0.32310744 0 0.024110945 1 1
27500 0.33115619 0 0.0025776713 1 1
27600 0.33295887 0 -0.010710764 1 1
27700 0.32968876 0 -0.0064595905 1 1
27800 0.34064581 0 -0.0086519116 1 1
27900 0.33559187 0 -0.0055753593 1 1
28000 0.32300727 0 -0.0004153384 1 1
28100 0.32147461 0 -0.0058543412 1 1
28200 0.35532383 0 0.013646951 1 1
28300 0.31507942 0 0.026532255 1 1
28400 0.32711006 0 0.033214981 1 1
28500 0.34472462 0 0.028050837 1 1
28600 0.33708059 0 0.019115676 1 1
28700 0.34478087 0 0.023743689 1 1
28800 0.34546686 0 0.0081772997 1 1
28900 0.34004886 0 0.017771865 1 1
29000 0.33604232 0 -0.010505671 1 1
29100 0.33541374 0 -0.016273261 1 1
29200 0.34347489 0 -0.010002306 1 1
29300 0.34083904 0 0.0089701784 1 1
29400 0.34846892 0 0.020765104 1 1
29500 0.3416255 0 0.022650856 1 1
29600 0.33725496 0 0.020693083 1 1
29700 0.34480638 0 0.024317128 1 1
29800 0.31459471 0 0.023097895 1 1
29900 0.33014448 0 0.03114046 1 1
30000 0.33741498 0 0.015624314 1 1
30100 0.32598657 0 -0.0018860541 1 1
30200 0.34855815 0 0.0017983372 1 1
30300 0.33375921 0 0.0010991235 1 1
30400 0.35008944 0 -0.0027316177 1 1
30500 0.33279729 0 -0.0035788551 1 1
30600 0.33868746 0 -0.0016249482 1 1
30700 0.33597034 0 -0.0014524001 1 1
30800 0.3227257 0 0.016353457 1 1
30900 0.32676516 0 0.027396654 1 1
31000 0.34083982 0 0.031606413 1 1
31100 0.32165238 0 0.013583368 1 1
31200 0.3428492 0 0.020486611 1 1
31300 0.32372541 0 0.01215566 1 1
31400 0.32734692 0 0.016229397 1 1
31500 0.33089262 0 0.0060426618 1 1
31600 0.34273493 0 -0.013456537 1 1
31700 0.32723905 0 -0.019243766 1 1
31800 0.33636488 0 0.0027814902 1 1
31900 0.32834805 0 0.00706877 1 1
32000 0.33995148 0 0.0018383309 1 1
32100 0.33412282 0 0.0076455933 1 1
32200 0.34334884 0 0.023586129 1 1
32300 0.32778925 0 0.020564321 1 1
32400 0.33163443 0 0.038878463 1 1
32500 0.32290345 0 0.022247461 1 1
32600 0.34113954 0 0.010966365 1 1
32700 0.33390633 0 0.0037777555 1 1
32800 0.34385341 0 0.010556575 1 1
32900 0.32137047 0 0.00022027143 1 1
33000 0.32079172 0 -0.017261272 1 1
33100 0.33570882 0 -0.0051942206 1 1
33200 0.34320894 0 -0.011515281 1 1
33300 0.32794746 0 -0.0018153673 1 1
33400 0.33060982 0 0.027118146 1 1
33500 0.33641809 0 0.02143035 1 1
33600 0.33643061 0 0.020833068 1 1
33700 0.3485949 0 0.030918751 1 1
33800 0.3283985 0 0.01947613 1 1
33900 0.31959761 0 0.021128147 1 1
34000 0.33897984 0 0.015270986 1 1
34100 0.32392267 0 0.0020130852 1 1
34200 0.33084514 0 -0.024316708 1 1
34300 0.3342259 0 -0.0059047764 1 1
34400 0.33385098 0 0.0063818721 1 1
34500 0.33255603 0 -0.01023837 1 1
34600 0.34766173 0 0.0056703013 1 1
34700 0.339822 0 0.0061648559 1 1
34800 0.33902329 0 0.030037037 1 1
34900 0.3216153 0 0.027996689 1 1
35000 0.32701056 0 0.024778517 1 1
35100 0.3124942 0 0.011316548 1 1
35200 0.34486416 0 0.011670127 1 1
35300 0.33275353 0 0.020491246 1 1
35400 0.33618763 0 0.014678874 1 1
35500 0.32352282 0 -0.018568683 1 1
35600 0.32617903 0 -0.012796912 1 1
35700 0.32378048 0 -0.021318585 1 1
35800 0.3371086 0 -0.0023678632 1 1
35900 0.33818476 0 0.011197742 1 1
36000 0.35142144 0 0.022520935 1 1
36100 0.35147297 0 0.020277852 1 1
36200 0.33489465 0 0.014564878 1 1
36300 0.33841515 0 0.036439962 1 1
36400 0.32301096 0 0.019966746 1 1
36500 0.35612028 0 0.036509556 1 1
36600 0.33841597 0 -0.0042180605 1 1
36700 0.34477654 0 -0.0052770853 1 1
36800 0.33804317 0 -0.013751733 1 1
36900 0.35003816 0 -0.0021184393 1 1
37000 0.32965041 0 -0.020900951 1 1
37100 0.34653095 0 -0.013667977 1 1
37200 0.35019871 0 -0.0071740923 1 1
37300 0.34859745 0 0.02006041 1 1
37400 0.35739859 0 0.020892822 1 1
37500 0.34128859 0 0.041072111 1 1
37600 0.33781905 0 0.023376738 1 1
37700 0.32961874 0 0.030953741 1 1
37800 0.343987 0 0.029579795 1 1
37900 0.33610448 0 0.036836828 1 1
38000 0.32757228 0 0.020902031 1 1
38100 0.32735808 0 0.019544751 1 1
38200 0.35646953 0 0.044607528 1 1
38300 0.32509773 0 0.03610738 1 1
38400 0.32111741 0 0.034474043 1 1
38500 0.30590608 0 0.053461212 1 1
38600 0.32322402 0 0.053453832 1 1
38700 0.33843057 0 0.076264534 1 1
38800 0.31350741 0 0.064733869 1 1
38900 0.31943061 0 0.067836769 1 1
39000 0.33775583 0 0.0788316 1 1
39100 0.34256036 0 0.075874935 1 1
39200 0.33128527 0 0.071610976 1 1
39300 0.34519653 0 0.046257301 1 1
39400 0.34351844 0 0.052422917 1 1
39500 0.35716037 0 0.048916058 1 1
39600 0.34000737 0 0.016149089 1 1
39700 0.34587892 0 0.021619621 1 1
39800 0.34878036 0 0.0092881327 1 1
39900 0.35225411 0 -0.011341599 1 1
40000 0.36309266 0 0.0050869295 1 1
Loop time of 1.97426 on 1 procs for 40000 steps with 361 atoms
Pair time (%) = 0.0380814 (1.9289)
Bond time (%) = 0.963403 (48.7983)
Neigh time (%) = 0.514568 (26.0639)
Comm time (%) = 0.0160263 (0.811762)
Outpt time (%) = 0.00375032 (0.189961)
Other time (%) = 0.438426 (22.2072)
Nlocal: 361 ave 361 max 361 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: 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
Ave special neighs/atom = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0

502
examples/balance/log.balance.bond.slow.21Jan15.linux.4
View File

@ -1,502 +0,0 @@
LAMMPS (20 Jan 2015)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds all all 1 1.0 1.5
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Memory usage per processor = 6.41878 Mbytes
Step Temp E_pair Press 10[3] 10
0 0.57437856 0 0.26099453 3.2354571 1.0526316
100 0.29756515 0 0.10149401 1.0193906 1.0083102
200 0.35394813 0 0.075159099 1.0304709 1.0083102
300 0.39245849 0 0.033002384 1.0304709 1.0193906
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2200 0.34893142 0 -0.036853228 1.0304709 1.0193906
2300 0.35379341 0 0.021124847 1.0304709 1.0304709
2400 0.34829744 0 0.09230184 1.0304709 1.0193906
2500 0.33038141 0 0.1399855 1.0193906 1.0193906
2600 0.30983019 0 0.12754742 1.0193906 1.0083102
2700 0.32992561 0 0.10485138 1.0415512 1.0304709
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3500 0.34257038 0 -0.021612062 1.0304709 1.0083102
3600 0.32838009 0 0.030131228 1.0083102 1.0083102
3700 0.34462142 0 0.074586378 1.0415512 1.0083102
3800 0.30891825 0 0.10605673 1.0304709 1.0083102
3900 0.33847951 0 0.13956139 1.0415512 1.0193906
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4900 0.35187284 0 0.043645941 1.0193906 1.0083102
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5400 0.33288012 0 0.078356448 1.0083102 1.0193906
5500 0.35142492 0 0.036958063 1.0193906 1.0083102
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6300 0.35398766 0 0.087221238 1.0083102 1.0193906
6400 0.30963379 0 0.11990957 1.0193906 1.0083102
6500 0.3174541 0 0.14103528 1.0193906 1.0193906
6600 0.31989791 0 0.11575506 1.0415512 1.0193906
6700 0.33811477 0 0.060747353 1.0083102 1.0193906
6800 0.3424043 0 0.010357152 1.0304709 1.0083102
6900 0.34804319 0 -0.042621786 1.0193906 1.0083102
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7400 0.34577559 0 -0.01985432 1.0193906 1.0083102
7500 0.3498641 0 0.052289439 1.0526316 1.0083102
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7700 0.33093497 0 0.11924405 1.0193906 1.0083102
7800 0.31435814 0 0.12701724 1.0083102 1.0304709
7900 0.33132217 0 0.10793075 1.0193906 1.0083102
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8300 0.3415632 0 -0.098067982 1.0304709 1.0083102
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8500 0.34446484 0 -0.098084709 1.0083102 1.0083102
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8800 0.33502983 0 0.027742411 1.0304709 1.0083102
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10100 0.32955942 0 0.04258493 1.0083102 1.0083102
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10900 0.35552287 0 -0.084955999 1.0193906 1.0304709
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11700 0.33555094 0 0.12738686 1.0083102 1.0304709
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11900 0.33836678 0 0.067253864 1.0193906 1.0193906
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12700 0.34673866 0 0.036734645 1.0193906 1.0083102
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12900 0.34271431 0 0.12415522 1.0304709 1.0083102
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15900 0.34289757 0 0.013849092 1.0304709 1.0083102
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16900 0.32183338 0 0.11680626 1.0193906 1.0083102
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17900 0.34255705 0 0.046794555 1.0304709 1.0193906
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19900 0.33903644 0 0.034788638 1.0083102 1.0193906
20000 0.32590125 0 0.011383785 1.0193906 1.0083102
20100 0.30358859 0 0.0030743554 1.0526316 1.0083102
20200 0.31830224 0 0.017637826 1.0193906 1.0193906
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20900 0.29447212 0 0.0967165 1.0193906 1.0193906
21000 0.31159961 0 0.067307231 1.0083102 1.0083102
21100 0.30490648 0 0.017689358 1.0083102 1.0193906
21200 0.30687262 0 -0.016055512 1.0193906 1.0193906
21300 0.30083286 0 -0.0014988997 1.0193906 1.0083102
21400 0.32070426 0 0.015960302 1.0083102 1.0083102
21500 0.31439311 0 0.038170385 1.0304709 1.0083102
21600 0.32617832 0 0.043263788 1.0083102 1.0083102
21700 0.35151793 0 0.066302727 1.0193906 1.0083102
21800 0.35912885 0 0.070099103 1.0193906 1.0083102
21900 0.32451958 0 0.068935768 1.0304709 1.0304709
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22500 0.34174625 0 -0.025019717 1.0083102 1.0083102
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22800 0.33973405 0 -0.0024705835 1.0193906 1.0083102
22900 0.33813085 0 0.0077527467 1.0083102 1.0193906
23000 0.33339981 0 0.028340744 1.0193906 1.0083102
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23200 0.33074548 0 0.032378405 1.0193906 1.0083102
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24100 0.31368736 0 -0.020818372 1.0304709 1.0083102
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24300 0.32530627 0 0.018183931 1.0415512 1.0083102
24400 0.31930662 0 0.027446878 1.0083102 1.0083102
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25100 0.32706871 0 -0.021196623 1.0415512 1.0193906
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25500 0.33002601 0 0.0080974022 1.0193906 1.0083102
25600 0.34127655 0 0.014296091 1.0526316 1.0193906
25700 0.34048065 0 0.022513032 1.0193906 1.0193906
25800 0.33029079 0 0.038733531 1.0193906 1.0083102
25900 0.33031324 0 0.026156982 1.0304709 1.0193906
26000 0.32967371 0 0.028727383 1.0083102 1.0193906
26100 0.33775718 0 0.015607478 1.0083102 1.0193906
26200 0.35097144 0 0.012291703 1.0083102 1.0083102
26300 0.34303792 0 0.00094823191 1.0083102 1.0193906
26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906
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26800 0.32998532 0 0.015932208 1.0304709 1.0193906
26900 0.33825444 0 0.010428603 1.0304709 1.0083102
27000 0.32081518 0 0.019818223 1.0304709 1.0193906
27100 0.31448098 0 0.020093416 1.0193906 1.0083102
27200 0.32643684 0 0.021934917 1.0083102 1.0083102
27300 0.33289466 0 0.023713072 1.0415512 1.0083102
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29900 0.33014448 0 0.03114046 1.0193906 1.0083102
30000 0.33741498 0 0.015624314 1.0083102 1.0193906
30100 0.32598657 0 -0.0018860541 1.0415512 1.0193906
30200 0.34855815 0 0.0017983372 1.0083102 1.0083102
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31000 0.34083982 0 0.031606413 1.0415512 1.0193906
31100 0.32165238 0 0.013583368 1.0193906 1.0083102
31200 0.3428492 0 0.020486611 1.0304709 1.0193906
31300 0.32372541 0 0.01215566 1.0083102 1.0083102
31400 0.32734692 0 0.016229397 1.0083102 1.0083102
31500 0.33089262 0 0.0060426618 1.0083102 1.0083102
31600 0.34273493 0 -0.013456537 1.0083102 1.0193906
31700 0.32723905 0 -0.019243766 1.0193906 1.0083102
31800 0.33636488 0 0.0027814902 1.0083102 1.0083102
31900 0.32834805 0 0.00706877 1.0083102 1.0193906
32000 0.33995148 0 0.0018383309 1.0193906 1.0193906
32100 0.33412282 0 0.0076455933 1.0083102 1.0083102
32200 0.34334884 0 0.023586129 1.0083102 1.0083102
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
32400 0.33163443 0 0.038878463 1.0193906 1.0083102
32500 0.32290345 0 0.022247461 1.0193906 1.0083102
32600 0.34113954 0 0.010966365 1.0304709 1.0083102
32700 0.33390633 0 0.0037777555 1.0193906 1.0083102
32800 0.34385341 0 0.010556575 1.0193906 1.0193906
32900 0.32137047 0 0.00022027143 1.0526316 1.0193906
33000 0.32079172 0 -0.017261272 1.0193906 1.0193906
33100 0.33570882 0 -0.0051942206 1.0083102 1.0083102
33200 0.34320894 0 -0.011515281 1.0304709 1.0083102
33300 0.32794746 0 -0.0018153673 1.0083102 1.0193906
33400 0.33060982 0 0.027118146 1.0193906 1.0083102
33500 0.33641809 0 0.02143035 1.0083102 1.0083102
33600 0.33643061 0 0.020833068 1.0193906 1.0083102
33700 0.3485949 0 0.030918751 1.0193906 1.0083102
33800 0.3283985 0 0.01947613 1.0193906 1.0083102
33900 0.31959761 0 0.021128147 1.0083102 1.0304709
34000 0.33897984 0 0.015270986 1.0193906 1.0083102
34100 0.32392267 0 0.0020130852 1.0304709 1.0193906
34200 0.33084514 0 -0.024316708 1.0193906 1.0193906
34300 0.3342259 0 -0.0059047764 1.0193906 1.0304709
34400 0.33385098 0 0.0063818721 1.0193906 1.0083102
34500 0.33255603 0 -0.01023837 1.0083102 1.0304709
34600 0.34766173 0 0.0056703013 1.0193906 1.0083102
34700 0.339822 0 0.0061648559 1.0083102 1.0193906
34800 0.33902329 0 0.030037037 1.0415512 1.0193906
34900 0.3216153 0 0.027996689 1.0304709 1.0083102
35000 0.32701056 0 0.024778517 1.0193906 1.0193906
35100 0.3124942 0 0.011316548 1.0193906 1.0193906
35200 0.34486416 0 0.011670127 1.0193906 1.0193906
35300 0.33275353 0 0.020491246 1.0193906 1.0193906
35400 0.33618763 0 0.014678874 1.0083102 1.0083102
35500 0.32352282 0 -0.018568683 1.0193906 1.0193906
35600 0.32617903 0 -0.012796912 1.0193906 1.0193906
35700 0.32378048 0 -0.021318585 1.0193906 1.0083102
35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906
35900 0.33818476 0 0.011197742 1.0193906 1.0083102
36000 0.35142144 0 0.022520935 1.0083102 1.0193906
36100 0.35147297 0 0.020277852 1.0193906 1.0083102
36200 0.33489465 0 0.014564878 1.0415512 1.0083102
36300 0.33841515 0 0.036439962 1.0193906 1.0193906
36400 0.32301096 0 0.019966746 1.0304709 1.0083102
36500 0.35612028 0 0.036509556 1.0083102 1.0083102
36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906
36700 0.34477654 0 -0.0052770853 1.0193906 1.0193906
36800 0.33804317 0 -0.013751733 1.0083102 1.0083102
36900 0.35003816 0 -0.0021184393 1.0083102 1.0193906
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
37200 0.35019871 0 -0.0071740923 1.0083102 1.0193906
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
37400 0.35739859 0 0.020892822 1.0193906 1.0083102
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
37800 0.343987 0 0.029579795 1.0083102 1.0083102
37900 0.33610448 0 0.036836828 1.0415512 1.0304709
38000 0.32757228 0 0.020902031 1.0193906 1.0193906
38100 0.32735808 0 0.019544751 1.0193906 1.0083102
38200 0.35646953 0 0.044607528 1.0083102 1.0193906
38300 0.32509773 0 0.03610738 1.0193906 1.0083102
38400 0.32111741 0 0.034474043 1.0193906 1.0193906
38500 0.30590608 0 0.053461212 1.0304709 1.0083102
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
39300 0.34519653 0 0.046257301 1.0193906 1.0083102
39400 0.34351844 0 0.052422917 1.0304709 1.0304709
39500 0.35716037 0 0.048916058 1.0304709 1.0083102
39600 0.34000737 0 0.016149089 1.0304709 1.0083102
39700 0.34587892 0 0.021619621 1.0526316 1.0083102
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
39900 0.35225411 0 -0.011341599 1.0083102 1.0083102
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
Loop time of 1.09412 on 4 procs for 40000 steps with 361 atoms
Pair time (%) = 0.0126024 (1.15184)
Bond time (%) = 0.234326 (21.417)
Neigh time (%) = 0.165015 (15.082)
Comm time (%) = 0.324642 (29.6716)
Outpt time (%) = 0.0075146 (0.686818)
Other time (%) = 0.350016 (31.9908)
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 59.25 ave 61 max 56 min
Histogram: 1 0 0 0 0 0 0 0 2 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
Ave special neighs/atom = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 2d polygon nparticle bodies
units lj
dimension 2
atom_style body nparticle 2 6
read_data data.body
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
1 by 1 by 1 MPI processor grid
reading atoms ...
100 atoms
100 bodies
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
fix 1 all nve/body
fix 2 all enforce2d
#compute 1 all body/local type 1 2 3
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Memory usage per processor = 3.22547 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5537157 -1.5243356 0 0.013843001 0.2654775
1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
1500 1.6994347 -1.7246456 0 -0.04220525 0.3664501
2000 1.6587022 -1.6970163 0 -0.054901081 0.10137795
2500 1.7859516 -1.8212698 0 -0.053177671 0.35400181
3000 1.7865459 -1.730183 0 0.038497352 0.28330983
3500 2.0521408 -1.98222 0 0.049399375 0.088928245
4000 1.721448 -1.7409775 0 -0.036743968 0.12815274
4500 1.6189244 -1.7257177 0 -0.12298249 0.21501422
5000 1.5828072 -1.6501894 0 -0.083210213 0.33447691
5500 1.8562352 -1.7632936 0 0.074379269 0.24273308
6000 1.4818079 -1.6942298 0 -0.22723999 0.22470999
6500 1.5229137 -1.6249423 0 -0.11725778 -0.043041211
7000 1.5930761 -1.5349749 0 0.04217044 0.072621368
7500 1.7251412 -1.7620322 0 -0.05414237 -0.052083575
8000 1.7843737 -1.6422594 0 0.12427062 0.3924994
8500 1.9344759 -1.7880774 0 0.12705368 0.32652919
9000 1.6338929 -1.6889133 0 -0.071359354 0.3793827
9500 1.5180082 -1.7729127 0 -0.27008457 0.27223707
10000 1.6133128 -1.7939587 0 -0.19677903 0.18983194
Loop time of 2.02213 on 1 procs for 10000 steps with 100 atoms
Pair time (%) = 1.79877 (88.9544)
Neigh time (%) = 0.0161726 (0.799784)
Comm time (%) = 0.0302939 (1.49812)
Outpt time (%) = 0.000165939 (0.00820618)
Other time (%) = 0.176724 (8.7395)
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 85 ave 85 max 85 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 424 ave 424 max 424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 424
Ave neighs/atom = 4.24
Neighbor list builds = 795
Dangerous builds = 83

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LAMMPS (1 Feb 2014)
# 2d polygon nparticle bodies
units lj
dimension 2
atom_style body nparticle 2 6
read_data data.body
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
2 by 2 by 1 MPI processor grid
reading atoms ...
100 atoms
100 bodies
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
fix 1 all nve/body
fix 2 all enforce2d
#compute 1 all body/local type 1 2 3
#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Memory usage per processor = 3.19797 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5537157 -1.5243356 0 0.013843001 0.2654775
1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
1500 1.6994347 -1.7246456 0 -0.042205239 0.36645011
2000 1.6586974 -1.6970115 0 -0.054901078 0.10137999
2500 1.7878623 -1.8213737 0 -0.051390011 0.35530747
3000 1.7043715 -1.6613359 0 0.025991881 0.27048518
3500 1.6313416 -1.5250929 0 0.089935264 0.10510436
4000 1.5883641 -1.7692022 0 -0.1967218 0.50882304
4500 1.5897207 -1.5634198 0 0.010403642 0.24598267
5000 1.4849734 -1.5512049 0 -0.081081244 -0.028399888
5500 1.6074988 -1.7000582 0 -0.10863448 0.42879191
6000 1.6106093 -1.5850749 0 0.0094282394 0.4115976
6500 1.8169151 -1.7996899 0 -0.00094400747 0.21677584
7000 1.5487579 -1.6028263 0 -0.069555913 0.23742891
7500 1.7231927 -1.8001082 0 -0.094147408 -0.016712191
8000 1.5832288 -1.7242109 0 -0.15681439 0.33204
8500 1.9002455 -1.866332 0 0.014911066 0.28393405
9000 1.5916225 -1.6032424 0 -0.027536096 0.48213053
9500 1.6326075 -1.7974673 0 -0.18118584 0.078132294
10000 1.3851677 -1.49406 0 -0.12274404 0.18606978
Loop time of 0.730152 on 4 procs for 10000 steps with 100 atoms
Pair time (%) = 0.464131 (63.5663)
Neigh time (%) = 0.00445265 (0.609824)
Comm time (%) = 0.204234 (27.9714)
Outpt time (%) = 0.000480056 (0.0657474)
Other time (%) = 0.0568546 (7.78668)
Nlocal: 25 ave 25 max 25 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 43.75 ave 48 max 40 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 101.5 ave 113 max 91 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 406
Ave neighs/atom = 4.06
Neighbor list builds = 805
Dangerous builds = 97

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LAMMPS (1 Feb 2014)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
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 temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.96579 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
6000 2.1073992 0.0076702433 2.1127279 0.097655997 21544.211
7000 2.084579 -0.0022304831 2.0800323 0.11014552 17791.284
8000 2.0677538 0.00059800188 2.0660543 0.12718796 15494.44
9000 2.0545977 0.0064465732 2.0587614 0.15002732 13864.665
10000 2.0482054 0.010661731 2.0565913 0.17497885 12553.11
11000 2.0360539 0.022283053 2.0560747 0.18608443 11469.573
12000 2.0488819 0.012601482 2.0592068 0.20752397 10547.355
13000 2.0307724 0.027945421 2.0564614 0.23492616 9791.6008
14000 2.0291712 0.024760645 2.0516772 0.25749445 9166.0223
15000 2.0421329 0.011858836 2.0517227 0.26019128 8645.5059
16000 2.0321296 0.023089154 2.0529608 0.30100779 8173.8988
17000 2.0339883 0.020841935 2.0525702 0.31937035 7749.9866
18000 2.0165994 0.039101369 2.0534601 0.33206939 7399.5633
19000 2.0174571 0.03075954 2.045975 0.37582663 7115.1621
20000 2.0235743 0.033645074 2.054971 0.37789661 6779.655
21000 2.0086918 0.052575979 2.0590359 0.47587927 6468.3757
22000 2.0186512 0.035185664 2.0515939 0.39489244 6270.2423
23000 2.0159704 0.037209936 2.0509404 0.42372164 6090.2568
24000 2.0262103 0.034411154 2.0583702 0.46377965 5878.6019
25000 2.0136031 0.040396972 2.0517627 0.49998462 5706.6657
26000 2.0118123 0.04348596 2.0530629 0.52601904 5555.535
27000 2.0483861 0.010622163 2.0567323 0.46408289 5439.3763
28000 1.9775694 0.0880593 2.0634314 0.60451974 5303.7986
29000 2.0161573 0.051647461 2.0655645 0.55856521 5154.8346
30000 2.0154349 0.045614723 2.0588102 0.55640547 5067.2252
31000 2.0264636 0.042015926 2.0662279 0.58323212 4966.2146
32000 1.9946148 0.074464523 2.0668631 0.64405663 4840.3505
33000 2.016998 0.046624054 2.0613809 0.6520715 4765.5247
34000 2.0086574 0.060996501 2.067422 0.6530397 4666.4569
35000 2.0203252 0.05402663 2.0721071 0.69134002 4595.6514
36000 2.0271451 0.041489394 2.0663822 0.65114797 4526.2978
37000 2.0183469 0.064565854 2.0806701 0.70724758 4446.6465
38000 2.0049133 0.065280115 2.0679658 0.76328332 4389.5655
39000 2.0254497 0.05173788 2.0749371 0.75604831 4332.6535
40000 2.0019046 0.080413589 2.0800938 0.78175962 4254.5071
41000 2.0246809 0.05297341 2.0754047 0.77404015 4193.7093
42000 2.0254595 0.058651302 2.0818603 0.81823656 4135.9705
43000 2.0007241 0.083353246 2.0818543 0.82002543 4082.2245
44000 1.994415 0.089912333 2.0821113 0.98373573 4051.5787
45000 2.0130937 0.07986583 2.0907228 0.97054142 3991.453
46000 1.9997536 0.094509733 2.0920414 0.90955799 3926.3675
47000 2.0026833 0.086980098 2.0874382 1.1140455 3885.3495
48000 2.0217273 0.077640083 2.0971211 0.94719095 3829.7776
49000 1.9778606 0.11563852 2.0913015 1.1107597 3798.5114
50000 2.038067 0.060063696 2.0958661 1.0030415 3763.2003
Loop time of 8.766 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 4.14446 (47.2788)
Neigh time (%) = 1.10557 (12.612)
Comm time (%) = 0.423719 (4.83366)
Outpt time (%) = 0.000560045 (0.00638883)
Other time (%) = 3.09169 (35.2691)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 515 ave 515 max 515 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5990 ave 5990 max 5990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5990
Ave neighs/atom = 6.65556
Neighbor list builds = 3145
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
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 temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.8708 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076740311 2.112728 0.097657373 21544.21
7000 2.0843684 -0.001996932 2.0800555 0.11036967 17791.247
8000 2.0640518 0.0014998478 2.0632583 0.1290879 15498.836
9000 2.0466103 0.010705612 2.0550419 0.15352798 13893.115
10000 2.0318438 0.028356097 2.0579423 0.18270659 12603.157
11000 2.0483114 0.011317082 2.0573526 0.18793572 11521.407
12000 2.0465451 0.011178196 2.0554494 0.20917582 10593.908
13000 2.0339418 0.020973133 2.052655 0.22462811 9837.666
14000 2.0352875 0.021186021 2.054212 0.25973065 9169.0201
15000 2.0397627 0.016745562 2.0542419 0.26379715 8580.3575
16000 2.0306726 0.019939485 2.0483558 0.30415554 8135.4142
17000 2.0303715 0.023425678 2.0515413 0.29717285 7732.4398
18000 2.0091196 0.046353117 2.0532404 0.4201013 7321.9473
19000 2.0069004 0.044794224 2.0494648 0.37207191 7008.5252
20000 2.0293906 0.02286811 2.0500038 0.37743862 6770.2412
21000 2.0151565 0.035150252 2.0480677 0.42245372 6563.7655
22000 1.9931286 0.061233296 2.0521473 0.44215378 6387.0047
23000 2.0095257 0.04877004 2.0560629 0.4359382 6146.7894
24000 2.0244673 0.041537999 2.0637559 0.47433783 5904.2578
25000 2.0411374 0.014657985 2.0535275 0.42934196 5714.3163
26000 2.0101343 0.048931921 2.0568327 0.58433419 5557.1491
27000 2.010355 0.044833431 2.0529547 0.53172163 5441.607
28000 2.0075626 0.056527165 2.0618592 0.54811055 5312.0333
29000 2.0279913 0.036953425 2.0626914 0.53888357 5165.8026
30000 2.0014479 0.062210877 2.0614349 0.61283256 5028.4409
31000 2.0072038 0.060184255 2.0651578 0.62321627 4918.8388
32000 2.0250392 0.043276173 2.0660653 0.61454026 4822.6538
33000 2.0225382 0.041253335 2.0615443 0.61742775 4746.3484
34000 2.0079979 0.060100013 2.0658668 0.7196627 4668.3612
35000 1.9869444 0.081389753 2.0661264 0.69301002 4630.1772
36000 2.0080612 0.068966773 2.0747968 0.75807989 4524.4316
37000 2.016828 0.059785388 2.0743725 0.73797084 4436.8809
38000 1.9923438 0.084178865 2.074309 0.83179043 4358.5286
39000 2.0144256 0.058962222 2.0711496 0.72841391 4318.0019
40000 2.0205458 0.063834805 2.0821355 0.79611444 4233.3053
41000 1.9895557 0.088139599 2.0754847 0.77982219 4183.6801
42000 1.9862976 0.097665639 2.0817562 0.9527169 4136.6273
43000 1.9845679 0.10838021 2.0907431 0.84567001 4063.3971
44000 2.0058015 0.079068928 2.0826418 0.87879853 4013.8417
45000 2.01267 0.072607353 2.083041 0.84521964 3983.104
46000 2.0028119 0.088952749 2.0895393 0.86809738 3907.9426
47000 2.0219141 0.069213747 2.0888813 0.88288894 3868.029
48000 1.9820914 0.1111149 2.091004 1.0650645 3812.8502
49000 2.0161896 0.077389897 2.0913393 0.94940244 3771.6873
50000 2.0216994 0.071211384 2.0906645 0.99837694 3771.8545
Loop time of 3.69238 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.08079 (29.2708)
Neigh time (%) = 0.286304 (7.75391)
Comm time (%) = 0.855729 (23.1756)
Outpt time (%) = 0.000957787 (0.0259396)
Other time (%) = 1.4686 (39.7738)
Nlocal: 225 ave 251 max 199 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 295.25 ave 304 max 283 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 1477.25 ave 1684 max 1286 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 5909
Ave neighs/atom = 6.56556
Neighbor list builds = 3138
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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examples/comb/log.comb.Cu.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Memory usage per processor = 5.13167 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.180117 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.179547 (99.6834)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000333071 (0.184919)
Outpt time (%) = 0.000129461 (0.0718762)
Other time (%) = 0.000107765 (0.0598306)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb.Cu.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Memory usage per processor = 4.62535 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.0488312 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.0467316 (95.7003)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0016737 (3.42752)
Outpt time (%) = 0.000292957 (0.599938)
Other time (%) = 0.000132918 (0.2722)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

316
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 11.5578 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.302742 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.102108 (33.7277)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000131845 (0.0435504)
Outpt time (%) = 4.91142e-05 (0.0162231)
Other time (%) = 0.200453 (66.2125)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 12.8548 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
Loop time of 1.30625 on 1 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544021729 -3.84546110694 -3.84546110755
Force two-norm initial, final = 14.2445 25.7656
Force max component initial, final = 8.22308 14.8753
Final line search alpha, max atom move = 1.64125e-08 2.4414e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.772175 (59.1137)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000988007 (0.0756367)
Outpt time (%) = 2.5034e-05 (0.00191647)
Other time (%) = 0.533065 (40.8087)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 11.7345 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
5 0.9945563 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
Loop time of 0.169246 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0514591 (30.4049)
Neigh time (%) = 0 (0)
Comm time (%) = 6.58035e-05 (0.0388804)
Outpt time (%) = 2.40803e-05 (0.014228)
Other time (%) = 0.117697 (69.542)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
run 10
Memory usage per processor = 8.71237 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.844 -66760.744 -48482.078
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.702 -66759.409 -48477.317
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.56 -66758.075 -48472.557
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.418 -66756.741 -48467.797
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.278 -66755.407 -48463.036
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.137 -66754.073 -48458.277
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.997 -66752.739 -48453.517
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.858 -66751.404 -48448.758
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.718 -66750.07 -48443.999
Loop time of 0.623819 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.619949 (99.3796)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000663996 (0.10644)
Outpt time (%) = 0.00292301 (0.468567)
Other time (%) = 0.000283003 (0.0453662)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 9.22946 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.979 -66747.401 -48438.271
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.38 -66746.066 -48437.301
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.782 -66744.731 -48436.331
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.183 -66743.396 -48435.361
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.585 -66742.061 -48434.392
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.986 -66740.726 -48433.423
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.388 -66739.391 -48432.453
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.79 -66738.056 -48431.485
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.192 -66736.721 -48430.516
Loop time of 0.623835 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.620008 (99.3865)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000666618 (0.106858)
Outpt time (%) = 0.00287819 (0.46137)
Other time (%) = 0.000282288 (0.0452504)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 9.74655 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.588 -66735.38 -48165.079
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.582 -66735.374 -47900.611
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.577 -66735.368 -47636.143
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.571 -66735.362 -47371.676
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.565 -66735.356 -47107.208
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.56 -66735.35 -46842.74
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.554 -66735.344 -46578.272
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.548 -66735.338 -46313.805
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.542 -66735.332 -46049.337
Loop time of 0.624007 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.620168 (99.3848)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000666857 (0.106867)
Outpt time (%) = 0.00289488 (0.463918)
Other time (%) = 0.000277042 (0.0443973)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 10.2636 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.131 -66735.322 -45784.862
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.725 -66735.318 -45784.855
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.318 -66735.314 -45784.848
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.912 -66735.31 -45784.841
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.506 -66735.306 -45784.834
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.1 -66735.302 -45784.827
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.694 -66735.298 -45784.82
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.288 -66735.294 -45784.813
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.882 -66735.29 -45784.806
Loop time of 0.623936 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.620081 (99.3821)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000681162 (0.109172)
Outpt time (%) = 0.00288105 (0.461754)
Other time (%) = 0.000293016 (0.0469626)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

316
examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 6.52912 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.079618 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0258412 (32.4565)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000640452 (0.804406)
Outpt time (%) = 7.51615e-05 (0.0944026)
Other time (%) = 0.0530612 (66.6447)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 7.71427 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
Loop time of 0.349189 on 4 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544021729 -3.84546110694 -3.84546110755
Force two-norm initial, final = 14.2445 25.7656
Force max component initial, final = 8.22308 14.8753
Final line search alpha, max atom move = 1.64125e-08 2.4414e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.20012 (57.31)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00572902 (1.64066)
Outpt time (%) = 4.15444e-05 (0.0118974)
Other time (%) = 0.143298 (41.0374)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 6.68714 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
5 0.9945563 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
Loop time of 0.0451097 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.013331 (29.5524)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000361264 (0.800855)
Outpt time (%) = 3.72529e-05 (0.0825828)
Other time (%) = 0.0313802 (69.5642)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
run 10
Memory usage per processor = 5.93235 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.844 -66760.744 -48482.078
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.702 -66759.409 -48477.317
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.56 -66758.075 -48472.557
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.418 -66756.741 -48467.797
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.278 -66755.407 -48463.036
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.137 -66754.073 -48458.277
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.997 -66752.739 -48453.517
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.858 -66751.404 -48448.758
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.718 -66750.07 -48443.999
Loop time of 0.168408 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.161152 (95.6913)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0040102 (2.38124)
Outpt time (%) = 0.00308657 (1.83279)
Other time (%) = 0.000159502 (0.0947117)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 6.40641 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.979 -66747.401 -48438.271
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.38 -66746.066 -48437.301
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.782 -66744.731 -48436.331
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.183 -66743.396 -48435.361
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.585 -66742.061 -48434.392
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.986 -66740.726 -48433.423
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.388 -66739.391 -48432.453
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.79 -66738.056 -48431.485
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.192 -66736.721 -48430.516
Loop time of 0.168435 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.161198 (95.7033)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00402051 (2.38698)
Outpt time (%) = 0.00305879 (1.81601)
Other time (%) = 0.000157833 (0.0937056)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 6.88047 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.588 -66735.38 -48165.079
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.582 -66735.374 -47900.611
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.577 -66735.368 -47636.143
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.571 -66735.362 -47371.676
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.565 -66735.356 -47107.208
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.56 -66735.35 -46842.74
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.554 -66735.344 -46578.272
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.548 -66735.338 -46313.805
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.542 -66735.332 -46049.337
Loop time of 0.168295 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.161186 (95.776)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0039618 (2.35408)
Outpt time (%) = 0.0029906 (1.777)
Other time (%) = 0.000156462 (0.0929689)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 7.35453 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.131 -66735.322 -45784.862
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.725 -66735.318 -45784.855
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.318 -66735.314 -45784.848
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.912 -66735.31 -45784.841
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.506 -66735.306 -45784.834
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.1 -66735.302 -45784.827
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.694 -66735.298 -45784.82
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.288 -66735.294 -45784.813
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.882 -66735.29 -45784.806
Loop time of 0.16841 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.161244 (95.7444)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00396228 (2.35275)
Outpt time (%) = 0.00304365 (1.80728)
Other time (%) = 0.000160992 (0.0955951)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

185
examples/comb/log.comb.HfO2.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 11.9784 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.121151 on 1 procs for 1 steps with 1500 atoms
Pair time (%) = 0.120976 (99.8556)
Neigh time (%) = 0 (0)
Comm time (%) = 8.29697e-05 (0.0684845)
Outpt time (%) = 3.09944e-05 (0.0255833)
Other time (%) = 6.10352e-05 (0.0503794)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 17.2999 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
Loop time of 0.836291 on 1 procs for 5 steps with 1500 atoms
Pair time (%) = 0.606207 (72.4875)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000421047 (0.050347)
Outpt time (%) = 0.000165939 (0.0198423)
Other time (%) = 0.229497 (27.4423)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 18.7762 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.471877 on 1 procs for 1 steps with 1500 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0941049618 -10.0941049618 -10.0949959801
Force two-norm initial, final = 5418.49 5437.46
Force max component initial, final = 4082.68 4098.38
Final line search alpha, max atom move = 4.89874e-08 0.000200769
Iterations, force evaluations = 1 1
Pair time (%) = 0.242309 (51.35)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000167131 (0.0354184)
Outpt time (%) = 0 (0)
Other time (%) = 0.229401 (48.6146)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Memory usage per processor = 17.2999 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 1.66905 on 1 procs for 10 steps with 1500 atoms
Pair time (%) = 1.20968 (72.4776)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000833511 (0.0499394)
Outpt time (%) = 0.000306129 (0.0183416)
Other time (%) = 0.458222 (27.4542)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0

185
examples/comb/log.comb.HfO2.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 5.22718 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0313838 on 4 procs for 1 steps with 1500 atoms
Pair time (%) = 0.0305235 (97.2589)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000760198 (2.42226)
Outpt time (%) = 4.77433e-05 (0.152127)
Other time (%) = 5.23329e-05 (0.166751)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 6.92136 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
Loop time of 0.215946 on 4 procs for 5 steps with 1500 atoms
Pair time (%) = 0.152745 (70.7329)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00467187 (2.16344)
Outpt time (%) = 0.000242293 (0.112201)
Other time (%) = 0.058287 (26.9915)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 7.6363 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.121192 on 4 procs for 1 steps with 1500 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0941049618 -10.0941049618 -10.0949959801
Force two-norm initial, final = 5418.49 5437.46
Force max component initial, final = 4082.68 4098.38
Final line search alpha, max atom move = 4.89874e-08 0.000200769
Iterations, force evaluations = 1 1
Pair time (%) = 0.0610258 (50.3547)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00184089 (1.51899)
Outpt time (%) = 0 (0)
Other time (%) = 0.0583253 (48.1264)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Memory usage per processor = 6.92136 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
Loop time of 0.431377 on 4 procs for 10 steps with 1500 atoms
Pair time (%) = 0.305476 (70.8142)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00917089 (2.12596)
Outpt time (%) = 0.000487924 (0.113108)
Other time (%) = 0.116242 (26.9467)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb.Si.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Memory usage per processor = 5.5122 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.134541 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.13386 (99.4939)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000366688 (0.272547)
Outpt time (%) = 0.000138283 (0.102781)
Other time (%) = 0.000175953 (0.13078)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb.Si.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Memory usage per processor = 4.66323 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.0370951 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.034411 (92.7644)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00227368 (6.12933)
Outpt time (%) = 0.000264704 (0.713583)
Other time (%) = 0.000145674 (0.392704)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

274
examples/comb/log.comb.Si.elastic.1Feb14.linux.1
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@ -1,274 +0,0 @@
LAMMPS (1 Feb 2014)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 6.19884 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.229516 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.22687 (98.8473)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000636816 (0.27746)
Outpt time (%) = 1.88351e-05 (0.00820643)
Other time (%) = 0.00199008 (0.867077)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
Memory usage per processor = 5.20702 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0133381 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0132809 (99.571)
Neigh time (%) = 0 (0)
Comm time (%) = 3.91006e-05 (0.29315)
Outpt time (%) = 1.00136e-05 (0.0750751)
Other time (%) = 8.10623e-06 (0.0607751)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
run 10
Memory usage per processor = 5.66478 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 4.2424409e-06 1.8970431e-06 5.2226895e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.0659899e-06 3.6846991e-06 4.9259641e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 3.8875089e-06 2.372335e-06 4.6875974e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 3.2832708e-06 3.8145125e-06 4.6443213e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 4.0254046e-06 3.7666561e-06 1.4753812e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.7956471e-06 -1.771899e-06 2.0927452e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.4378795e-06 3.6072928e-06 1.6693231e-06
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.4064842e-06 3.1661348e-06 1.1859415e-06
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 3.3766971e-06 3.2790869e-06 1.2694808e-06
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.7553942e-06 3.4602587e-06 1.8958276e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -5.8836668e-06 -5.4578803e-06 1.5156445e-06
Loop time of 0.159919 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.157728 (98.63)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000384331 (0.240328)
Outpt time (%) = 0.00167108 (1.04495)
Other time (%) = 0.000135422 (0.0846815)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 6.12255 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 4.4203553e-06 1.7546449e-06 3.8696804e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.4413815e-06 3.2045526e-06 3.765411e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 1.9121071e-06 7.2294681e-06 4.3210997e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.1284508e-06 3.8448888e-06 4.2955743e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 2.6951046e-06 3.4945075e-06 -4.5517214e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -5.9762705e-07 3.542375e-06 -3.0529456e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -6.9439231e-07 3.3859393e-06 4.3147517e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -4.5695573e-07 3.4108162e-06 3.953809e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -6.2504609e-07 4.0351804e-06 4.6966692e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 2.5898938e-07 4.0107779e-06 4.6632245e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -4.5460256e-07 3.6194737e-06 3.412469e-06
Loop time of 0.160066 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.157902 (98.6478)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000381947 (0.238618)
Outpt time (%) = 0.00164986 (1.03074)
Other time (%) = 0.000132561 (0.0828164)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 6.58031 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 3.1470723e-06 2.3932875e-06 3.3367488e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.7837353e-06 4.8243295e-06 2.5146962e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.8016568e-06 5.6512219e-06 243.65137
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 1.9900804e-06 4.0111151e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 1.762453e-06 6.1935142e-06 730.9542
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.3991797e-06 5.493982e-06 974.60552
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.2018322e-06 4.7607643e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.8680162e-06 5.6568584e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 2.2450268e-06 8.6579416e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 1.9691724e-06 8.970813e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.9802012e-06 8.483733e-06 2192.8625
Loop time of 0.15999 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.157806 (98.635)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000383854 (0.239924)
Outpt time (%) = 0.0016675 (1.04225)
Other time (%) = 0.000132561 (0.0828556)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 7.03807 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 3.1183118e-06 9.8932292e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.5429824e-06 1.089443e-05 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00011790196 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00024666123 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.0003778327 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00050731605 2436.5139
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00063724551 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00076799013 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00089693851 2436.5139
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010276841 2436.5139
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011569482 2436.5139
Loop time of 0.16096 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.158687 (98.5875)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000389814 (0.242181)
Outpt time (%) = 0.00174046 (1.0813)
Other time (%) = 0.00014329 (0.0890217)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

274
examples/comb/log.comb.Si.elastic.1Feb14.linux.4
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@ -1,274 +0,0 @@
LAMMPS (1 Feb 2014)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 5.35368 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0760608 on 4 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.0578517 (76.0599)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0166439 (21.8823)
Outpt time (%) = 3.75509e-05 (0.0493696)
Other time (%) = 0.00152761 (2.0084)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
Memory usage per processor = 4.36186 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.00442469 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.00335443 (75.8116)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00102764 (23.2252)
Outpt time (%) = 2.20537e-05 (0.498424)
Other time (%) = 2.05636e-05 (0.464747)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
run 10
Memory usage per processor = 4.81962 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.2585718e-06 8.1180987e-07 4.0306446e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 2.5758786e-06 1.8749159e-06 3.2724054e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 1.1168843e-07 -1.1628767e-06 4.899012e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 3.802339e-06 2.2938022e-06 3.4583539e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 3.6215267e-06 1.8435613e-06 -7.4389779e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.064601e-06 -6.209123e-06 4.5628869e-07
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.2041932e-06 1.4500411e-06 5.5267226e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.1624105e-06 1.8235057e-06 7.871368e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.4485703e-06 1.2810688e-06 2.6866887e-09
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.6571948e-06 2.3701116e-06 6.6957472e-07
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -3.6955126e-06 -5.5104616e-06 1.1388559e-06
Loop time of 0.0540757 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0405609 (75.0076)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0114365 (21.149)
Outpt time (%) = 0.00200176 (3.70178)
Other time (%) = 7.6592e-05 (0.141638)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 5.27739 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 3.5908688e-06 1.1023465e-06 4.3869032e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.1280098e-06 2.3099075e-06 3.2862947e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.7484085e-06 -8.7020552e-07 2.7979177e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.6676044e-06 2.2839782e-06 3.5535702e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 3.9701144e-06 2.7405115e-06 -3.8363284e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 6.9640455e-07 2.8451033e-06 -2.8508806e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 8.7021293e-07 2.342196e-06 3.7774214e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 1.346913e-06 2.6670815e-06 3.9313557e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 8.4825249e-08 2.741412e-06 3.3674586e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -3.353247e-07 1.6605663e-06 3.3399914e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 5.4012079e-07 2.5242571e-06 3.2038115e-06
Loop time of 0.054018 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.040496 (74.9676)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0114477 (21.1924)
Outpt time (%) = 0.00199842 (3.69955)
Other time (%) = 7.58767e-05 (0.140466)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 5.73515 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 2.8906214e-06 1.7666628e-06 2.9640551e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.9258037e-06 3.6230832e-06 1.33952e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.1740797e-06 5.2110496e-06 243.65137
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 2.60027e-06 4.4622713e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 2.3749106e-06 4.4580653e-06 730.9542
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.3993094e-06 2.1645558e-06 974.60552
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.787245e-06 4.7294171e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.691321e-06 5.1697154e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 2.9029135e-06 5.9089513e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 2.6120766e-06 3.8685242e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.5647131e-06 4.7043661e-06 2192.8625
Loop time of 0.0540408 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0404646 (74.8779)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0114999 (21.2801)
Outpt time (%) = 0.00199848 (3.6981)
Other time (%) = 7.77841e-05 (0.143936)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 6.19291 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.8976957e-06 5.6758319e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.1032622e-06 7.408283e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00012251553 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00025164456 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.00038452391 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.000513424 2436.5139
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064410321 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077446789 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.0009043182 2436.5139
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001034056 2436.5139
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011642879 2436.5139
Loop time of 0.0501781 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0406764 (81.0642)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00744313 (14.8334)
Outpt time (%) = 0.0019834 (3.95273)
Other time (%) = 7.51019e-05 (0.149671)
Nlocal: 128 ave 152 max 112 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3073 ave 3089 max 3049 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 63232 max 46592 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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examples/comb/log.comb3.1Feb14.linux.1
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LAMMPS (11 May 2014)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
#dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Memory usage per processor = 4.47117 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -2.3270126 -2.3657338 -1.7978067 -0.56792713 21594.196 17719.012 21.3 24.6 33.8162
10 478.0603 -2.3269803 -2.3886838 -1.8209127 -0.56777109 23710.285 17719.012 21.3 24.6 33.8162
20 814.80333 -2.3269776 -2.4321448 -1.8640442 -0.5681006 23470.546 17719.012 21.3 24.6 33.8162
30 1057.7976 -2.3270931 -2.4636237 -1.8952156 -0.56840806 21318.443 17719.012 21.3 24.6 33.8162
40 1181.0863 -2.3273291 -2.4797726 -1.9107617 -0.56901089 12287.617 17719.012 21.3 24.6 33.8162
50 1260.4426 -2.327182 -2.4898681 -1.9199876 -0.56988046 14920.176 17719.012 21.3 24.6 33.8162
60 1420.2752 -2.3273048 -2.5106206 -1.9398802 -0.57074041 34149.68 17719.012 21.3 24.6 33.8162
70 1637.2855 -2.3275266 -2.538852 -1.9673056 -0.57154647 48501.634 17719.012 21.3 24.6 33.8162
80 1842.2774 -2.3278122 -2.5655961 -1.9932476 -0.5723485 51133.322 17719.012 21.3 24.6 33.8162
90 2030.6604 -2.3282513 -2.5903498 -2.0173162 -0.57303362 50474.741 17719.012 21.3 24.6 33.8162
100 2148.8242 -2.3286078 -2.6059579 -2.0323384 -0.57361944 43730.685 17719.012 21.3 24.6 33.8162
Loop time of 17.3159 on 1 procs for 100 steps with 682 atoms
Pair time (%) = 7.25847 (41.918)
Neigh time (%) = 0.0360692 (0.208301)
Comm time (%) = 0.00386763 (0.0223357)
Outpt time (%) = 0.000226736 (0.00130941)
Other time (%) = 10.0172 (57.85)
Nlocal: 682 ave 682 max 682 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4150 ave 4150 max 4150 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 355236 ave 355236 max 355236 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 355236
Ave neighs/atom = 520.874
Neighbor list builds = 1
Dangerous builds = 0

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examples/comb/log.comb3.1Feb14.linux.4
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LAMMPS (11 May 2014)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 33.8162) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
#dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Memory usage per processor = 4.95436 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -2.3270126 -2.3657338 -1.7978067 -0.56792713 21594.196 17719.012 21.3 24.6 33.8162
10 478.0603 -2.3269803 -2.3886838 -1.8209127 -0.56777109 23710.285 17719.012 21.3 24.6 33.8162
20 814.80333 -2.3269776 -2.4321448 -1.8640442 -0.5681006 23470.546 17719.012 21.3 24.6 33.8162
30 1057.7976 -2.3270931 -2.4636237 -1.8952156 -0.56840806 21318.443 17719.012 21.3 24.6 33.8162
40 1181.0863 -2.3273291 -2.4797726 -1.9107617 -0.56901089 12287.617 17719.012 21.3 24.6 33.8162
50 1260.4426 -2.327182 -2.4898681 -1.9199876 -0.56988046 14920.176 17719.012 21.3 24.6 33.8162
60 1420.2752 -2.3273048 -2.5106206 -1.9398802 -0.57074041 34149.68 17719.012 21.3 24.6 33.8162
70 1637.2855 -2.3275266 -2.538852 -1.9673056 -0.57154647 48501.634 17719.012 21.3 24.6 33.8162
80 1842.2774 -2.3278122 -2.5655961 -1.9932476 -0.5723485 51133.322 17719.012 21.3 24.6 33.8162
90 2030.6604 -2.3282513 -2.5903498 -2.0173162 -0.57303362 50474.741 17719.012 21.3 24.6 33.8162
100 2148.8242 -2.3286078 -2.6059579 -2.0323384 -0.57361944 43730.685 17719.012 21.3 24.6 33.8162
Loop time of 8.04903 on 4 procs for 100 steps with 682 atoms
Pair time (%) = 2.56114 (31.8192)
Neigh time (%) = 0.022868 (0.284109)
Comm time (%) = 0.897084 (11.1452)
Outpt time (%) = 0.000355363 (0.00441498)
Other time (%) = 4.56758 (56.747)
Nlocal: 170.5 ave 259 max 100 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 2869 ave 3578 max 2147 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 88809 ave 139203 max 48175 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 355236
Ave neighs/atom = 520.874
Neighbor list builds = 1
Dangerous builds = 0

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examples/crack/log.crack.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 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 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
run 5000
Memory usage per processor = 2.06456 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917
200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101
400 0.060533553 -3.2509973 0 -3.1949623 -0.4305406 8679.2464
600 0.06082965 -3.2466949 0 -3.1903858 -0.6028531 8716.7569
800 0.061677224 -3.2413215 0 -3.1842278 -0.7482749 8756.226
1000 0.062383731 -3.2349273 0 -3.1771796 -0.87425132 8793.1116
1200 0.063709246 -3.2276094 0 -3.1686347 -0.98020161 8828.8863
1400 0.065404552 -3.2196608 0 -3.1591168 -1.0695384 8866.4893
1600 0.067579602 -3.2110378 0 -3.1484804 -1.1456387 8900.6772
1800 0.069324241 -3.2018536 0 -3.1376812 -1.2020999 8933.017
2000 0.071014927 -3.1921108 0 -3.1263733 -1.2430105 8963.9853
2200 0.072992881 -3.1818701 0 -3.1143017 -1.2701297 9004.4136
2400 0.075000723 -3.1712313 0 -3.1018043 -1.2830866 9034.9991
2600 0.076843477 -3.1601004 0 -3.0889675 -1.27924 9072.1325
2800 0.078671706 -3.1487747 0 -3.0759495 -1.2659604 9103.9526
3000 0.080713586 -3.1373277 0 -3.0626123 -1.2440673 9134.552
3200 0.08309469 -3.1260242 0 -3.0491047 -1.214547 9169.0003
3400 0.085424766 -3.1146623 0 -3.0355859 -1.1839326 9206.909
3600 0.087396485 -3.1029493 0 -3.0220477 -1.143412 9233.783
3800 0.089007987 -3.090822 0 -3.0084286 -1.1000791 9259.0348
4000 0.089813071 -3.0794078 0 -2.9962692 -1.062847 9281.82
4200 0.08584753 -3.0668559 0 -2.9873882 -1.037972 9308.8113
4400 0.086197517 -3.0559678 0 -2.9761761 -1.028843 9328.9666
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637
Loop time of 6.86201 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 5.71043 (83.218)
Neigh time (%) = 0.29686 (4.32613)
Comm time (%) = 0.00569272 (0.0829599)
Outpt time (%) = 0.000731707 (0.0106631)
Other time (%) = 0.8483 (12.3623)
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: 71389 ave 71389 max 71389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 71389
Ave neighs/atom = 8.76907
Neighbor list builds = 100
Dangerous builds = 0

138
examples/crack/log.crack.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 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 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
run 5000
Memory usage per processor = 2.06601 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917
200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331
400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288
600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131
800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512
1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575
1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488
1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358
1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607
1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591
2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463
2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559
2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932
2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997
2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245
3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862
3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322
3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205
3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656
3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143
4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799
4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135
4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075
4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
Loop time of 1.93628 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 1.46785 (75.8079)
Neigh time (%) = 0.0816418 (4.21643)
Comm time (%) = 0.13282 (6.85954)
Outpt time (%) = 0.000654757 (0.0338153)
Other time (%) = 0.253311 (13.0823)
Nlocal: 2035.25 ave 2064 max 2015 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 198 ave 248 max 150 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 17850 ave 18247 max 17601 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 71400
Ave neighs/atom = 8.77042
Neighbor list builds = 106
Dangerous builds = 0

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examples/dipole/log.dipole.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style lj/cut/dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
#dump 1 all custom 500 dump.dipole id type x y z mux muy
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 3.28197 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019973 -2.7914873 0.22407026 -2.4032386 -0.40914143
2500 0.40242274 -2.8142159 0.24281467 -2.4138053 -0.3391299
3000 0.42771065 -2.8535488 0.25848739 -2.4279767 -0.2500108
3500 0.44706195 -2.7890555 0.18446345 -2.3442289 -0.1005632
4000 0.4041733 -2.7741037 0.22161024 -2.3719512 -0.13373446
4500 0.47549052 -2.8368758 0.21740299 -2.3637627 -0.14246916
5000 0.42071015 -2.7518085 0.20821432 -2.3332019 -0.047522754
5500 0.43520504 -2.8042986 0.24366805 -2.3712696 -0.22180582
6000 0.42802195 -2.7822398 0.24060881 -2.3563579 -0.35350862
6500 0.4479767 -2.8175363 0.25806495 -2.3717994 0.07885849
7000 0.39538519 -2.7246562 0.23766993 -2.331248 -0.098542228
7500 0.40716663 -2.7115371 0.21917238 -2.3064063 -0.14844207
8000 0.42814546 -2.7318282 0.23188976 -2.3058235 -0.37209482
8500 0.46175735 -2.7607768 0.23020837 -2.3013282 -0.33381513
9000 0.48360992 -2.758533 0.21927619 -2.2773411 -0.016767257
9500 0.47646809 -2.7812073 0.24046809 -2.3071216 -0.12582235
10000 0.48207466 -2.7437285 0.20973254 -2.2640642 0.51612253
Loop time of 1.03017 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 0.838452 (81.3899)
Neigh time (%) = 0.03585 (3.48002)
Comm time (%) = 0.0484488 (4.703)
Outpt time (%) = 0.000171423 (0.0166403)
Other time (%) = 0.107245 (10.4105)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1673 ave 1673 max 1673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1673
Ave neighs/atom = 8.365
Neighbor list builds = 679
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style lj/cut/dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
#dump 1 all custom 500 dump.dipole id type x y z mux muy
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 3.2813 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019968 -2.7914873 0.22407029 -2.4032386 -0.4091395
2500 0.40237391 -2.8138968 0.24276582 -2.4135348 -0.33901619
3000 0.42595202 -2.8621684 0.26812111 -2.4383462 -0.19493812
3500 0.41153448 -2.8070419 0.23860803 -2.397565 -0.032395966
4000 0.40867238 -2.7790568 0.22331133 -2.3724278 0.014462986
4500 0.39803378 -2.7718651 0.23536245 -2.3758215 -0.25429533
5000 0.42736901 -2.8476039 0.2824171 -2.4223718 0.12187395
5500 0.41115816 -2.7810177 0.24508517 -2.3719153 -0.1925336
6000 0.43184788 -2.8015292 0.24726776 -2.3718406 -0.014489672
6500 0.45955478 -2.8340069 0.26105652 -2.3767499 -0.16015969
7000 0.43826613 -2.7488226 0.20031236 -2.3127478 0.071480756
7500 0.45738321 -2.7892162 0.23337255 -2.3341199 -0.17245012
8000 0.46107991 -2.7322063 0.18569571 -2.2734318 -0.21563894
8500 0.40367385 -2.7623279 0.27023252 -2.3606724 -0.038576129
9000 0.43104207 -2.7672424 0.25452132 -2.3383555 0.044351007
9500 0.38924411 -2.7231541 0.24926613 -2.3358562 -0.21910634
10000 0.44421944 -2.7677489 0.23376321 -2.3257506 0.034770807
Loop time of 0.443194 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.217619 (49.1024)
Neigh time (%) = 0.00970978 (2.19086)
Comm time (%) = 0.157952 (35.6394)
Outpt time (%) = 0.000405192 (0.0914255)
Other time (%) = 0.0575083 (12.9759)
Nlocal: 50 ave 55 max 41 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 87.75 ave 92 max 78 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 415 ave 481 max 301 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 1660
Ave neighs/atom = 8.3
Neighbor list builds = 671
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 512 27
Memory usage per processor = 7.97163 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 2.14577e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 203708 ave 203708 max 203708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 392 12
Memory usage per processor = 6.52754 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
Loop time of 5.24521e-06 on 4 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 5.24521e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 50927 ave 55516 max 46073 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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LAMMPS (1 Feb 2014)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 1 by 1 MPI processor grid
reading atoms ...
2000 atoms
reading velocities ...
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
#dump id all atom 100 dump.eim
#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Na Cl
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Na Cl
run 500
Memory usage per processor = 2.19121 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
Loop time of 5.87275 on 1 procs for 500 steps with 2000 atoms
Pair time (%) = 5.39652 (91.8909)
Neigh time (%) = 0.377995 (6.43642)
Comm time (%) = 0.023782 (0.404955)
Outpt time (%) = 0.000288486 (0.00491229)
Other time (%) = 0.0741594 (1.26277)
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4194 ave 4194 max 4194 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99537 ave 99537 max 99537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99537
Ave neighs/atom = 49.7685
Neighbor list builds = 89
Dangerous builds = 10

72
examples/eim/log.eim.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 2 by 2 MPI processor grid
reading atoms ...
2000 atoms
reading velocities ...
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
#dump id all atom 100 dump.eim
#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Na Cl
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Na Cl
run 500
Memory usage per processor = 1.87327 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
Loop time of 1.52681 on 4 procs for 500 steps with 2000 atoms
Pair time (%) = 1.36826 (89.6153)
Neigh time (%) = 0.0933943 (6.11695)
Comm time (%) = 0.0370625 (2.42744)
Outpt time (%) = 0.000231683 (0.0151743)
Other time (%) = 0.0278663 (1.82513)
Nlocal: 500 ave 501 max 498 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2179.25 ave 2182 max 2175 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 24884.2 ave 25164 max 24622 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 99537
Ave neighs/atom = 49.7685
Neighbor list builds = 89
Dangerous builds = 10

163
examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
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
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.4108 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
Loop time of 0.725952 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.503768 (69.3941)
Neigh time (%) = 0.0126507 (1.74264)
Comm time (%) = 0.0136161 (1.87562)
Outpt time (%) = 0.000351191 (0.0483765)
Other time (%) = 0.195566 (26.9393)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 232 ave 232 max 232 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2868 ave 2868 max 2868 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.42095 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981994 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222377 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099841 1187.4615
2500 2.0866909 -3.2692047 -1.1766063 0.67971438 1187.4615
2600 2.0982853 -3.2774461 -1.1869918 0.9045362 1187.4615
2700 2.0482743 -3.2229418 -1.1928883 0.69426343 1187.4615
2800 1.9676269 -3.1400321 -1.1685787 0.7578428 1187.4615
2900 2.0421127 -3.2182014 -1.1866875 0.79386471 1187.4615
3000 2.1074286 -3.2870176 -1.2012732 0.18871121 1187.4615
3100 2.0466481 -3.2227223 -1.1821678 0.70482646 1187.4615
3200 2.1159694 -3.2976371 -1.1588561 0.52105755 1187.4615
3300 2.150544 -3.3366154 -1.179448 0.45837229 1187.4615
3400 2.1035378 -3.2868896 -1.1614884 0.72339226 1187.4615
3500 2.0665964 -3.2481259 -1.1351878 0.77887358 1187.4615
3600 2.0079794 -3.183204 -1.1647668 0.49419048 1187.4615
3700 2.0028597 -3.1740178 -1.1738107 0.38011763 1187.4615
3800 1.9501131 -3.1191211 -1.1785414 0.77609881 1187.4615
3900 2.0648034 -3.2412864 -1.1750708 0.55412858 1187.4615
4000 2.0161932 -3.1865719 -1.1939133 0.6656145 1187.4615
Loop time of 0.763192 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.621734 (81.4649)
Neigh time (%) = 0.0058322 (0.764184)
Comm time (%) = 0.0142851 (1.87175)
Outpt time (%) = 0.000369549 (0.0484215)
Other time (%) = 0.120971 (15.8507)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 220 ave 220 max 220 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2901 ave 2901 max 2901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2901
Ave neighs/atom = 7.2525
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

163
examples/ellipse/log.ellipse.gayberne.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
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
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.39986 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.9525477 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
Loop time of 0.247263 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.132236 (53.4797)
Neigh time (%) = 0.00340456 (1.3769)
Comm time (%) = 0.0404702 (16.3672)
Outpt time (%) = 0.000372708 (0.150733)
Other time (%) = 0.0707802 (28.6254)
Nlocal: 100 ave 113 max 79 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 139.75 ave 151 max 132 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 717 ave 880 max 487 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.4007 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981993 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222388 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099822 1187.4615
2500 2.0866909 -3.2692048 -1.1766063 0.67971376 1187.4615
2600 2.098286 -3.2774469 -1.1869922 0.90453433 1187.4615
2700 2.0482737 -3.2229412 -1.1928882 0.69426669 1187.4615
2800 1.9676254 -3.1400305 -1.1685788 0.75785389 1187.4615
2900 2.0421207 -3.2182098 -1.1866861 0.79382733 1187.4615
3000 2.1074356 -3.2870234 -1.2012809 0.18867661 1187.4615
3100 2.0466079 -3.2226774 -1.1821925 0.7048821 1187.4615
3200 2.1158976 -3.2976855 -1.1589624 0.5209376 1187.4615
3300 2.1508115 -3.3368934 -1.1793489 0.45871464 1187.4615
3400 2.1046063 -3.2881336 -1.1615171 0.71895972 1187.4615
3500 2.066052 -3.2475413 -1.1359344 0.77760912 1187.4615
3600 2.0042504 -3.1791312 -1.1647191 0.50555439 1187.4615
3700 1.9888544 -3.1596354 -1.1679759 0.4059197 1187.4615
3800 1.9919683 -3.1636959 -1.1860197 0.70259722 1187.4615
3900 2.056542 -3.2325648 -1.1700712 0.43059703 1187.4615
4000 1.9958145 -3.1666798 -1.2556316 0.87469089 1187.4615
Loop time of 0.272762 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.159981 (58.6524)
Neigh time (%) = 0.00155282 (0.569295)
Comm time (%) = 0.0710112 (26.0341)
Outpt time (%) = 0.000505924 (0.185482)
Other time (%) = 0.0397106 (14.5587)
Nlocal: 100 ave 118 max 69 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 139 ave 156 max 130 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 729.75 ave 951 max 409 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 2919
Ave neighs/atom = 7.2975
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

160
examples/ellipse/log.ellipse.resquared.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 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
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.4108 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 1.42748 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.20681 (84.541)
Neigh time (%) = 0.0122275 (0.856581)
Comm time (%) = 0.0100107 (0.701285)
Outpt time (%) = 0.000345707 (0.024218)
Other time (%) = 0.198091 (13.8769)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 207 ave 207 max 207 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1886 ave 1886 max 1886 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.41282 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
2600 1.9450942 0.15744768 2.0838764 1.2106282 1657.9242
2700 1.9229729 0.18066635 2.1170011 1.3384024 1657.9242
2800 1.9512215 0.15099705 2.0988077 1.2134331 1657.9242
2900 1.9211263 0.18279158 2.0994515 1.3620719 1657.9242
3000 1.9067872 0.19775144 2.0931298 1.4157496 1657.9242
3100 1.9114595 0.19296361 2.1126574 1.4113475 1657.9242
3200 1.9427389 0.15998511 2.0865325 1.3075162 1657.9242
3300 1.9111626 0.19317346 2.1216597 1.430974 1657.9242
3400 1.9538368 0.14833057 2.1210144 1.2276261 1657.9242
3500 1.9244329 0.17929291 2.0825169 1.3186835 1657.9242
3600 1.9511869 0.15107062 2.1197982 1.2271623 1657.9242
3700 1.9369647 0.16601964 2.0970193 1.2813174 1657.9242
3800 1.9418163 0.16093067 2.1231369 1.2354415 1657.9242
3900 1.9450511 0.15759761 2.1394612 1.2392 1657.9242
4000 1.9350034 0.1681995 2.1142685 1.2676915 1657.9242
Loop time of 2.43595 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 2.29204 (94.0923)
Neigh time (%) = 0.00481176 (0.197532)
Comm time (%) = 0.0134215 (0.550978)
Outpt time (%) = 0.000373363 (0.0153272)
Other time (%) = 0.125302 (5.14388)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 209 ave 209 max 209 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

160
examples/ellipse/log.ellipse.resquared.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 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
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.39986 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 0.435333 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.307563 (70.65)
Neigh time (%) = 0.00319058 (0.732905)
Comm time (%) = 0.0498152 (11.443)
Outpt time (%) = 0.00043124 (0.0990598)
Other time (%) = 0.0743331 (17.075)
Nlocal: 100 ave 109 max 96 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 116 ave 120 max 109 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 471.5 ave 499 max 455 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.4007 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
2800 1.9512215 0.15099706 2.0988077 1.2134331 1657.9242
2900 1.9211263 0.18279161 2.0994515 1.362072 1657.9242
3000 1.9067874 0.19775131 2.0931298 1.415749 1657.9242
3100 1.9114597 0.1929634 2.1126573 1.4113467 1657.9242
3200 1.9427391 0.15998497 2.0865325 1.3075156 1657.9242
3300 1.9111628 0.19317321 2.1216596 1.4309722 1657.9242
3400 1.9538367 0.14833072 2.1210148 1.2276275 1657.9242
3500 1.9244321 0.17929374 2.0825174 1.3186878 1657.9242
3600 1.9511866 0.15107093 2.1197989 1.2271649 1657.9242
3700 1.9369592 0.16602536 2.0970215 1.2813456 1657.9242
3800 1.9418194 0.16092741 2.1231381 1.2354327 1657.9242
3900 1.9450474 0.15760145 2.1394611 1.2392217 1657.9242
4000 1.9350001 0.16820285 2.114271 1.2677094 1657.9242
Loop time of 0.68978 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.582906 (84.5062)
Neigh time (%) = 0.0012635 (0.183174)
Comm time (%) = 0.0669423 (9.70488)
Outpt time (%) = 0.000495672 (0.0718595)
Other time (%) = 0.0381718 (5.53392)
Nlocal: 100 ave 107 max 97 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 117.5 ave 121 max 115 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 475.75 ave 511 max 446 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

130
examples/flow/log.flow.couette.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# 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
# Poiseuille 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
#dump_modify 3 pad 5
run 10000
Memory usage per processor = 2.05833 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286
1000 1 -0.42965445 0 0.28225032 2.9612165 571.54286
1500 1.0739874 -0.41189772 0 0.35267901 2.5621951 571.54286
2000 1 -0.40814276 0 0.303762 2.9229578 571.54286
2500 1.193111 -0.38495952 0 0.46442186 2.8338993 571.54286
3000 1 -0.45584623 0 0.25605853 2.6569248 571.54286
3500 0.98858828 -0.44619629 0 0.25758441 2.6526913 571.54286
4000 1 -0.43273535 0 0.27916941 2.4570212 571.54286
4500 1.0805289 -0.34947719 0 0.41975647 2.5797635 571.54286
5000 1 -0.44623035 0 0.26567441 2.3488673 571.54286
5500 1.0821688 -0.41710054 0 0.35330058 2.6341553 571.54286
6000 1 -0.435398 0 0.27650676 2.496566 571.54286
6500 1.0788214 -0.46009514 0 0.30792295 2.3714035 571.54286
7000 1 -0.46345696 0 0.2484478 2.5780441 571.54286
7500 1.0331063 -0.436765 0 0.29870828 2.2415868 571.54286
8000 1 -0.42418776 0 0.287717 2.3469791 571.54286
8500 1.0898295 -0.42615905 0 0.3496958 2.6162262 571.54286
9000 1 -0.42341477 0 0.28849 2.5134824 571.54286
9500 1.0851884 -0.4442208 0 0.32833001 2.4872143 571.54286
10000 1 -0.39800556 0 0.3138992 2.5008138 571.54286
Loop time of 0.281453 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.123218 (43.7794)
Neigh time (%) = 0.0488372 (17.3518)
Comm time (%) = 0.00895357 (3.1812)
Outpt time (%) = 0.000183105 (0.0650572)
Other time (%) = 0.100261 (35.6226)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 943 ave 943 max 943 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 943
Ave neighs/atom = 2.24524
Neighbor list builds = 983
Dangerous builds = 0

130
examples/flow/log.flow.couette.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# 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
# Poiseuille 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
#dump_modify 3 pad 5
run 10000
Memory usage per processor = 2.06206 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286
1000 1 -0.3731019 0 0.33880286 2.8561715 571.54286
1500 1.0366879 -0.36031105 0 0.37771198 3.0196355 571.54286
2000 1 -0.41052955 0 0.30137522 2.865194 571.54286
2500 1.1228407 -0.37042187 0 0.4289338 2.9445246 571.54286
3000 1 -0.38445444 0 0.32745032 2.5935182 571.54286
3500 0.9837004 -0.45271556 0 0.24758544 2.7982195 571.54286
4000 1 -0.39733214 0 0.31457262 2.5610834 571.54286
4500 1.1185501 -0.40471335 0 0.39158777 2.4136693 571.54286
5000 1 -0.41474863 0 0.29715613 2.5475686 571.54286
5500 1.0417966 -0.3742507 0 0.36740927 2.4667154 571.54286
6000 1 -0.45012825 0 0.26177652 2.569894 571.54286
6500 1.1544519 -0.3964682 0 0.42539161 2.5635202 571.54286
7000 1 -0.44665963 0 0.26524513 2.4335307 571.54286
7500 0.97729968 -0.47377977 0 0.22196453 2.7482936 571.54286
8000 1 -0.42864525 0 0.28325951 2.3927949 571.54286
8500 1.0967901 -0.40513897 0 0.37567113 2.612602 571.54286
9000 1 -0.3847711 0 0.32713366 2.6900106 571.54286
9500 1.0085423 -0.4393538 0 0.27863229 2.4411599 571.54286
10000 1 -0.44847346 0 0.26343131 2.4997148 571.54286
Loop time of 0.163524 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0304542 (18.6237)
Neigh time (%) = 0.0127853 (7.81863)
Comm time (%) = 0.0743965 (45.4959)
Outpt time (%) = 0.00036943 (0.225918)
Other time (%) = 0.0455183 (27.8359)
Nlocal: 105 ave 115 max 94 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 40.25 ave 43 max 39 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 235.75 ave 297 max 170 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 943
Ave neighs/atom = 2.24524
Neighbor list builds = 965
Dangerous builds = 0

130
examples/flow/log.flow.pois.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# 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
# Poiseuille 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 10000
Memory usage per processor = 2.05833 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806
1000 1 -0.34609791 0 0.36580685 1.9736175 584.67179
1500 1.2112861 -0.39062708 0 0.47169327 1.521881 587.24778
2000 1 -0.39956949 0 0.31233527 1.2496669 583.00676
2500 1.2236323 -0.40128446 0 0.46982521 1.4276891 570.03729
3000 1 -0.48849341 0 0.22341135 1.5091366 553.64637
3500 1.2404531 -0.63017461 0 0.25290984 1.7681313 535.22607
4000 1 -0.71551407 0 -0.003609313 2.2075137 516.73151
4500 1.2253143 -0.76279415 0 0.10951296 2.6154841 503.20466
5000 1 -0.79031519 0 -0.078410425 3.0914492 499.10917
5500 1.2025432 -0.74031121 0 0.115785 2.5889437 502.17138
6000 1 -0.64454518 0 0.067359583 2.0907022 510.47702
6500 1.2112733 -0.65703634 0 0.20527486 2.054449 515.41213
7000 1 -0.61856581 0 0.093338954 1.9843361 516.79512
7500 1.2212907 -0.67431193 0 0.19513077 1.9939559 517.17301
8000 1 -0.69966668 0 0.012238083 2.1559293 510.52934
8500 1.2245982 -0.73461969 0 0.13717758 2.4482542 506.2679
9000 1 -0.697338 0 0.014566762 2.4757604 503.86953
9500 1.1882 -0.66622491 0 0.17966032 2.3295348 505.67684
10000 1 -0.70364194 0 0.008262826 2.218568 507.64681
Loop time of 0.325207 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.13604 (41.8317)
Neigh time (%) = 0.0279303 (8.58846)
Comm time (%) = 0.00756764 (2.32702)
Outpt time (%) = 0.00018692 (0.0574773)
Other time (%) = 0.153482 (47.1953)
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: 1116 ave 1116 max 1116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1116
Ave neighs/atom = 2.65714
Neighbor list builds = 563
Dangerous builds = 0

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examples/flow/log.flow.pois.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# 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
# Poiseuille 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 10000
Memory usage per processor = 2.06206 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659
1000 1 -0.35701441 0 0.35489035 2.0575313 585.71407
1500 1.2368663 -0.37709732 0 0.50343367 1.4865879 587.193
2000 1 -0.39362939 0 0.31827537 1.4236 578.9418
2500 1.2272957 -0.423819 0 0.44989866 1.454461 570.15856
3000 1 -0.49143403 0 0.22047073 1.5345951 554.98633
3500 1.2444908 -0.59761803 0 0.28834092 1.875379 537.01606
4000 1 -0.70133161 0 0.010573147 2.1395416 521.46845
4500 1.2212352 -0.74763375 0 0.1217694 2.7598268 507.63512
5000 1 -0.7889135 0 -0.077008742 2.9809426 501.21601
5500 1.1965673 -0.78262115 0 0.069220825 2.8192028 505.3984
6000 1 -0.71434201 0 -0.0024372499 2.346053 512.05291
6500 1.203859 -0.67621716 0 0.18081576 2.1621043 518.624
7000 1 -0.66493592 0 0.046968842 1.8459166 519.01312
7500 1.2065975 -0.69903932 0 0.15994317 2.0439995 515.42888
8000 1 -0.71320172 0 -0.0012969589 2.1303566 511.98833
8500 1.2146567 -0.72062191 0 0.144098 2.4268382 504.80659
9000 1 -0.74806158 0 -0.036156822 2.5758196 502.43487
9500 1.1970932 -0.73220717 0 0.1200092 2.585169 504.06803
10000 1 -0.71105178 0 0.00085297794 2.3528576 507.92052
Loop time of 0.221735 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0346093 (15.6084)
Neigh time (%) = 0.0078088 (3.52168)
Comm time (%) = 0.0817159 (36.8529)
Outpt time (%) = 0.000392079 (0.176823)
Other time (%) = 0.097209 (43.8402)
Nlocal: 105 ave 107 max 103 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 42.75 ave 46 max 37 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 276.5 ave 295 max 257 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 1106
Ave neighs/atom = 2.63333
Neighbor list builds = 564
Dangerous builds = 0

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examples/friction/log.friction.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 MPI 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 112 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
862 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
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# 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
fix 4 all enforce2d
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.friction
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 20000
Memory usage per processor = 2.05872 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.1 -3.0915465 0 -3.0503052 0.010015559 2444.9333
2000 0.1 -3.0826487 0 -3.0414074 -0.42012889 2444.9333
3000 0.089819692 -3.07584 0 -3.0387972 -0.25252108 2444.9333
4000 0.098489874 -3.0667093 0 -3.0260907 -0.25506538 2444.9333
5000 0.11379986 -3.0557087 0 -3.0087762 -0.080871179 2444.9333
6000 0.11269179 -3.04532 0 -2.9988445 -0.33381202 2444.9333
7000 0.1 -3.0380598 0 -2.9968185 -0.32423909 2444.9333
8000 0.1 -3.0346453 0 -2.993404 -0.38015347 2444.9333
9000 0.1 -3.0324305 0 -2.9911892 -0.42940009 2444.9333
10000 0.11811429 -3.0334969 0 -2.984785 -0.32538147 2444.9333
11000 0.11627653 -3.0344827 0 -2.9865288 -0.45037424 2444.9333
12000 0.11250787 -3.0472157 0 -3.000816 -0.27347069 2444.9333
13000 0.11429889 -3.0455404 0 -2.9984021 -0.28832736 2444.9333
14000 0.11292741 -3.0466673 0 -3.0000946 -0.38939496 2444.9333
15000 0.11239299 -3.0460428 0 -2.9996905 -0.35437935 2444.9333
16000 0.11775554 -3.0457709 0 -2.997207 -0.14263984 2444.9333
17000 0.11456908 -3.0459128 0 -2.998663 -0.3686153 2444.9333
18000 0.1165453 -3.0454305 0 -2.9973657 -0.3572725 2444.9333
19000 0.11403056 -3.0440495 0 -2.9970218 -0.25462158 2444.9333
20000 0.11801421 -3.0462201 0 -2.9975495 -0.23484136 2444.9333
Loop time of 5.81332 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 4.61616 (79.4065)
Neigh time (%) = 0.319022 (5.48777)
Comm time (%) = 0.0435834 (0.749715)
Outpt time (%) = 0.000309229 (0.00531931)
Other time (%) = 0.834251 (14.3507)
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 147 ave 147 max 147 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14384 ave 14384 max 14384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14384
Ave neighs/atom = 8.34339
Neighbor list builds = 723
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
2 by 2 by 1 MPI 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 112 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
862 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
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# 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
fix 4 all enforce2d
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 500 dump.friction
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 20000
Memory usage per processor = 2.06213 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.081958665 -3.0927273 0 -3.0589265 -0.021846131 2444.9333
2000 0.082641883 -3.0850764 0 -3.0509938 -0.44960195 2444.9333
3000 0.092293442 -3.0748001 0 -3.0367371 -0.25353161 2444.9333
4000 0.096012911 -3.0565129 0 -3.0169159 -0.027669541 2444.9333
5000 0.1 -3.0465555 0 -3.0053142 -0.099323956 2444.9333
6000 0.11642983 -3.0390782 0 -2.991061 -0.21034609 2444.9333
7000 0.11597774 -3.0331763 0 -2.9853456 -0.46345898 2444.9333
8000 0.11937899 -3.0305561 0 -2.9813226 -0.30773083 2444.9333
9000 0.111108 -3.0274067 0 -2.9815843 -0.5243749 2444.9333
10000 0.11666452 -3.0170603 0 -2.9689463 -0.37436916 2444.9333
11000 0.11005147 -3.0140407 0 -2.9686541 -0.46293236 2444.9333
12000 0.11286668 -3.0174735 0 -2.9709258 -0.28406396 2444.9333
13000 0.11280782 -3.0238036 0 -2.9772802 -0.41208934 2444.9333
14000 0.1 -3.0332072 0 -2.9919659 -0.1785001 2444.9333
15000 0.1148413 -3.0339717 0 -2.9866096 -0.4418584 2444.9333
16000 0.11194137 -3.0322089 0 -2.9860428 -0.29354474 2444.9333
17000 0.10699902 -3.0395654 0 -2.9954376 -0.37176577 2444.9333
18000 0.11091428 -3.0400366 0 -2.9942941 -0.19329155 2444.9333
19000 0.1094118 -3.0432032 0 -2.9980803 -0.38516174 2444.9333
20000 0.11137857 -3.0442022 0 -2.9982683 -0.37419199 2444.9333
Loop time of 1.88423 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 1.16936 (62.0606)
Neigh time (%) = 0.0789706 (4.19113)
Comm time (%) = 0.359838 (19.0974)
Outpt time (%) = 0.00038904 (0.0206471)
Other time (%) = 0.275667 (14.6302)
Nlocal: 431 ave 493 max 377 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 96 ave 125 max 77 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 3596 ave 4228 max 3139 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 14384
Ave neighs/atom = 8.34339
Neighbor list builds = 700
Dangerous builds = 0

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examples/hugoniostat/log.hugoniostat.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.80047 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4827806e-13 -4.9289339e-13 -4.9887818e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0800641 on 1 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.85376e-10
Force max component initial, final = 1960.27 3.43538e-10
Final line search alpha, max atom move = 1 3.43538e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0630546 (78.7551)
Neigh time (%) = 0.00099206 (1.23908)
Comm time (%) = 0.00194621 (2.43082)
Outpt time (%) = 2.00272e-05 (0.0250139)
Other time (%) = 0.0140512 (17.5499)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

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LAMMPS (1 Feb 2014)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.77703 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4436885e-13 -4.8889278e-13 -4.8955934e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0301411 on 4 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.75073e-10
Force max component initial, final = 1960.27 3.37121e-10
Final line search alpha, max atom move = 1 3.37121e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0164203 (54.4781)
Neigh time (%) = 0.000260174 (0.863187)
Comm time (%) = 0.00554258 (18.3888)
Outpt time (%) = 2.22921e-05 (0.0739592)
Other time (%) = 0.00789577 (26.196)
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6445 max 4305 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
# 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
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 250 dump.indent
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 30000
Memory usage per processor = 2.05408 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771
2000 0.12086797 -3.0886512 0 -2.9853378 -0.39883289 444.3556
3000 0.11671309 -3.0840074 0 -2.9842455 -0.34859991 442.95428
4000 0.12339115 -3.1000529 0 -2.9945828 -0.049696765 438.99297
5000 0.10860594 -3.0866045 0 -2.9937722 -0.47973882 443.99855
6000 0.11839788 -3.0929689 0 -2.9917669 -0.033454196 442.70339
7000 0.12194527 -3.0835584 0 -2.9793242 -0.13981611 443.36261
8000 0.11671309 -3.0862884 0 -2.9865265 0.073952568 441.71327
9000 0.12449823 -3.0880806 0 -2.9816643 0.28647997 439.28167
10000 0.12475263 -3.0830722 0 -2.9764384 0.38101457 440.50309
11000 0.11198118 -3.0743549 0 -2.9786377 0.67583952 438.50252
12000 0.10823034 -3.0621355 0 -2.9696244 0.66485024 441.13781
13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805
14000 0.12310403 -3.051382 0 -2.9461573 0.87077702 445.54011
15000 0.11148462 -3.0402208 0 -2.944928 1.0040645 451.90788
16000 0.12322336 -3.041552 0 -2.9362254 0.75818853 456.90372
17000 0.12311108 -3.0300339 0 -2.9248033 1.0483106 452.91666
18000 0.12062525 -3.0261654 0 -2.9230595 1.3983603 451.71885
19000 0.11959317 -3.0143074 0 -2.9120838 1.3960468 457.92611
20000 0.122338 -3.001592 0 -2.8970221 1.1237176 470.12398
21000 0.1209773 -3.028491 0 -2.9250842 0.76640926 472.90657
22000 0.11587369 -3.0270707 0 -2.9280263 0.5800164 474.83158
23000 0.11060033 -3.0277028 0 -2.9331659 0.96792829 471.43258
24000 0.11282983 -3.0192428 0 -2.9228001 1.3053189 467.06167
25000 0.11096642 -3.0068579 0 -2.912008 1.4340346 468.26071
26000 0.12109501 -3.0023534 0 -2.898846 1.2871412 469.14748
27000 0.12624077 -3.0033907 0 -2.8954849 1.3874279 469.76742
28000 0.1267503 -3.0016483 0 -2.893307 1.4306934 469.29832
29000 0.11992821 -2.9799464 0 -2.8774363 1.4301585 478.04046
30000 0.1193433 -2.9677931 0 -2.865783 1.7313522 478.97844
Loop time of 2.34072 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.74973 (74.752)
Neigh time (%) = 0.0712562 (3.0442)
Comm time (%) = 0.0313151 (1.33784)
Outpt time (%) = 0.000312567 (0.0133535)
Other time (%) = 0.488101 (20.8526)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 110 ave 110 max 110 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3703 ave 3703 max 3703 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3703
Ave neighs/atom = 8.81667
Neighbor list builds = 619
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.05417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.1193433 -2.9677931 0 -2.865783 1.728905 479.6564
31000 0.10869597 -3.0331255 0 -2.9402164 -0.36614133 491.53109
32000 0.11671309 -3.003635 0 -2.903873 -0.37717771 490.3049
33000 0.11357386 -3.0277987 0 -2.9307201 0.46609243 478.52907
34000 0.11325318 -3.0277136 0 -2.9309091 0.14887789 487.01132
35000 0.11614873 -3.0302671 0 -2.9309876 -0.36332093 487.84102
36000 0.11196694 -3.0411493 0 -2.9454442 -0.067640849 486.96511
37000 0.12006386 -3.0481451 0 -2.945519 -0.23342373 480.40191
38000 0.11842139 -3.0466238 0 -2.9454017 -0.34243775 488.71437
39000 0.1198706 -3.0605588 0 -2.9580979 -0.19385979 484.35217
40000 0.11191157 -3.0647812 0 -2.9691234 -0.48040337 491.82885
41000 0.11291708 -3.065682 0 -2.9691648 -0.2494499 487.47298
42000 0.12242643 -3.0738126 0 -2.9691672 -0.36376783 487.84689
43000 0.12095077 -3.0725493 0 -2.9691652 -0.36977815 488.33432
44000 0.11671309 -3.0789107 0 -2.9791488 -0.22354617 486.65601
45000 0.11671309 -3.0688305 0 -2.9690686 -0.25626357 486.86098
46000 0.12233634 -3.0703788 0 -2.9658103 -0.26550413 487.14029
47000 0.11077381 -3.0604929 0 -2.9658077 -0.1338011 487.70423
48000 0.11616048 -3.0761007 0 -2.9768111 -0.26861141 487.1961
49000 0.11232937 -3.0728268 0 -2.976812 -0.27614358 488.13299
50000 0.11890619 -3.0784515 0 -2.9768151 -0.35807475 488.7576
51000 0.1139473 -3.0742097 0 -2.9768119 -0.3599846 488.14034
52000 0.11570005 -3.0757089 0 -2.9768129 -0.20273147 488.2635
53000 0.11622085 -3.0761556 0 -2.9768145 -0.29363039 485.22966
54000 0.11721028 -3.0770006 0 -2.9768137 -0.35379322 486.02806
55000 0.11816386 -3.0778183 0 -2.9768164 -0.26890935 486.25412
56000 0.12138263 -3.0805663 0 -2.976813 -0.43809353 486.45992
57000 0.11368036 -3.0739797 0 -2.9768101 -0.3784405 487.68779
58000 0.12624247 -3.0714284 0 -2.9635212 -0.28330741 487.44043
59000 0.10749507 -3.0655101 0 -2.9736274 -0.30239742 490.08649
60000 0.11976607 -3.0760024 0 -2.9736309 -0.22323075 486.62515
Loop time of 2.11157 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.71606 (81.2693)
Neigh time (%) = 0.0706546 (3.34607)
Comm time (%) = 0.0320117 (1.51602)
Outpt time (%) = 0.000283957 (0.0134476)
Other time (%) = 0.292562 (13.8552)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3561 ave 3561 max 3561 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3561
Ave neighs/atom = 8.47857
Neighbor list builds = 629
Dangerous builds = 0

179
examples/indent/log.indent.1Feb14.linux.4
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@ -1,179 +0,0 @@
LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
60 settings made for type
# 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
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 250 dump.indent
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 30000
Memory usage per processor = 2.06074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732
2000 0.11519605 -3.0960246 0 -2.9975594 -0.38133491 442.33058
3000 0.11367906 -3.0839597 0 -2.9867912 -0.42579765 444.59119
4000 0.11618844 -3.0860897 0 -2.9867762 -0.041580916 439.84614
5000 0.11327789 -3.0848614 0 -2.9880358 -0.48898867 446.19202
6000 0.12058424 -3.0869438 0 -2.983873 0.011477134 440.56887
7000 0.11772522 -3.0833477 0 -2.9827207 -0.090378245 442.56787
8000 0.12533514 -3.0970033 0 -2.9898715 0.13263189 441.23478
9000 0.1198683 -3.0867062 0 -2.9842473 0.34046664 439.4706
10000 0.12234014 -3.0835007 0 -2.9789291 0.28399731 441.94307
11000 0.11082436 -3.0754796 0 -2.9807511 0.62194284 441.32012
12000 0.10842719 -3.0646379 0 -2.9719584 0.65383569 442.64668
13000 0.11686417 -3.0600388 0 -2.9601477 1.0041123 438.50135
14000 0.12557378 -3.0570017 0 -2.949666 0.85709167 442.10189
15000 0.11934084 -3.0498848 0 -2.9478768 1.0392199 451.74396
16000 0.12576904 -3.0452178 0 -2.9377152 1.3479499 441.27019
17000 0.11546522 -3.0348362 0 -2.936141 1.6318206 439.4846
18000 0.12148312 -3.0221147 0 -2.9182755 1.6088803 449.25447
19000 0.11884301 -3.0036771 0 -2.9020946 1.5201596 447.11858
20000 0.11165616 -3.0037969 0 -2.9083575 1.4074721 461.75507
21000 0.11360221 -2.9898243 0 -2.8927215 1.1326553 473.96356
22000 0.12149681 -3.024808 0 -2.9209571 0.78922351 473.43584
23000 0.11891429 -3.0140734 0 -2.91243 1.2020863 469.92437
24000 0.12003368 -3.0195801 0 -2.9169798 0.76069021 473.29691
25000 0.12286633 -3.0215711 0 -2.9165496 0.67406806 485.07199
26000 0.1177073 -3.0094446 0 -2.9088329 0.33348438 486.6152
27000 0.11671309 -3.0183329 0 -2.918571 0.70486163 484.63284
28000 0.12675659 -3.0429799 0 -2.9346332 0.66897197 483.34837
29000 0.1156808 -3.0381771 0 -2.9392975 0.56595774 485.98334
30000 0.11265389 -3.0300644 0 -2.9337722 0.97207041 485.94269
Loop time of 1.04821 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.450331 (42.9618)
Neigh time (%) = 0.01888 (1.80116)
Comm time (%) = 0.314544 (30.0076)
Outpt time (%) = 0.000509083 (0.0485668)
Other time (%) = 0.263949 (25.1809)
Nlocal: 105 ave 120 max 89 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 91.25 ave 99 max 83 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 900.5 ave 1089 max 720 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3602
Ave neighs/atom = 8.57619
Neighbor list builds = 616
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.06085 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11265389 -3.0300644 0 -2.9337722 0.97234223 485.80685
31000 0.11759958 -3.0552427 0 -2.954723 -0.45428585 489.01075
32000 0.1244223 -3.031587 0 -2.9252355 -0.55586882 497.58671
33000 0.11512011 -3.045739 0 -2.9473387 0.20493313 482.45319
34000 0.12011045 -3.0498103 0 -2.9471445 -0.20993642 490.60496
35000 0.12168423 -3.0402933 0 -2.9362822 -0.56627306 496.84137
36000 0.12206115 -3.054588 0 -2.9502548 0.024107079 488.42757
37000 0.1183082 -3.0513368 0 -2.9502114 -0.049466566 490.53247
38000 0.10909549 -3.043269 0 -2.9500183 -0.4203535 494.85852
39000 0.11529806 -3.0486455 0 -2.9500931 0.018737728 493.31601
40000 0.11343932 -3.0471365 0 -2.9501729 -0.22971202 492.54675
41000 0.11812961 -3.0411142 0 -2.9401415 -0.32514863 495.25905
42000 0.12105766 -3.0434615 0 -2.939986 -0.040665394 492.97267
43000 0.10525203 -3.0425539 0 -2.9525885 -0.16326985 494.40556
44000 0.10613869 -3.0431187 0 -2.9523954 -0.16981593 495.58301
45000 0.11561112 -3.0514123 0 -2.9525924 -0.17742887 493.63953
46000 0.11018146 -3.046615 0 -2.9524361 -0.32577677 498.4112
47000 0.10570042 -3.043205 0 -2.9528564 -0.14894466 491.63488
48000 0.11339264 -3.049744 0 -2.9528203 -0.09546935 491.51042
49000 0.10630296 -3.0434874 0 -2.9526237 -0.18683154 494.0362
50000 0.10854184 -3.0455192 0 -2.9527418 -0.23688088 495.39066
51000 0.10953314 -3.0512975 0 -2.9576727 -0.083732144 495.75424
52000 0.12374024 -3.0529561 0 -2.9471877 -0.32091022 494.47207
53000 0.11492903 -3.0453421 0 -2.9471052 -0.23510307 496.33496
54000 0.11401393 -3.0339003 0 -2.9364455 0.0060137449 496.63695
55000 0.11651709 -3.0359636 0 -2.9363692 -0.32187304 495.2289
56000 0.12583256 -3.0438852 0 -2.9363284 -0.18360885 495.28665
57000 0.11188382 -3.0423929 0 -2.9467589 -0.097898762 496.68295
58000 0.11603787 -3.045827 0 -2.9466422 -0.31359664 498.05865
59000 0.12070545 -3.0496657 0 -2.9464913 -0.17444968 494.22795
60000 0.11476903 -3.0445911 0 -2.9464909 -0.146398 493.56692
Loop time of 0.943008 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.442427 (46.9166)
Neigh time (%) = 0.0189115 (2.00544)
Comm time (%) = 0.326607 (34.6345)
Outpt time (%) = 0.000496209 (0.0526198)
Other time (%) = 0.154567 (16.3908)
Nlocal: 105 ave 121 max 86 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 92 ave 99 max 86 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 892.25 ave 1084 max 682 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 620
Dangerous builds = 0

404
examples/indent/log.indent.min.1Feb14.linux.1
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@ -1,404 +0,0 @@
LAMMPS (1 Feb 2014)
# 2d indenter simulation with minimization instead of dynamics
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 orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 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 group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
#dump 1 all atom 10 dump.indent
#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
60 0 -3.1906458 0 -3.1906458 -0.7837635 435.62268
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
74 0 -3.1908431 0 -3.1908431 -0.73877396 435.62268
Loop time of 0.0425239 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058073 -3.19084306284
Force two-norm initial, final = 6.74302 0.560627
Force max component initial, final = 1.46877 0.0659033
Final line search alpha, max atom move = 0.00643442 0.00042405
Iterations, force evaluations = 74 411
Pair time (%) = 0.037972 (89.2957)
Neigh time (%) = 0.000494957 (1.16395)
Comm time (%) = 0.000413179 (0.971641)
Outpt time (%) = 7.00951e-05 (0.164837)
Other time (%) = 0.00357366 (8.40388)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624129 -0.73807217 436.03689
80 0 -3.1521235 0 -3.1418193 -0.26103179 436.03693
90 0 -3.172501 0 -3.1715058 -0.36498503 436.19
100 0 -3.1770944 0 -3.1759303 -0.36782131 436.15772
110 0 -3.179003 0 -3.1778726 -0.34159509 436.07263
120 0 -3.1801625 0 -3.1792123 -0.29559493 435.77089
130 0 -3.1809815 0 -3.1802941 -0.20023556 434.9421
140 0 -3.181069 0 -3.180391 -0.1867988 434.23462
149 0 -3.1811854 0 -3.1804775 -0.17149229 434.62963
Loop time of 0.0426731 on 1 procs for 75 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241291025 -3.18047516326 -3.18047748467
Force two-norm initial, final = 1731.02 0.601744
Force max component initial, final = 1265.65 0.297585
Final line search alpha, max atom move = 0.00267208 0.000795171
Iterations, force evaluations = 75 368
Pair time (%) = 0.0337248 (79.0305)
Neigh time (%) = 0.00306416 (7.18053)
Comm time (%) = 0.000451803 (1.05875)
Outpt time (%) = 6.48499e-05 (0.151969)
Other time (%) = 0.00536752 (12.5782)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3584 ave 3584 max 3584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3584
Ave neighs/atom = 8.53333
Neighbor list builds = 27
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
149 0 -3.1811854 0 -0.18581133 -0.1714388 434.76522
150 0 -3.1643579 0 -0.9039795 0.013604142 434.76522
160 0 -2.9896502 0 -2.8476201 1.7049354 434.75857
170 0 -3.0638049 0 -3.0412807 1.3613793 434.71626
180 0 -3.0925759 0 -3.0805454 1.2078809 434.84134
190 0 -3.0992403 0 -3.0902396 1.1565899 435.28172
200 0 -3.1006774 0 -3.0922078 1.1563293 434.85279
210 0 -3.1021512 0 -3.0942343 1.1847386 433.5255
220 0 -3.1034865 0 -3.0957045 1.2437301 433.5255
Loop time of 0.0324862 on 1 procs for 71 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.185811329671 -3.09570333014 -3.0957044814
Force two-norm initial, final = 1763.73 6.22486
Force max component initial, final = 924.34 1.95519
Final line search alpha, max atom move = 1.23202e-05 2.40883e-05
Iterations, force evaluations = 71 282
Pair time (%) = 0.0262792 (80.8935)
Neigh time (%) = 0.00164843 (5.07423)
Comm time (%) = 0.000334263 (1.02894)
Outpt time (%) = 6.07967e-05 (0.187146)
Other time (%) = 0.0041635 (12.8162)
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: 3633 ave 3633 max 3633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3633
Ave neighs/atom = 8.65
Neighbor list builds = 14
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
220 0 -3.1034865 0 2.0778483 1.2452636 432.99162
230 0 -2.5109892 0 -2.3349564 6.16399 433.43161
240 0 -2.8436954 0 -2.7695635 3.9188746 440.0748
250 0 -2.8958915 0 -2.859753 3.5873163 443.3911
260 0 -2.9335258 0 -2.9180699 3.2586768 446.93395
270 0 -2.9587555 0 -2.9449067 3.0495207 450.7898
280 0 -2.9632665 0 -2.9508012 2.9704184 455.18424
290 0 -2.9663937 0 -2.9548266 2.9251605 455.18424
300 0 -2.9815499 0 -2.972728 2.690073 461.16274
310 0 -2.998615 0 -2.9900703 2.5025287 462.28498
320 0 -3.0171338 0 -3.0096079 2.2589518 464.76762
330 0 -3.066495 0 -3.0615455 1.6037908 468.05879
340 0 -3.0915645 0 -3.0882311 1.3314881 470.4116
350 0 -3.1067793 0 -3.1027465 1.1863784 468.66537
360 0 -3.111438 0 -3.1085634 1.133372 471.4241
370 0 -3.1144779 0 -3.1118395 1.0503928 471.4241
380 0 -3.1187534 0 -3.115652 0.89135021 473.74678
390 0 -3.1198286 0 -3.1164385 0.84502104 473.74678
400 0 -3.1202166 0 -3.1166667 0.82342171 474.96181
410 0 -3.1206604 0 -3.1169627 0.79018217 475.00074
418 0 -3.1207429 0 -3.1171141 0.77776922 473.85863
Loop time of 0.089386 on 1 procs for 198 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.07784826507 -3.11711145486 -3.11711413336
Force two-norm initial, final = 2348.2 0.758541
Force max component initial, final = 1038.98 0.227243
Final line search alpha, max atom move = 0.00310726 0.000706103
Iterations, force evaluations = 198 764
Pair time (%) = 0.0712759 (79.7395)
Neigh time (%) = 0.00549102 (6.14304)
Comm time (%) = 0.00098896 (1.10639)
Outpt time (%) = 0.000168562 (0.188578)
Other time (%) = 0.0114615 (12.8225)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 107 ave 107 max 107 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3612 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3612
Ave neighs/atom = 8.6
Neighbor list builds = 46
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74073 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
418 0 -3.1207429 0 4.5511735 0.77738319 474.09394
420 0 -3.0629926 0 1.9444704 1.3379171 473.98211
430 0 -2.6813506 0 -2.4214349 4.7277839 473.31189
440 0 -2.8631611 0 -2.7958919 3.6555407 477.0175
450 0 -2.9314239 0 -2.897992 3.1393288 481.94369
460 0 -2.9620386 0 -2.9480925 2.7967516 491.0709
470 0 -2.9748225 0 -2.9605783 2.6387787 491.13394
480 0 -2.984083 0 -2.9712966 2.5491081 491.9717
490 0 -2.9886661 0 -2.9779169 2.4836251 493.12793
500 0 -2.9929304 0 -2.9843848 2.4179024 493.50247
510 0 -3.0014663 0 -2.9928884 2.3117132 495.11638
520 0 -3.0255297 0 -3.0197482 2.0516501 496.59829
530 0 -3.0475992 0 -3.0428515 1.8691696 496.97347
540 0 -3.0552715 0 -3.0499976 1.7904182 496.00133
550 0 -3.061395 0 -3.0556631 1.6863886 495.72563
560 0 -3.0651 0 -3.0590723 1.6279321 495.24659
570 0 -3.0673019 0 -3.0610166 1.5949476 494.64061
580 0 -3.0687599 0 -3.0621893 1.5269488 497.3911
586 0 -3.0694654 0 -3.0627953 1.5123574 497.3911
Loop time of 0.0674939 on 1 procs for 168 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
4.55117353041 -3.06279311906 -3.06279529487
Force two-norm initial, final = 2972.98 2.60071
Force max component initial, final = 1399.42 0.742189
Final line search alpha, max atom move = 0.00013057 9.69073e-05
Iterations, force evaluations = 168 577
Pair time (%) = 0.0539668 (79.958)
Neigh time (%) = 0.0038271 (5.67028)
Comm time (%) = 0.00071764 (1.06327)
Outpt time (%) = 0.000156879 (0.232435)
Other time (%) = 0.00882554 (13.0761)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 118 ave 118 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3637 ave 3637 max 3637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3637
Ave neighs/atom = 8.65952
Neighbor list builds = 32
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74081 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
586 0 -3.0694654 0 -2.5610272 1.5148154 496.584
590 0 -2.9807015 0 -2.8962768 2.3098422 496.58447
600 0 -2.9891378 0 -2.966537 2.3737377 496.58482
610 0 -2.9927542 0 -2.9765217 2.3647514 496.68053
620 0 -3.0027846 0 -2.9911735 2.3024398 496.99879
630 0 -3.0120047 0 -3.0013041 2.2445443 497.3327
640 0 -3.0199795 0 -3.0109861 2.2085552 497.48784
650 0 -3.0252192 0 -3.0168447 2.1840453 497.61838
660 0 -3.0285753 0 -3.020419 2.1577783 498.09493
670 0 -3.032151 0 -3.0245432 2.1160278 498.75158
680 0 -3.0334423 0 -3.0260628 2.0715843 498.99145
690 0 -3.0348442 0 -3.0277896 2.0397454 499.38565
700 0 -3.0373291 0 -3.0303879 1.950985 499.35774
710 0 -3.0413907 0 -3.034156 1.8600169 501.53756
714 0 -3.0418366 0 -3.0343319 1.8536192 501.53756
Loop time of 0.060724 on 1 procs for 128 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.56102720477 -3.0343306266 -3.03433194949
Force two-norm initial, final = 485.313 7.6949
Force max component initial, final = 233.682 1.75894
Final line search alpha, max atom move = 0.000202561 0.000356292
Iterations, force evaluations = 128 518
Pair time (%) = 0.048727 (80.2434)
Neigh time (%) = 0.0034678 (5.71075)
Comm time (%) = 0.000708818 (1.16728)
Outpt time (%) = 0.000118494 (0.195135)
Other time (%) = 0.00770187 (12.6834)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 117 ave 117 max 117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3707 ave 3707 max 3707 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3707
Ave neighs/atom = 8.82619
Neighbor list builds = 29
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74081 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
714 0 -3.0418366 0 -2.5647674 1.8523771 501.87385
720 0 -2.9615831 0 -2.9005481 2.6557784 501.89551
730 0 -2.9642041 0 -2.9367288 2.732803 502.11719
740 0 -2.9666385 0 -2.9495445 2.7501461 501.9651
750 0 -2.972902 0 -2.9544262 2.6982499 501.913
760 0 -2.9761809 0 -2.9613793 2.7071736 501.90871
770 0 -2.9840571 0 -2.9666566 2.6500893 501.90871
780 0 -2.9871658 0 -2.9704099 2.6464522 501.59836
790 0 -2.9969968 0 -2.9807461 2.6151906 501.40924
800 0 -3.0051819 0 -2.9894906 2.5702395 501.37371
810 0 -3.0071904 0 -2.9916568 2.5671087 501.33912
820 0 -3.0079125 0 -2.9925277 2.5615763 502.01846
827 0 -3.0081656 0 -2.9928086 2.5580601 502.05698
Loop time of 0.0602961 on 1 procs for 113 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.56476735837 -2.99280857633 -2.9928086311
Force two-norm initial, final = 447.674 1.83102
Force max component initial, final = 195.835 0.221915
Final line search alpha, max atom move = 6.85287e-06 1.52076e-06
Iterations, force evaluations = 113 508
Pair time (%) = 0.0482583 (80.0356)
Neigh time (%) = 0.00370264 (6.14077)
Comm time (%) = 0.000731945 (1.21392)
Outpt time (%) = 0.000100374 (0.166469)
Other time (%) = 0.00750279 (12.4433)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 119 ave 119 max 119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3803 ave 3803 max 3803 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3803
Ave neighs/atom = 9.05476
Neighbor list builds = 31
Dangerous builds = 0

405
examples/indent/log.indent.min.1Feb14.linux.4
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@ -1,405 +0,0 @@
LAMMPS (1 Feb 2014)
# 2d indenter simulation with minimization instead of dynamics
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 orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 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 group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
#dump 1 all atom 10 dump.indent
#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
60 0 -3.1906458 0 -3.1906458 -0.78376348 435.62268
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
74 0 -3.1908431 0 -3.1908431 -0.73877366 435.62268
Loop time of 0.0168951 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058192 -3.19084306553
Force two-norm initial, final = 6.74302 0.560405
Force max component initial, final = 1.46877 0.0658777
Final line search alpha, max atom move = 0.00643452 0.000423891
Iterations, force evaluations = 74 411
Pair time (%) = 0.00975549 (57.7417)
Neigh time (%) = 0.000121534 (0.719346)
Comm time (%) = 0.00325423 (19.2615)
Outpt time (%) = 0.00011605 (0.686889)
Other time (%) = 0.00364774 (21.5906)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 84 ave 90 max 79 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 895 ave 909 max 887 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624137 -0.73807188 436.03689
80 0 -3.1521235 0 -3.1418193 -0.26103149 436.03693
90 0 -3.1725009 0 -3.1715057 -0.36498447 436.19
100 0 -3.1770919 0 -3.1759284 -0.3678025 436.15756
110 0 -3.1795983 0 -3.1785044 -0.32326426 436.06295
120 0 -3.180804 0 -3.180035 -0.20918126 435.18508
130 0 -3.1809911 0 -3.1802835 -0.19952199 435.02873
140 0 -3.1812648 0 -3.1804983 -0.1536603 433.52101
146 0 -3.1812507 0 -3.1805455 -0.14792876 435.60369
Loop time of 0.0170696 on 4 procs for 72 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241374157 -3.1805424084 -3.18054549688
Force two-norm initial, final = 1731.02 0.648868
Force max component initial, final = 1265.65 0.243588
Final line search alpha, max atom move = 0.00411247 0.00100175
Iterations, force evaluations = 72 345
Pair time (%) = 0.00818044 (47.9241)
Neigh time (%) = 0.000614583 (3.60046)
Comm time (%) = 0.00340056 (19.9218)
Outpt time (%) = 0.000127673 (0.747957)
Other time (%) = 0.00474632 (27.8057)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 93 ave 95 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 900.5 ave 991 max 795 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3602
Ave neighs/atom = 8.57619
Neighbor list builds = 20
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
146 0 -3.1812507 0 -0.19362668 -0.14835915 434.34002
150 0 -3.0139224 0 -2.1509399 1.2746122 434.3403
160 0 -3.0194803 0 -2.9695748 1.6379418 434.34235
170 0 -3.0791621 0 -3.0643991 1.2982776 434.34066
180 0 -3.0976992 0 -3.0876817 1.1785055 434.99297
190 0 -3.1011034 0 -3.0933162 1.177501 434.36151
196 0 -3.101384 0 -3.093552 1.1763591 434.56832
Loop time of 0.00935769 on 4 procs for 50 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.193626681647 -3.09355173343 -3.09355201119
Force two-norm initial, final = 1761.84 3.77378
Force max component initial, final = 925.281 0.741268
Final line search alpha, max atom move = 8.16442e-06 6.05202e-06
Iterations, force evaluations = 50 179
Pair time (%) = 0.00431252 (46.0853)
Neigh time (%) = 0.000466645 (4.98675)
Comm time (%) = 0.0018518 (19.789)
Outpt time (%) = 8.27312e-05 (0.884099)
Other time (%) = 0.002644 (28.2549)
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 94.5 ave 97 max 92 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 912.75 ave 1012 max 810 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 3651
Ave neighs/atom = 8.69286
Neighbor list builds = 15
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
196 0 -3.101384 0 2.0685206 1.175426 434.91329
200 0 -2.7636455 0 -1.0998236 3.845322 434.90722
210 0 -2.7400198 0 -2.5636998 4.5111706 434.85438
220 0 -2.8544322 0 -2.8143558 3.8164599 441.10314
230 0 -2.9053821 0 -2.8748243 3.4509052 443.16362
240 0 -2.9336393 0 -2.9178903 3.1887133 446.32345
250 0 -2.9476213 0 -2.9353019 3.0616994 448.49386
260 0 -2.9570838 0 -2.9455155 2.9376727 451.97386
270 0 -2.9689281 0 -2.9578275 2.8316438 457.18765
280 0 -2.9748011 0 -2.9654648 2.7862357 457.989
290 0 -2.9889836 0 -2.9806176 2.5953846 459.49997
300 0 -3.0041161 0 -2.9952343 2.4349847 462.63608
310 0 -3.011901 0 -3.003921 2.3164192 462.63608
320 0 -3.0576072 0 -3.0503749 1.6137857 468.46632
330 0 -3.0797 0 -3.0755735 1.4331912 469.59287
340 0 -3.0978292 0 -3.0935875 1.2415604 471.43131
350 0 -3.1030388 0 -3.0994817 1.1855922 471.43131
360 0 -3.1128512 0 -3.1097503 1.096837 469.69029
370 0 -3.1148659 0 -3.1119534 1.0489288 470.95557
380 0 -3.1166378 0 -3.1136569 0.98288209 473.66763
390 0 -3.1193105 0 -3.1160328 0.87791426 471.97237
400 0 -3.1206215 0 -3.1170125 0.78375684 473.92596
410 0 -3.1208112 0 -3.117148 0.76964642 475.39426
416 0 -3.1208738 0 -3.1171963 0.763393 474.17968
Loop time of 0.0445333 on 4 procs for 220 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.06852056346 -3.11719356011 -3.11719629261
Force two-norm initial, final = 2343.13 0.489927
Force max component initial, final = 1038.51 0.0921925
Final line search alpha, max atom move = 0.00296916 0.000273734
Iterations, force evaluations = 220 848
Pair time (%) = 0.0204562 (45.9347)
Neigh time (%) = 0.00166583 (3.74064)
Comm time (%) = 0.0099439 (22.3292)
Outpt time (%) = 0.000369072 (0.828756)
Other time (%) = 0.0120983 (27.1668)
Nlocal: 105 ave 122 max 89 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 89.5 ave 98 max 82 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 901.5 ave 1096 max 713 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3606
Ave neighs/atom = 8.58571
Neighbor list builds = 53
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
416 0 -3.1208738 0 4.5726242 0.76329108 474.24299
420 0 -2.7921115 0 0.12554168 3.208605 473.97607
430 0 -2.7757713 0 -2.5174284 4.1005727 473.9787
440 0 -2.8622562 0 -2.8246751 3.6723228 477.12966
450 0 -2.937786 0 -2.909592 3.0648237 484.85615
460 0 -2.97273 0 -2.9564121 2.7383277 488.78876
470 0 -2.9835994 0 -2.9700404 2.563441 491.80148
480 0 -2.9879154 0 -2.9761033 2.5160526 491.96498
490 0 -2.9916932 0 -2.9820721 2.4627562 493.83702
500 0 -3.001486 0 -2.9936395 2.3293593 494.85915
510 0 -3.0335777 0 -3.0270601 1.9771348 497.06866
520 0 -3.0489472 0 -3.0436257 1.8483891 497.01921
530 0 -3.0557407 0 -3.0503519 1.7746631 496.65321
540 0 -3.0607842 0 -3.0547376 1.6643506 497.17452
550 0 -3.0667068 0 -3.0598216 1.4983736 500.95093
560 0 -3.0695111 0 -3.0626813 1.4851269 499.05662
570 0 -3.0728017 0 -3.0657511 1.4648801 498.07014
580 0 -3.0738418 0 -3.0668835 1.4561546 498.07014
590 0 -3.0764099 0 -3.0693885 1.4545514 497.99673
600 0 -3.0818748 0 -3.0747706 1.43346 498.38846
610 0 -3.0822295 0 -3.0751338 1.4354444 498.38846
620 0 -3.082426 0 -3.0753487 1.4397055 497.93724
622 0 -3.0824212 0 -3.0753552 1.4395296 497.93724
Loop time of 0.038512 on 4 procs for 206 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
4.57262417707 -3.07535244818 -3.07535522656
Force two-norm initial, final = 2978.09 1.12104
Force max component initial, final = 1400.85 0.44337
Final line search alpha, max atom move = 0.00595121 0.00263859
Iterations, force evaluations = 206 720
Pair time (%) = 0.0172448 (44.7778)
Neigh time (%) = 0.00121301 (3.14971)
Comm time (%) = 0.00913364 (23.7163)
Outpt time (%) = 0.000345349 (0.896732)
Other time (%) = 0.0105752 (27.4594)
Nlocal: 105 ave 123 max 89 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 95.5 ave 105 max 87 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 904.75 ave 1103 max 718 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3619
Ave neighs/atom = 8.61667
Neighbor list builds = 39
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
622 0 -3.0824212 0 -2.5558044 1.4393841 497.98759
630 0 -2.9990709 0 -2.9502024 2.2860407 498.00801
640 0 -3.0064013 0 -2.9810478 2.2922801 497.90024
650 0 -3.0097157 0 -2.9948668 2.314644 497.75126
660 0 -3.0165998 0 -3.0052994 2.3153482 497.51161
670 0 -3.0231017 0 -3.012251 2.2916257 497.00169
680 0 -3.0304422 0 -3.0203383 2.2695844 497.00368
690 0 -3.0346029 0 -3.0248205 2.2468155 497.00368
700 0 -3.036641 0 -3.0270583 2.2296664 497.6363
710 0 -3.037401 0 -3.0277122 2.2211151 498.04962
711 0 -3.0374016 0 -3.0277127 2.221111 498.04962
Loop time of 0.019655 on 4 procs for 89 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.55580440685 -3.02771223773 -3.02771273695
Force two-norm initial, final = 490.137 4.69177
Force max component initial, final = 232.239 2.5669
Final line search alpha, max atom move = 9.39778e-06 2.41232e-05
Iterations, force evaluations = 89 359
Pair time (%) = 0.00871509 (44.3404)
Neigh time (%) = 0.000852227 (4.33593)
Comm time (%) = 0.00470811 (23.9538)
Outpt time (%) = 0.0001598 (0.813025)
Other time (%) = 0.00521976 (26.5569)
Nlocal: 105 ave 122 max 88 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 96.75 ave 107 max 86 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 935.5 ave 1131 max 760 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3742
Ave neighs/atom = 8.90952
Neighbor list builds = 27
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Memory usage per processor = 2.74744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
711 0 -3.0374016 0 -2.5400948 2.2234368 497.52862
720 0 -2.9467221 0 -2.9050784 3.1683023 497.59856
730 0 -2.9511837 0 -2.9319657 3.2028566 497.43904
740 0 -2.9618885 0 -2.9417829 3.10431 498.05306
750 0 -2.9627467 0 -2.9447731 3.0959012 498.05306
760 0 -2.9641239 0 -2.9470922 3.0777312 498.32613
770 0 -2.9700494 0 -2.9509269 3.0196934 498.5897
780 0 -2.9749707 0 -2.9573574 2.997151 498.94648
790 0 -2.9845528 0 -2.9661482 2.9379015 499.2991
800 0 -2.994962 0 -2.9772454 2.8800592 499.10677
810 0 -2.9980155 0 -2.9808077 2.8692662 499.10677
820 0 -2.9989391 0 -2.9817793 2.8656279 499.65704
825 0 -2.9991788 0 -2.9820879 2.8660089 499.65704
Loop time of 0.0272222 on 4 procs for 114 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.54009483624 -2.98208743291 -2.98208787345
Force two-norm initial, final = 458.759 2.33644
Force max component initial, final = 204.211 0.365055
Final line search alpha, max atom move = 3.33864e-05 1.21879e-05
Iterations, force evaluations = 114 498
Pair time (%) = 0.0122632 (45.0484)
Neigh time (%) = 0.00070715 (2.59769)
Comm time (%) = 0.00696242 (25.5762)
Outpt time (%) = 0.000183165 (0.672851)
Other time (%) = 0.0071063 (26.1048)
Nlocal: 105 ave 125 max 86 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 99.5 ave 109 max 90 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 948.25 ave 1245 max 710 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 3793
Ave neighs/atom = 9.03095
Neighbor list builds = 22
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 MPI processor grid
reading atoms ...
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 50 dump.meam
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Memory usage per processor = 5.10824 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0835102 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.0802212 (96.0616)
Neigh time (%) = 0.00220895 (2.64513)
Comm time (%) = 0.000565529 (0.677198)
Outpt time (%) = 0.000127792 (0.153026)
Other time (%) = 0.000386715 (0.463075)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 543 ave 543 max 543 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1526 ave 1526 max 1526 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3052 ave 3052 max 3052 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

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LAMMPS (1 Feb 2014)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 MPI processor grid
reading atoms ...
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 50 dump.meam
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Memory usage per processor = 4.99306 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0331262 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.0293604 (88.6321)
Neigh time (%) = 0.000602961 (1.82019)
Comm time (%) = 0.00270861 (8.17666)
Outpt time (%) = 0.000221252 (0.667908)
Other time (%) = 0.000232935 (0.703175)
Nlocal: 32 ave 36 max 30 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 293.75 ave 305 max 285 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 381.5 ave 413 max 334 min
Histogram: 1 0 0 0 1 0 0 0 0 2
FullNghs: 763 ave 866 max 678 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI 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 box
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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 6.77654 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
Loop time of 1.5888 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 1.56768 (98.671)
Neigh time (%) = 0.0145421 (0.915289)
Comm time (%) = 0.0015583 (0.0980806)
Outpt time (%) = 6.31809e-05 (0.00397665)
Other time (%) = 0.00495219 (0.311694)
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 500 dump.meam.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 6.95312 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4992.9811 19894.297
100 292.0799 -8177.7235 0 -8142.9266 2566.6872 19871.516
200 306.71233 -8177.1504 0 -8140.6103 872.78764 20047.2
300 295.7806 -8172.9505 0 -8137.7127 -1053.769 20091.657
400 309.18439 -8169.6374 0 -8132.8028 -1784.5443 20122.178
500 304.51122 -8163.9147 0 -8127.6369 -160.26993 20183.44
600 300 -8158.55 0 -8122.8096 1555.2344 20279.887
700 304.32794 -8149.4746 0 -8113.2185 3700.5984 20430.504
800 304.79621 -8138.8368 0 -8102.5249 3721.6015 20510.74
900 303.87706 -8128.16 0 -8091.9576 4387.1435 20638.992
1000 300 -8113.4908 0 -8077.7503 6186.7017 20755.029
1100 306.13485 -8097.1731 0 -8060.7018 8904.6623 20879.616
1200 309.15674 -8081.8589 0 -8045.0276 10523.683 20996.875
1300 304.48415 -8064.5597 0 -8028.2851 10063.026 21126.348
1400 300 -8046.7606 0 -8011.0202 10972.46 21238.721
1500 300 -8041.3545 0 -8005.614 11939.553 21374.301
1600 309.60382 -8035.2271 0 -7998.3425 11340.231 21530.1
1700 300 -8029.1688 0 -7993.4284 11298.984 21635.492
1800 300 -8034.2178 0 -7998.4773 9635.8998 21737.07
1900 299.69156 -8037.3123 0 -8001.6086 6094.2811 21857.993
2000 308.23519 -8030.0074 0 -7993.2859 3176.5086 21983.182
2100 300 -8031.5977 0 -7995.8573 1352.4566 22112.054
2200 300 -8039.3918 0 -8003.6514 2078.9229 22231.755
2300 305.77226 -8038.7518 0 -8002.3237 3408.6101 22345.35
2400 300 -8034.7719 0 -7999.0314 5324.2456 22468.716
2500 300 -8034.9187 0 -7999.1782 7770.9385 22588.417
2600 300 -8034.3037 0 -7998.5633 10402.367 22709.34
2700 304.22676 -8032.9652 0 -7996.7213 11603.947 22840.035
2800 306.55646 -8032.2292 0 -7995.7077 10585.627 22959.736
2900 304.12756 -8031.7372 0 -7995.505 7574.3331 23087.988
3000 301.87833 -8033.9958 0 -7998.0316 4111.4578 23197.918
Loop time of 50.7057 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 49.8856 (98.3827)
Neigh time (%) = 0.619792 (1.22233)
Comm time (%) = 0.0500011 (0.0986104)
Outpt time (%) = 0.00052166 (0.0010288)
Other time (%) = 0.14977 (0.295371)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1657 ave 1657 max 1657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23337 ave 23337 max 23337 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46674 ave 46674 max 46674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46674
Ave neighs/atom = 24.4111
Neighbor list builds = 219
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI 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 box
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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 5.96074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
Loop time of 0.443615 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.425855 (95.9965)
Neigh time (%) = 0.00376439 (0.848572)
Comm time (%) = 0.0119869 (2.7021)
Outpt time (%) = 0.000107288 (0.024185)
Other time (%) = 0.00190133 (0.428599)
Nlocal: 478 ave 492 max 465 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 809 ave 822 max 795 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 5916 ave 6133 max 5658 min
Histogram: 1 0 0 1 0 0 0 0 1 1
FullNghs: 11832 ave 12277 max 11299 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 47328
Ave neighs/atom = 24.7531
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 500 dump.meam.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 6.00501 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 295.42794 -8176.5141 0 -8141.3183 3169.3113 19886.93
100 292.02876 -8176.5475 0 -8141.7567 -826.45881 19918.758
200 306.10676 -8176.7837 0 -8140.3158 -1371.1065 19948.794
300 300 -8172.6378 0 -8136.8974 -1736.2602 20086.712
400 306.48529 -8168.4581 0 -8131.9451 -957.8783 20111.985
500 309.89005 -8166.3097 0 -8129.391 -1024.7828 20200.517
600 302.35862 -8157.8008 0 -8121.7794 540.69714 20316.092
700 292.46062 -8149.9463 0 -8115.1041 1709.248 20448.424
800 306.03297 -8139.326 0 -8102.8669 4197.3195 20522.955
900 302.01714 -8127.2712 0 -8091.2905 6337.0018 20634.106
1000 300 -8112.4155 0 -8076.675 7383.2425 20759.915
1100 303.06207 -8097.0321 0 -8060.9268 7921.3462 20879.616
1200 300.99295 -8079.4118 0 -8043.5531 10534.001 20995.654
1300 300 -8065.6269 0 -8029.8865 10683.83 21125.127
1400 300 -8050.6108 0 -8014.8704 9586.4735 21255.821
1500 300 -8041.9686 0 -8006.2281 9655.7424 21365.751
1600 308.48003 -8031.9005 0 -7995.1498 10878.449 21496.446
1700 300 -8018.8868 0 -7983.1463 11313.466 21610.04
1800 300 -8011.819 0 -7976.0786 11545.414 21730.963
1900 300 -8008.9295 0 -7973.1891 9195.9922 21861.658
2000 300 -8013.4803 0 -7977.7399 5835.8211 21977.695
2100 300 -8024.1289 0 -7988.3885 1247.1291 22107.168
2200 300 -8035.3879 0 -7999.6475 755.15155 22219.541
2300 300 -8039.784 0 -8004.0436 990.04968 22355.121
2400 300 -8044.0207 0 -8008.2803 -798.93073 22469.937
2500 300 -8045.7015 0 -8009.9611 -2282.7 22588.417
2600 309.16599 -8043.0604 0 -8006.228 -1333.726 22713.005
2700 297.78976 -8035.0476 0 -7999.5705 -1819.5883 22842.478
2800 306.30156 -8029.889 0 -7993.3979 -155.02495 22962.179
2900 300 -8028.0102 0 -7992.2698 731.08083 23083.102
3000 300 -8025.8905 0 -7990.15 2169.2725 23200.361
Loop time of 13.8878 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 13.3534 (96.1521)
Neigh time (%) = 0.160926 (1.15876)
Comm time (%) = 0.316833 (2.28138)
Outpt time (%) = 0.000683129 (0.00491891)
Other time (%) = 0.0559426 (0.402818)
Nlocal: 478 ave 511 max 445 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 787.5 ave 833 max 753 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 5805 ave 6124 max 5486 min
Histogram: 1 1 0 0 0 0 0 0 1 1
FullNghs: 11610 ave 12225 max 11027 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 46440
Ave neighs/atom = 24.2887
Neighbor list builds = 222
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 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 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Memory usage per processor = 2.35377 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.723551 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 0.608158 (84.0518)
Neigh time (%) = 0.0826616 (11.4244)
Comm time (%) = 0.0138171 (1.90962)
Outpt time (%) = 9.58443e-05 (0.0132464)
Other time (%) = 0.0188186 (2.60087)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 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 50 dump.melt
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Memory usage per processor = 1.88303 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.209819 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.159745 (76.1344)
Neigh time (%) = 0.0218451 (10.4114)
Comm time (%) = 0.0226035 (10.7728)
Outpt time (%) = 0.000118613 (0.0565311)
Other time (%) = 0.00550741 (2.62483)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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 fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.47979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.161192 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.10344 (64.1721)
Bond time (%) = 0.00639391 (3.96664)
Neigh time (%) = 0.019408 (12.0403)
Comm time (%) = 0.00402379 (2.49627)
Outpt time (%) = 0.00023222 (0.144064)
Other time (%) = 0.0276937 (17.1806)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# 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 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.63238 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727753 0.058614052 -1.4645362 1.9980678
2000 0.45 -2.001583 0.074586381 -1.4773716 1.677722
3000 0.45 -2.01376 0.065369685 -1.4987654 1.5672632
4000 0.44978364 -2.0284623 0.069543994 -1.5095095 1.3255914
5000 0.4515788 -2.0213579 0.063453981 -1.5067015 1.2898067
6000 0.44084238 -2.0220208 0.059857725 -1.5216881 1.3664878
7000 0.45280746 -2.0465582 0.056091161 -1.538037 1.1247107
8000 0.45575503 -2.0556878 0.056250977 -1.5440615 1.2847641
9000 0.45541476 -2.0383734 0.062759047 -1.5205791 1.4205644
10000 0.43553889 -2.0491499 0.064724759 -1.5492492 1.2479479
11000 0.46199123 -2.0775949 0.05294824 -1.5630404 0.91003048
12000 0.45116812 -2.0484232 0.065204884 -1.5324262 1.1225658
13000 0.44686952 -2.0599878 0.049287713 -1.564203 1.1154998
14000 0.45212998 -2.0625951 0.058683349 -1.5521586 0.98441931
15000 0.4556105 -2.0756197 0.059200748 -1.5611881 0.95502443
16000 0.45043625 -2.0824009 0.064992475 -1.5673475 1.1101553
17000 0.44547914 -2.0937506 0.063134923 -1.5855078 1.0387966
18000 0.44560114 -2.0932092 0.063158377 -1.584821 0.92976825
19000 0.46409216 -2.0998691 0.063095466 -1.5730682 0.74222038
20000 0.43356947 -2.079761 0.058993704 -1.5875591 0.98809322
21000 0.43970509 -2.0772972 0.063415284 -1.5745433 1.1679023
22000 0.45439796 -2.0869643 0.060942539 -1.5720025 0.95309247
23000 0.46436648 -2.0865877 0.062283763 -1.5603244 0.82847808
24000 0.45179512 -2.099375 0.057554155 -1.5904022 0.81341216
25000 0.45 -2.1028977 0.053292072 -1.5999806 0.8167413
26000 0.44379478 -2.0953332 0.065257482 -1.5866508 0.79986647
27000 0.45233801 -2.0995326 0.060977813 -1.5865937 0.8732284
28000 0.45416333 -2.0995467 0.051944425 -1.5938174 0.84546945
29000 0.44235173 -2.0819112 0.063209787 -1.5767183 0.7973497
30000 0.463297 -2.1019723 0.052828108 -1.5862333 0.83736896
31000 0.46237603 -2.114332 0.059492046 -1.5928492 0.6791076
32000 0.46010313 -2.1067583 0.06500768 -1.5820309 0.73245227
33000 0.45581512 -2.106217 0.054623133 -1.5961586 0.77209258
34000 0.46132621 -2.1005582 0.063679478 -1.5759369 0.79365061
35000 0.44457465 -2.1009737 0.063096958 -1.5936726 0.77684088
36000 0.46892599 -2.1283119 0.063349886 -1.5964267 0.66757096
37000 0.43919893 -2.117133 0.061828288 -1.6164718 0.82728955
38000 0.46347483 -2.1095945 0.053697761 -1.5928082 0.6018967
39000 0.46560699 -2.134901 0.051889552 -1.6177925 0.61468453
40000 0.45486545 -2.1082829 0.05921023 -1.5945863 0.67314005
41000 0.46926414 -2.1056671 0.052918097 -1.5838759 0.72673846
42000 0.44801848 -2.1122598 0.053198288 -1.6114163 0.7515948
43000 0.44733537 -2.1143993 0.048691802 -1.6187449 0.64883126
44000 0.44330158 -2.0946395 0.063057453 -1.5886499 0.74170615
45000 0.44616358 -2.1212538 0.054840602 -1.6206214 0.72390736
46000 0.43298663 -2.0977927 0.063259619 -1.6019073 0.75151063
47000 0.45 -2.093575 0.062292347 -1.5816576 0.83230853
48000 0.43668769 -2.1011039 0.055608008 -1.6091721 0.81680002
49000 0.43402566 -2.1180572 0.0705711 -1.6138221 0.61733524
50000 0.45870183 -2.1234461 0.061839249 -1.6032873 0.71893984
51000 0.46897063 -2.1240109 0.056638825 -1.5987922 0.57223633
52000 0.44547026 -2.114712 0.066830872 -1.6027821 0.88042497
53000 0.45698191 -2.1088353 0.055900552 -1.5963336 0.73302935
54000 0.46105819 -2.1164732 0.053844244 -1.6019549 0.52305471
55000 0.46526131 -2.1168922 0.053629683 -1.5983889 0.74647219
56000 0.4610805 -2.1203778 0.060044544 -1.5996369 0.56764901
57000 0.43539083 -2.1162246 0.058878039 -1.6223185 0.63599171
58000 0.45613812 -2.1341668 0.059717309 -1.6186914 0.5752578
59000 0.45035503 -2.1066421 0.056509876 -1.6001524 0.69875083
60000 0.46528439 -2.1306197 0.058828427 -1.6068946 0.47995479
Loop time of 13.5248 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 9.22542 (68.2113)
Bond time (%) = 0.386645 (2.85879)
Neigh time (%) = 1.98116 (14.6484)
Comm time (%) = 0.342358 (2.53134)
Outpt time (%) = 0.000705719 (0.00521797)
Other time (%) = 1.58848 (11.745)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9799 ave 9799 max 9799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9799
Ave neighs/atom = 8.16583
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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 fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.79957 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
600 0.45 0.58193041 0.088386617 1.119942 5.131481
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
Loop time of 0.0566852 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0265669 (46.8675)
Bond time (%) = 0.00169075 (2.98269)
Neigh time (%) = 0.00560409 (9.88633)
Comm time (%) = 0.0120407 (21.2413)
Outpt time (%) = 0.000412762 (0.728166)
Other time (%) = 0.01037 (18.294)
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# 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 2000 dump.micelle
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.79957 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727852 0.0586182 -1.464542 1.9980664
2000 0.46082446 -1.977605 0.057039794 -1.4601247 1.726013
3000 0.45 -2.0006402 0.05562923 -1.495386 1.511225
4000 0.4623338 -2.0091993 0.059138048 -1.4881127 1.3542907
5000 0.45 -2.0395585 0.061066034 -1.5288674 1.1830193
6000 0.45905159 -2.0634848 0.058991931 -1.5458239 1.1082099
7000 0.45 -2.0508705 0.061559594 -1.5396859 1.2020831
8000 0.44666556 -2.0397402 0.066632486 -1.5268144 1.2612013
9000 0.45034184 -2.03446 0.064174681 -1.5203188 1.1644088
10000 0.44920732 -2.0856804 0.059525789 -1.5773216 0.93583471
11000 0.45896474 -2.063989 0.064678373 -1.5407284 1.0732096
12000 0.45848122 -2.0752398 0.061533665 -1.555607 1.0281395
13000 0.46738009 -2.0629007 0.067132245 -1.5287778 0.96711354
14000 0.44988856 -2.062354 0.062693783 -1.5501466 1.0123189
15000 0.45098377 -2.072531 0.051120563 -1.5708025 0.97044948
16000 0.45 -2.1017479 0.064909547 -1.5872134 0.90299146
17000 0.4552102 -2.0765865 0.056648474 -1.5651072 0.91280438
18000 0.44824933 -2.0828037 0.058978706 -1.5759492 0.92795752
19000 0.44079166 -2.0556475 0.059088524 -1.5561347 1.1454216
20000 0.44463382 -2.0859907 0.057486911 -1.5842405 0.92599126
21000 0.44406551 -2.0826296 0.056776522 -1.5821577 0.99925665
22000 0.44911834 -2.0711967 0.059641892 -1.5628107 0.95834342
23000 0.43655144 -2.0909928 0.062696368 -1.5921088 0.91119509
24000 0.44867934 -2.1018259 0.055592487 -1.597928 0.76348634
25000 0.45260844 -2.0937068 0.059149636 -1.5823259 0.89135412
26000 0.44898273 -2.1016995 0.066566046 -1.5865249 0.74284381
27000 0.43221936 -2.084773 0.062900549 -1.5900132 0.87821534
28000 0.46292457 -2.0965745 0.055816359 -1.5782193 0.74158202
29000 0.45 -2.1306418 0.063790424 -1.6172264 0.53967764
30000 0.44871717 -2.0907319 0.055486729 -1.586902 0.99873528
31000 0.46125755 -2.0755203 0.056517719 -1.5581294 0.9347469
32000 0.45941056 -2.0914092 0.057505763 -1.5748757 0.89468013
33000 0.46026614 -2.0984679 0.056646234 -1.5819391 0.80740251
34000 0.46916633 -2.1193229 0.054211886 -1.5963356 0.61039936
35000 0.43884901 -2.0922975 0.061924634 -1.5918896 0.79377862
36000 0.43947177 -2.0909805 0.053228588 -1.5986464 0.90484301
37000 0.45414812 -2.1030789 0.055686423 -1.5936228 0.87060399
38000 0.44280127 -2.0908535 0.058003408 -1.5904178 0.8046892
39000 0.45516585 -2.1008067 0.058183565 -1.5878366 0.6089312
40000 0.43067796 -2.0848319 0.062869447 -1.5916434 0.74412702
41000 0.44165418 -2.1259603 0.064019775 -1.6206544 0.6221064
42000 0.43982239 -2.1055547 0.064067567 -1.6020312 0.62130789
43000 0.46586098 -2.1382757 0.05819116 -1.6146118 0.54791918
44000 0.45469796 -2.1328327 0.066699087 -1.6118146 0.52752596
45000 0.45358824 -2.1251041 0.063138554 -1.6087553 0.64714368
46000 0.44191865 -2.1041137 0.059520035 -1.6030433 0.62417966
47000 0.45804456 -2.1075048 0.066124313 -1.5837176 0.82334648
48000 0.45700413 -2.1298865 0.065741607 -1.6075216 0.58174639
49000 0.45842123 -2.1362735 0.056849019 -1.6213852 0.51934277
50000 0.44239274 -2.1182037 0.053635135 -1.6225444 0.59636555
51000 0.45869721 -2.1176213 0.059785615 -1.5995207 0.62467419
52000 0.45 -2.1136347 0.062713868 -1.6012959 0.71773796
53000 0.44480469 -2.1070829 0.061995737 -1.6006531 0.72790523
54000 0.45834924 -2.1352139 0.056517736 -1.6207289 0.64257865
55000 0.44776128 -2.1167768 0.051321782 -1.6180669 0.52184371
56000 0.46087785 -2.1186123 0.059414538 -1.598704 0.72628855
57000 0.44514743 -2.1107461 0.062138072 -1.6038315 0.68847034
58000 0.44897344 -2.1218568 0.056966905 -1.6162906 0.66787759
59000 0.43532599 -2.1262526 0.062848971 -1.6284404 0.61398862
60000 0.44623012 -2.105934 0.05919675 -1.600879 0.73556885
Loop time of 4.35988 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 2.35274 (53.9636)
Bond time (%) = 0.0979231 (2.24601)
Neigh time (%) = 0.561045 (12.8684)
Comm time (%) = 0.839245 (19.2493)
Outpt time (%) = 0.00117868 (0.0270348)
Other time (%) = 0.507739 (11.6457)
Nlocal: 300 ave 320 max 287 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 218.75 ave 232 max 205 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 2461 ave 2617 max 2321 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 9844
Ave neighs/atom = 8.20333
Ave special neighs/atom = 0.5
Neighbor list builds = 4879
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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
pair_modify shift yes
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
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.199423 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.127195 (63.7817)
Neigh time (%) = 0.0478823 (24.0104)
Comm time (%) = 0.00542498 (2.72034)
Outpt time (%) = 0.000106335 (0.0533212)
Other time (%) = 0.0188138 (9.43415)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
#dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74946 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
1050 3.3134849 -2.808351 0 0.50099208 1.7334413
1100 3.3134849 -2.8586611 0 0.45068195 1.6058414
1150 3.3134849 -2.8712625 0 0.43808058 1.6049732
1200 3.3134849 -2.8785429 0 0.43080018 1.5883814
1250 3.3134849 -2.8832131 0 0.42612994 1.6155122
1300 3.3134849 -2.8882533 0 0.42108976 1.6323994
1350 3.3134849 -2.8953262 0 0.41401689 1.5991374
1365 3.3134849 -2.895477 0 0.41386606 1.5988878
Loop time of 0.278112 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.231226 (83.1415)
Neigh time (%) = 0.0193577 (6.96039)
Comm time (%) = 0.00456548 (1.6416)
Outpt time (%) = 7.00951e-05 (0.0252039)
Other time (%) = 0.0228922 (8.2313)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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
pair_modify shift yes
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
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06115 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.066597 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0324514 (48.728)
Neigh time (%) = 0.012701 (19.0714)
Comm time (%) = 0.0137331 (20.6212)
Outpt time (%) = 0.000190914 (0.28667)
Other time (%) = 0.00752062 (11.2927)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
#dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.7478 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
1050 3.2803075 -2.8198371 0 0.45636995 1.6553949
1100 3.2803075 -2.8554989 0 0.42070813 1.6571551
1150 3.2803075 -2.8646695 0 0.41153758 1.7045388
1200 3.2803075 -2.8688213 0 0.40738582 1.6922085
1250 3.2803075 -2.8764988 0 0.39970826 1.6948532
1300 3.2803075 -2.8776606 0 0.39854651 1.6821387
1350 3.2803075 -2.8789379 0 0.39726915 1.6715024
1365 3.2803075 -2.879076 0 0.3971311 1.66923
Loop time of 0.100178 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.0639488 (63.8349)
Neigh time (%) = 0.00472444 (4.71603)
Comm time (%) = 0.015418 (15.3905)
Outpt time (%) = 0.000124454 (0.124233)
Other time (%) = 0.0159628 (15.9343)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 500 dump.min
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.200018 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.127843 (63.9158)
Neigh time (%) = 0.0480146 (24.0052)
Comm time (%) = 0.00542927 (2.71439)
Outpt time (%) = 0.000105858 (0.0529242)
Other time (%) = 0.018625 (9.31168)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74946 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.7783474 0 -0.7783474 12.864955
1050 0 -2.808351 0 -2.808351 -1.0603061
1100 0 -2.8586611 0 -2.8586611 -1.1879061
1150 0 -2.8712625 0 -2.8712625 -1.1887742
1200 0 -2.8785429 0 -2.8785429 -1.205366
1250 0 -2.8832131 0 -2.8832131 -1.1782352
1300 0 -2.8882533 0 -2.8882533 -1.1613481
1350 0 -2.8953262 0 -2.8953262 -1.19461
1365 0 -2.895477 0 -2.895477 -1.1948596
Loop time of 0.278073 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.231544 (83.2672)
Neigh time (%) = 0.0193498 (6.95854)
Comm time (%) = 0.00450826 (1.62125)
Outpt time (%) = 6.7234e-05 (0.0241786)
Other time (%) = 0.022604 (8.12879)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.74946 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.895477 -1.2253391 -1.16438 0.0029844696
1400 0 -2.9030976 -1.037803 -0.93005749 0.0031404612
1450 0 -2.9111551 -0.7499331 -0.56417894 0.0034000612
1500 0 -2.9156519 -0.43747438 -0.15725876 0.0035241132
1550 0 -2.9163188 -0.10113405 0.29275665 0.0032578192
1600 0 -2.9129142 0.25786755 0.78857369 0.0031418378
1650 0 -2.9052907 0.63122126 1.3305275 0.0027036138
1700 0 -2.8938515 0.97940259 1.9066628 0.0017474185
1750 0 -2.8934608 0.9929599 1.9909561 0.0022591527
1800 0 -2.8938899 1.0037689 2.0049399 0.0031549929
1850 0 -2.8950206 0.99253195 1.9899581 0.0044014083
1900 0 -2.8954835 0.99574288 1.9942509 0.0052643914
1950 0 -2.8957658 1.0003472 2.0004684 0.0058490005
2000 0 -2.8970438 0.97690958 1.9714991 0.0067217987
2050 0 -2.897073 0.99072137 1.9920898 0.0072873033
2100 0 -2.8972746 0.99651146 1.995402 0.0075817227
2150 0 -2.8975964 0.99381046 1.991681 0.007627454
2200 0 -2.8979803 0.99274725 1.9904104 0.007749339
2250 0 -2.8982086 0.99172995 1.9905936 0.0077177074
2300 0 -2.8983994 0.99377061 1.9899673 0.0076946648
2350 0 -2.8985769 0.99172845 1.9896457 0.0074117889
2400 0 -2.8986693 0.99578192 1.992246 0.0071806046
2450 0 -2.8988819 0.99128252 1.9903378 0.0069177704
2500 0 -2.8989812 0.99522115 1.991489 0.0068121239
2550 0 -2.8991564 0.99146083 1.990657 0.0065352609
2600 0 -2.8992555 0.99538317 1.9914926 0.0062558371
2650 0 -2.8994204 0.99157917 1.9907942 0.0059727799
2700 0 -2.8995111 0.9953798 1.9917332 0.0057516669
2750 0 -2.899661 0.9919244 1.9913158 0.005332134
2800 0 -2.8997549 0.99504761 1.9916688 0.0050046256
2850 0 -2.8999018 0.99193526 1.9912547 0.004492394
2900 0 -2.8999871 0.99565899 1.9922087 0.0040528402
2950 0 -2.9001422 0.99213366 1.9916425 0.0035862563
3000 0 -2.9002325 0.99582487 1.9924604 0.0032829497
3050 0 -2.9003895 0.99227644 1.9918388 0.0029100217
3100 0 -2.9004934 0.9954142 1.9922624 0.0026581626
3150 0 -2.9006459 0.99232395 1.9918443 0.0023680976
3200 0 -2.9007414 0.99623688 1.99297 0.0020662395
3250 0 -2.9009264 0.99256898 1.991983 0.0018040717
3300 0 -2.9009986 0.99800399 1.9945846 0.0015930444
3350 0 -2.9011372 0.99321268 1.9969898 0.001407703
3400 0 -2.9013641 0.99622318 1.9930656 0.0014563979
3450 0 -2.9015832 0.99282311 1.9924118 0.0014454286
3500 0 -2.9017596 0.99595378 1.992875 0.0016105573
3550 0 -2.9020182 0.99269026 1.9918179 0.0017633837
3600 0 -2.9022093 0.99607639 1.9930845 0.0020441612
3650 0 -2.9024948 0.99278561 1.9922635 0.0022606286
3700 0 -2.9027328 0.99606872 1.9930129 0.0026414228
3750 0 -2.9030541 0.99270955 1.9922055 0.0030676238
3800 0 -2.9033283 0.99509621 1.9917886 0.0034492628
3850 0 -2.9036436 0.99265445 1.9918333 0.0039194462
3900 0 -2.9039245 0.99611739 1.9930579 0.0043794142
3950 0 -2.9043033 0.99262403 1.9918954 0.0048733419
4000 0 -2.9046124 0.99585905 1.9928584 0.0054448584
4050 0 -2.9050077 0.99265871 1.9918589 0.0059527585
4100 0 -2.9053408 0.99596017 1.992967 0.0066819293
4150 0 -2.9057612 0.99271888 1.9920143 0.0074538661
4200 0 -2.9061208 0.99585342 1.9928494 0.0083030126
4250 0 -2.9065583 0.99276056 1.9921715 0.0091760837
4300 0 -2.9069587 0.99569608 1.9928109 0.010563215
4350 0 -2.9074386 0.99294112 1.9923317 0.012242263
4400 0 -2.9079159 0.99617793 1.9929836 0.014425511
4450 0 -2.9084828 0.99335369 1.9912818 0.017137841
4500 0 -2.9088005 0.99954722 1.9956616 0.019873686
4550 0 -2.9092238 0.99844962 1.9944461 0.022380697
4600 0 -2.9096299 0.99300644 1.9925264 0.024687168
4650 0 -2.9100061 0.99370577 1.9934207 0.027508267
4700 0 -2.9104263 0.99565636 1.9926298 0.030664353
4750 0 -2.9109614 0.99284169 1.9919846 0.034334378
4800 0 -2.9114155 0.9960171 1.9931707 0.038040635
4850 0 -2.9119649 0.99287594 1.9919796 0.041618415
4900 0 -2.9125125 0.99631202 1.9935981 0.046177605
4950 0 -2.9134822 0.99545012 1.9963436 0.055551769
5000 0 -2.9138087 1.0016464 1.9978697 0.059129043
5050 0 -2.9138895 1.0005328 2.0066685 0.060919794
5100 0 -2.9144557 0.99415884 1.9925195 0.062934069
5150 0 -2.9143897 0.99900082 2.0070401 0.06446803
5200 0 -2.9150165 0.99737915 1.9943189 0.066857536
5250 0 -2.9154332 0.9999712 2.0021875 0.069632138
5300 0 -2.9157558 0.99795158 1.9974044 0.070422281
5350 0 -2.9158439 1.0016699 2.0035502 0.071049397
5400 0 -2.9164666 0.99255654 1.9908929 0.071776886
5450 0 -2.9168846 1.0018915 1.9938812 0.072677356
5500 0 -2.9173241 0.99707078 1.9957969 0.072868177
5550 0 -2.9179842 0.99391224 1.9978813 0.073182143
5600 0 -2.9184699 0.99532518 1.9933732 0.073208315
5650 0 -2.9188477 1.0063118 2.0052442 0.073258803
5700 0 -2.919468 1.0026929 2.0041254 0.073010391
5750 0 -2.9202844 1.0035994 2.0008607 0.072352512
5800 0 -2.9204309 1.0072764 2.008335 0.072056645
5850 0 -2.9213742 0.99720824 1.9925634 0.071173036
5900 0 -2.9216129 1.0000335 2.001122 0.070609448
5950 0 -2.9223916 1.0003501 2.0032975 0.069559273
6000 0 -2.9227892 1.0043807 2.0050332 0.069077943
6050 0 -2.9233982 1.004802 2.0050324 0.068450588
6100 0 -2.9237721 1.0066363 2.0070477 0.06823504
6150 0 -2.9245074 1.0063392 2.0068761 0.068112243
6200 0 -2.9258589 0.99455185 1.9953413 0.06865518
6250 0 -2.9261201 1.0042987 2.0031819 0.069636648
6300 0 -2.9270045 0.99564956 1.9901358 0.071020033
6350 0 -2.9270282 1.007771 2.0049483 0.072360652
6400 0 -2.9279953 0.99228232 1.9927028 0.074781454
6450 0 -2.9280616 1.0017566 2.0022453 0.076142216
6500 0 -2.9288249 0.99408967 1.9888019 0.078305191
6550 0 -2.9286973 1.0065411 2.0049519 0.079618619
6600 0 -2.9291183 0.99372953 1.9985414 0.080448942
6650 0 -2.9292204 1.0023178 2.0050015 0.081907164
6700 0 -2.9301292 0.99992006 2.0016415 0.085917352
6750 0 -2.9302372 1.00613 2.004525 0.086946884
6800 0 -2.9305702 1.0074557 1.9965127 0.087976601
6850 0 -2.9313326 1.0050252 2.0080944 0.092584504
6900 0 -2.9317498 1.0087999 1.9958456 0.094058095
6950 0 -2.9318279 0.99688134 2.002508 0.094400121
7000 0 -2.9318978 1.0034321 2.0052797 0.095451664
7050 0 -2.9322652 0.99758568 2.0037109 0.097238969
7100 0 -2.9327121 0.99815697 1.9914701 0.098802948
7150 0 -2.9327437 1.0038622 2.0011895 0.10050304
7200 0 -2.9329063 1.004612 2.0032044 0.10185804
7250 0 -2.9335997 0.98168701 1.9864884 0.10300105
7300 0 -2.9336515 0.99279141 1.992742 0.10470943
7350 0 -2.9337138 1.003092 2.000106 0.10653676
7400 0 -2.9340414 1.0023845 1.9946755 0.10808147
7450 0 -2.9342536 0.99920061 1.9983417 0.10966697
7500 0 -2.9344657 0.99656006 2.002306 0.11134193
7550 0 -2.9346812 1.0009774 2.0059445 0.11345836
7600 0 -2.9352073 0.99664019 2.0028997 0.116237
7650 0 -2.9355092 1.0067299 2.0052137 0.11889963
7700 0 -2.9359369 1.000096 2.0038144 0.12089102
7750 0 -2.936237 1.0071591 2.0077241 0.12334687
7800 0 -2.9367687 1.0047286 2.0037322 0.12562793
7850 0 -2.9372513 0.99839299 2.0008738 0.1271966
7900 0 -2.93781 1.0013489 1.9924309 0.12900725
7950 0 -2.9382206 0.99271028 1.9910513 0.12995672
8000 0 -2.9385111 0.99261038 1.9917151 0.13094744
8050 0 -2.9388605 0.99256847 1.9933576 0.13194246
8100 0 -2.9391752 0.99421545 1.9941225 0.13291935
8150 0 -2.9394092 0.9997332 1.9965286 0.13397127
8200 0 -2.939821 0.99876146 1.9939496 0.13501447
8250 0 -2.9403015 0.99313692 1.9903144 0.13588404
8300 0 -2.9406524 0.99504174 1.9916891 0.13709102
8350 0 -2.9411077 0.99272049 1.9917049 0.13823709
8400 0 -2.9414976 0.99650126 1.9935111 0.13948558
8450 0 -2.9419844 0.9928859 1.9921827 0.14058516
8500 0 -2.9424055 0.9957698 1.9928898 0.14199174
8550 0 -2.9428963 0.99297812 1.9922564 0.14329168
8600 0 -2.9431968 0.99693087 1.9947462 0.14458722
8650 0 -2.9435631 0.99940154 1.9944064 0.14582129
8700 0 -2.9441466 0.99396641 1.9935763 0.14733962
8750 0 -2.9449093 0.99592155 1.9932061 0.15025209
8800 0 -2.9461707 0.99237436 1.9925136 0.15595847
8850 0 -2.9462853 1.000815 2.007233 0.15828028
8900 0 -2.9469511 1.0000829 1.9986375 0.16055827
8950 0 -2.9473161 1.0004185 1.9954916 0.16178098
9000 0 -2.9476848 1.0002902 1.9955333 0.16283909
9050 0 -2.9476782 1.0024581 2.0035957 0.16324604
9100 0 -2.9477989 1.0030916 2.0059473 0.16365445
9150 0 -2.9482536 0.99281175 1.9946546 0.16370039
9200 0 -2.9481416 1.00865 2.0073808 0.16435272
9250 0 -2.9486901 0.99494204 1.9953024 0.16410446
9300 0 -2.9486493 0.99953893 2.0056513 0.16419403
9350 0 -2.949079 1.003429 1.997895 0.16444925
9400 0 -2.9491509 1.0064853 2.0082985 0.16432267
9450 0 -2.9494699 1.0048863 2.001313 0.16433478
9500 0 -2.9496103 1.0059455 2.0060809 0.16420418
9550 0 -2.9499432 1.0037986 1.9989587 0.16406824
9600 0 -2.9501927 1.0010447 2.0005638 0.16375939
9650 0 -2.9511285 0.98322543 1.9801177 0.16290463
9700 0 -2.9506509 1.0102419 2.0082163 0.16328052
9750 0 -2.9511779 0.99511265 1.9950262 0.16251764
9800 0 -2.9512164 0.99608392 2.0052439 0.16186521
9850 0 -2.9517206 0.99656506 1.9966162 0.16144425
9900 0 -2.9519451 1.0066635 2.0043954 0.16101155
9950 0 -2.9520952 1.0051178 2.0087197 0.16058558
10000 0 -2.9531155 1.0041379 2.0031534 0.15982682
10050 0 -2.9537418 0.99448829 1.9904993 0.15928106
10100 0 -2.9540875 1.0000256 1.9948928 0.1590648
10150 0 -2.9545724 0.99595476 1.9920689 0.15859113
10200 0 -2.9550866 0.9945366 1.9940695 0.15788443
10250 0 -2.955721 0.99319075 1.9905041 0.15710363
10300 0 -2.9560458 0.99598109 1.9939645 0.15650198
10350 0 -2.9565093 0.99480453 1.9979782 0.15542386
10400 0 -2.9570486 0.99396171 1.9942613 0.15473357
10450 0 -2.9576457 0.99301571 1.9922208 0.1541236
10500 0 -2.9583596 0.9956042 1.992646 0.15365553
10550 0 -2.9591414 0.99318206 1.9923162 0.15326877
10600 0 -2.959942 0.99596727 1.9933176 0.15282597
10650 0 -2.9609186 0.99353471 1.9930306 0.1521666
10700 0 -2.9620307 0.99594782 1.9932886 0.1508232
10750 0 -2.9637166 0.99482397 1.9947588 0.14649906
10800 0 -2.9662462 0.99407822 1.9953083 0.13351206
10850 0 -2.9665593 1.0027673 1.9995492 0.13140588
10900 0 -2.9667709 1.0023406 2.0013835 0.12981724
10950 0 -2.9670159 1.0033354 2.0040861 0.12797651
11000 0 -2.9672441 1.0037572 2.004755 0.12647524
11050 0 -2.967593 0.99874092 1.9995822 0.12495147
11100 0 -2.9681165 0.99125559 1.9863869 0.1236617
11150 0 -2.9679478 1.0024409 2.0014347 0.12298067
11200 0 -2.968096 1.0083556 2.0040025 0.12211851
11250 0 -2.96854 0.99060368 1.9933029 0.12097655
11300 0 -2.968643 0.99899132 2.0034915 0.11986456
11350 0 -2.9687697 1.0018133 2.0075949 0.11899469
11365 0 -2.9688638 1.0116402 2.005578 0.11895715
Loop time of 2.59925 on 1 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.89547702741 -2.96928950062 -2.96886378746
Force two-norm initial, final = 3665.97 11.745
Force max component initial, final = 2998.7 10.1406
Final line search alpha, max atom move = 6.36291e-05 0.00064524
Iterations, force evaluations = 10000 10063
Pair time (%) = 1.93873 (74.5878)
Neigh time (%) = 0.00854492 (0.328745)
Comm time (%) = 0.0286736 (1.10315)
Outpt time (%) = 0.00297666 (0.11452)
Other time (%) = 0.620332 (23.8658)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 330 ave 330 max 330 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7336 ave 7336 max 7336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7336
Ave neighs/atom = 9.17
Neighbor list builds = 36
Dangerous builds = 0

356
examples/min/log.min.box.1Feb14.linux.4
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@ -1,356 +0,0 @@
LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
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
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 500 dump.min
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06115 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.0672228 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0325756 (48.4591)
Neigh time (%) = 0.012749 (18.9652)
Comm time (%) = 0.0136126 (20.25)
Outpt time (%) = 0.000190377 (0.283203)
Other time (%) = 0.00809526 (12.0424)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.7478 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.74465936 0 -0.74465936 13.069823
1050 0 -2.8198371 0 -2.8198371 -1.1103791
1100 0 -2.8554989 0 -2.8554989 -1.1086189
1150 0 -2.8646695 0 -2.8646695 -1.0612352
1200 0 -2.8688213 0 -2.8688213 -1.0735655
1250 0 -2.8764988 0 -2.8764988 -1.0709208
1300 0 -2.8776606 0 -2.8776606 -1.0836353
1350 0 -2.8789379 0 -2.8789379 -1.0942716
1365 0 -2.879076 0 -2.879076 -1.096544
Loop time of 0.103336 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.0650657 (62.9653)
Neigh time (%) = 0.00482118 (4.66555)
Comm time (%) = 0.0168168 (16.2739)
Outpt time (%) = 0.000125468 (0.121417)
Other time (%) = 0.0165067 (15.9739)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.7478 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
1400 0 -2.8859021 -0.86433583 -0.91383427 0.038857701
1450 0 -2.8929425 -0.58254768 -0.55566103 0.040538566
1500 0 -2.8966088 -0.28118754 -0.15988163 0.042020855
1550 0 -2.8967125 0.036820191 0.27480302 0.04324269
1600 0 -2.8931249 0.36718787 0.74943653 0.044424741
1650 0 -2.8858731 0.69688815 1.2623711 0.044835267
1700 0 -2.8755822 0.98073679 1.7977638 0.043907813
1750 0 -2.8722618 0.99796906 1.9978937 0.040932086
1800 0 -2.8731203 0.9972851 1.9960832 0.039723601
1850 0 -2.8733692 1.0063823 2.0084146 0.038402341
1900 0 -2.8747209 0.98521911 1.9798435 0.03629572
1950 0 -2.874625 1.0055823 2.0075042 0.034193545
2000 0 -2.8752902 0.99350208 1.9911933 0.03326557
2050 0 -2.8752769 1.0018946 2.0024682 0.03231859
2100 0 -2.8758319 0.99169935 1.9887983 0.031437471
2150 0 -2.8761892 0.99301192 1.9906401 0.029831022
2200 0 -2.8765018 0.99825416 1.9982587 0.027754052
2250 0 -2.8768461 0.99326761 1.9910275 0.027115046
2300 0 -2.8767423 1.0035487 2.0046857 0.026126393
2350 0 -2.8770655 0.99795811 1.9973107 0.025614851
2400 0 -2.877445 0.99163396 1.9870033 0.025156704
2450 0 -2.8774865 0.99148327 1.9905808 0.024719242
2500 0 -2.8775546 0.9950178 1.9915017 0.024486868
2550 0 -2.877691 0.9916018 1.9905624 0.02421693
2600 0 -2.8777627 0.99470414 1.9910618 0.023930399
2650 0 -2.8778782 0.99170595 1.9907118 0.023475253
2700 0 -2.877945 0.99480447 1.9913566 0.023271004
2750 0 -2.8780803 0.99164504 1.9902596 0.023000125
2800 0 -2.8781378 0.99501379 1.9915144 0.022773904
2850 0 -2.8782474 0.99219164 1.9915607 0.022481218
2900 0 -2.8783151 0.99550644 1.9921431 0.022359954
2950 0 -2.8784484 0.99224048 1.9913612 0.022193155
3000 0 -2.8785175 0.99532849 1.9920577 0.021941569
3050 0 -2.8786568 0.99222235 1.9910476 0.021737518
3100 0 -2.8787309 0.99525548 1.9920127 0.021688272
3150 0 -2.8788689 0.99228052 1.9913905 0.021446146
3200 0 -2.8789303 0.99616583 1.992901 0.021394358
3250 0 -2.8790946 0.99232091 1.9915574 0.02118161
3300 0 -2.8791847 0.99541221 1.9921056 0.021194771
3350 0 -2.8793341 0.9922686 1.9915267 0.021013055
3400 0 -2.8794452 0.99516725 1.9917199 0.021036976
3450 0 -2.8795969 0.99227386 1.9913259 0.021052828
3500 0 -2.8797075 0.99538375 1.9920724 0.02124209
3550 0 -2.8798796 0.99230271 1.9914458 0.021226686
3600 0 -2.8800015 0.99546439 1.9922124 0.02149345
3650 0 -2.880188 0.99227706 1.9913914 0.021617113
3700 0 -2.880312 0.99546322 1.9922772 0.021954501
3750 0 -2.8805126 0.99224941 1.991302 0.02213367
3800 0 -2.8806831 0.99459806 1.9906732 0.022675671
3850 0 -2.8808636 0.9921438 1.9909899 0.022992462
3900 0 -2.8810051 0.99533223 1.9921709 0.023485422
3950 0 -2.881225 0.99232174 1.9914377 0.023944603
4000 0 -2.8813892 0.99554805 1.992182 0.024545033
4050 0 -2.8816257 0.99218933 1.9910408 0.025105298
4100 0 -2.8817867 0.99546861 1.9923568 0.025863634
4150 0 -2.8820302 0.99242518 1.9914814 0.026365444
4200 0 -2.8822192 0.99526027 1.9919315 0.027062527
4250 0 -2.8824692 0.99223247 1.9913085 0.027610787
4300 0 -2.8826625 0.99537467 1.9921185 0.028217161
4350 0 -2.882922 0.99239179 1.9914342 0.028679998
4400 0 -2.8831241 0.99556357 1.9922663 0.029235596
4450 0 -2.8833989 0.9921938 1.9912448 0.029596184
4500 0 -2.8836067 0.99557381 1.9922188 0.030181
4550 0 -2.8838874 0.99214405 1.9912047 0.030371361
4600 0 -2.8840891 0.99568228 1.9925689 0.030873328
4650 0 -2.8843766 0.99222214 1.991537 0.031107839
4700 0 -2.8846039 0.99540851 1.9920535 0.031397701
4750 0 -2.8849039 0.99221886 1.9907361 0.031483457
4800 0 -2.8851163 0.99551704 1.9923517 0.031579764
4850 0 -2.8854144 0.99225442 1.9913169 0.031526446
4900 0 -2.8856452 0.99550052 1.9922005 0.031417289
4950 0 -2.8859485 0.99210587 1.9910919 0.03118115
5000 0 -2.8861801 0.99535546 1.9921671 0.030985542
5050 0 -2.8864881 0.99209875 1.9911885 0.030438838
5100 0 -2.8867336 0.99520939 1.9919538 0.029911151
5150 0 -2.8870413 0.99225176 1.9913023 0.029087623
5200 0 -2.8873039 0.99488953 1.9914722 0.0283991
5250 0 -2.8876062 0.99228521 1.991158 0.027574033
5300 0 -2.8878541 0.99556088 1.9922986 0.026813081
5350 0 -2.8881769 0.99220208 1.9912481 0.025847812
5400 0 -2.8884304 0.99556208 1.9922152 0.02492658
5450 0 -2.8887574 0.99219343 1.9912168 0.023790678
5500 0 -2.8890085 0.99566139 1.9925529 0.022691755
5550 0 -2.8893435 0.99223125 1.9912108 0.021332027
5600 0 -2.8895985 0.99555806 1.9925205 0.019969308
5650 0 -2.8899325 0.99238332 1.9915515 0.018334611
5700 0 -2.8902024 0.9950743 1.9920344 0.016688965
5750 0 -2.8905116 0.99266165 1.9920244 0.014675128
5800 0 -2.8907908 0.99538343 1.9922424 0.012898355
5850 0 -2.8911238 0.99274659 1.9916141 0.010718854
5900 0 -2.891395 0.99586743 1.992946 0.0084079793
5950 0 -2.8917377 0.99323184 1.9923269 0.0058847015
6000 0 -2.8920318 0.99618703 1.9931886 0.0031743443
6050 0 -2.8924173 0.99312644 1.9919607 0.00036370652
6100 0 -2.8927403 0.99609392 1.9932028 -0.0023282997
6150 0 -2.8931582 0.99334969 1.9924865 -0.0052253296
6200 0 -2.8931737 1.0044374 2.0036405 -0.0073374891
6250 0 -2.8933601 1.0053494 2.0084308 -0.0095543493
6300 0 -2.8937021 1.0040228 2.0072436 -0.011528379
6350 0 -2.8941162 1.0040963 2.0067291 -0.014066056
6400 0 -2.8946376 1.0056964 2.0065238 -0.016998255
6450 0 -2.8952383 1.002655 2.0052962 -0.019179448
6500 0 -2.8957747 1.0053824 2.0058467 -0.020794074
6550 0 -2.8963468 1.0031095 2.0056915 -0.021771701
6600 0 -2.8968938 1.0056478 2.0062435 -0.021988194
6650 0 -2.8976105 1.0027738 2.0056577 -0.022097734
6700 0 -2.8985813 1.0049044 2.0041091 -0.022978826
6750 0 -2.8993763 1.0013212 2.0046643 -0.024685401
6800 0 -2.8999352 0.99348555 1.9941849 -0.024745246
6850 0 -2.9002761 0.99611648 1.9915352 -0.024953484
6900 0 -2.9002655 1.0044443 2.0034446 -0.025004427
6950 0 -2.9006942 1.0038737 2.0062629 -0.024954287
7000 0 -2.9012609 1.0022744 2.0036566 -0.024819334
7050 0 -2.9016604 1.0051803 2.0055167 -0.024458964
7100 0 -2.9021771 1.0033287 2.0059127 -0.024041683
7150 0 -2.9026446 1.0051909 2.0057434 -0.023513487
7200 0 -2.9030997 1.003201 2.0057931 -0.022955905
7250 0 -2.9035001 1.0053534 2.006177 -0.022222879
7300 0 -2.9039398 1.003141 2.0056512 -0.021526869
7350 0 -2.9043194 1.0053552 2.0062897 -0.020600969
7400 0 -2.9047554 1.0029275 2.0053735 -0.019798089
7450 0 -2.9051394 1.0050723 2.0057785 -0.018810517
7500 0 -2.9055639 1.0030839 2.0056435 -0.018085221
7550 0 -2.9059506 1.00542 2.006424 -0.01743443
7600 0 -2.906389 1.0034617 2.0060075 -0.017038562
7650 0 -2.9068088 1.0052048 2.0059319 -0.01659861
7700 0 -2.907256 1.0032841 2.0057462 -0.016390423
7750 0 -2.9076758 1.0050008 2.0056173 -0.01606256
7800 0 -2.9081063 1.0033321 2.0058403 -0.016036071
7850 0 -2.9085325 1.0050458 2.0057159 -0.015738035
7900 0 -2.9089602 1.0033725 2.0057939 -0.015561818
7950 0 -2.9093746 1.00496 2.0055106 -0.015498031
8000 0 -2.9097997 1.0034291 2.0058947 -0.015471401
8050 0 -2.9102208 1.0049791 2.0055274 -0.015258479
8100 0 -2.9106489 1.0035304 2.0060557 -0.015178684
8150 0 -2.9110829 1.0052492 2.0060114 -0.014964657
8200 0 -2.9115393 1.0037164 2.006322 -0.014718896
8250 0 -2.9120088 1.0051472 2.0058765 -0.014430597
8300 0 -2.912515 1.0035172 2.0062174 -0.014197457
8350 0 -2.9130749 1.0054557 2.0059921 -0.013814584
8400 0 -2.9137199 1.0035594 2.0063641 -0.013128137
8450 0 -2.914514 1.0053008 2.0055891 -0.012076819
8500 0 -2.9153923 1.0020887 2.0048249 -0.010873863
8550 0 -2.9161681 1.005124 2.0041437 -0.009983199
8600 0 -2.9166232 1.0035103 2.0031583 -0.0098656588
8650 0 -2.9168935 1.0017735 2.0032739 -0.010137246
8700 0 -2.9176075 0.99350983 1.9942491 -0.010568888
8750 0 -2.9176655 1.0037509 2.0042507 -0.010929755
8800 0 -2.9180335 1.0034837 2.0006008 -0.011388
8850 0 -2.9184726 0.99722599 1.9972524 -0.012308771
8900 0 -2.9185896 1.0070137 2.0062244 -0.012981266
8950 0 -2.9189395 0.99775846 2.0046927 -0.013843916
9000 0 -2.9194348 0.99994718 1.9961545 -0.01430817
9050 0 -2.9199623 0.99913876 1.9945451 -0.015066366
9100 0 -2.9200915 1.0053667 2.0015458 -0.015628169
9150 0 -2.9203602 1.0029844 1.9981877 -0.015943776
9200 0 -2.9204472 1.007234 2.0012475 -0.01621898
9250 0 -2.9207559 1.0000323 1.9994854 -0.01673357
9300 0 -2.9208476 1.0070892 2.004772 -0.016969206
9350 0 -2.9212065 0.9954353 2.002531 -0.017293607
9400 0 -2.9213536 1.011464 1.9987715 -0.016468707
9450 0 -2.9216568 1.0004584 1.992812 -0.016331783
9500 0 -2.9215087 1.0030182 2.006723 -0.016328481
9550 0 -2.9218914 1.0097858 1.9978241 -0.01513886
9600 0 -2.9221223 1.0064187 1.9937476 -0.014411434
9650 0 -2.9224212 1.0060439 1.9885122 -0.013032442
9700 0 -2.9220952 1.00799 2.0115738 -0.012619136
9750 0 -2.9226088 0.99323702 1.9948387 -0.011548183
9800 0 -2.9225553 0.99626951 2.0047326 -0.010162452
9850 0 -2.9227332 1.006235 2.0036748 -0.0075392887
9900 0 -2.9232122 0.98911031 1.9917417 -0.0055326528
9950 0 -2.9231491 0.99681615 1.9994126 -0.0037310254
10000 0 -2.9235123 0.9884299 1.9875481 -0.0021912307
10050 0 -2.9237223 0.9999364 1.9825867 0.00099300384
10100 0 -2.9235973 0.99000996 1.9970993 0.0021504958
10150 0 -2.9233485 1.0077913 2.0121611 0.004525478
10200 0 -2.9236768 1.0032927 2.0035362 0.007071254
10250 0 -2.9238478 1.0002834 2.003131 0.0096263035
10300 0 -2.9240364 0.99131539 2.0026965 0.011952105
10350 0 -2.9242833 0.99641849 1.9947521 0.014575055
10400 0 -2.9244439 0.99508819 1.9965681 0.018000688
10450 0 -2.9243187 1.0124534 2.0090192 0.021804357
10500 0 -2.9246558 0.99263574 2.0030149 0.023531827
10550 0 -2.9250009 0.99916756 1.9950546 0.027624091
10600 0 -2.9248637 1.0079577 2.0069131 0.02964918
10650 0 -2.9253535 1.0010931 1.994458 0.032931815
10700 0 -2.925576 0.99564043 1.9973125 0.03610588
10750 0 -2.9255597 1.0108614 2.0075111 0.0396819
10800 0 -2.9261759 0.9865698 1.9969888 0.0427848
10850 0 -2.9265088 0.99539121 1.9933442 0.046588103
10900 0 -2.9270268 0.9946174 1.9930678 0.052105624
10950 0 -2.9270626 1.0042522 2.0070013 0.055801296
11000 0 -2.9274337 1.0073265 2.0057225 0.059701269
11050 0 -2.927977 0.99674096 1.9951088 0.062406122
11100 0 -2.9280496 1.0088979 2.0105292 0.066470787
11150 0 -2.928782 0.99018003 1.990749 0.068640734
11200 0 -2.9290447 0.99949136 2.0055469 0.073700453
11250 0 -2.9297585 1.0015608 1.9941199 0.078090219
11300 0 -2.929934 1.0057572 2.0034521 0.080757029
11350 0 -2.9305123 0.99951982 1.9941245 0.083214206
11365 0 -2.9302543 1.0058576 2.0105109 0.083648804
Loop time of 1.01754 on 4 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.8790759758 -2.93081588364 -2.93025426371
Force two-norm initial, final = 3556.23 12.2587
Force max component initial, final = 2979.1 9.18102
Final line search alpha, max atom move = 2.99243e-05 0.000274736
Iterations, force evaluations = 10000 10062
Pair time (%) = 0.498018 (48.9434)
Neigh time (%) = 0.0017876 (0.175679)
Comm time (%) = 0.107307 (10.5457)
Outpt time (%) = 0.00365829 (0.359524)
Other time (%) = 0.406768 (39.9757)
Nlocal: 200 ave 205 max 194 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 178 ave 181 max 173 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 1857.25 ave 1884 max 1824 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 7429
Ave neighs/atom = 9.28625
Neighbor list builds = 29
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 17.139 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.44651 -1917.3971 0 -149.11346 1306.17
20 539.94305 -1778.786 0 -150.72199 2492.7873
30 449.49509 -1506.4706 0 -151.12989 4667.6248
40 331.86049 -1151.7344 0 -151.09164 7379.764
50 258.27083 -929.8024 0 -151.05092 9103.558
60 256.1869 -923.58742 0 -151.1195 9252.9158
70 281.76061 -1000.7367 0 -151.1576 8739.2518
80 300.28534 -1056.589 0 -151.15321 8324.8812
90 305.83368 -1073.3097 0 -151.14426 8175.2478
100 304.06857 -1067.9843 0 -151.14112 8191.234
Loop time of 3.42543 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.27706 (95.6685)
Neigh time (%) = 0.0675609 (1.97233)
Comm time (%) = 0.0221717 (0.647268)
Outpt time (%) = 0.000853539 (0.0249177)
Other time (%) = 0.0577855 (1.68695)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22235 ave 22235 max 22235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183715
Ave neighs/atom = 93.6092
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.10679e+03
Fix MSST e0 = to be -1.51141e+02
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 17.1454 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
Loop time of 4.37563 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.2868 (75.1161)
Neigh time (%) = 0.136101 (3.11044)
Comm time (%) = 0.0217741 (0.497621)
Outpt time (%) = 0.0132105 (0.301912)
Other time (%) = 0.917742 (20.974)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22205 ave 22205 max 22205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183494
Ave neighs/atom = 93.5997
Neighbor list builds = 2
Dangerous builds = 0

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@ -1,138 +0,0 @@
LAMMPS (1 Feb 2014)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 5.52772 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.47212 -1917.4465 0 -149.08565 1305.7368
20 540.13678 -1779.3375 0 -150.68935 2488.8545
30 450.11466 -1508.2891 0 -151.08028 4655.1306
40 332.99843 -1155.1208 0 -151.04685 7357.5162
50 259.2571 -932.72753 0 -151.0022 9086.2087
60 256.22581 -923.67654 0 -151.0913 9257.1571
70 281.12085 -998.79866 0 -151.14863 8759.7887
80 299.37658 -1053.8476 0 -151.1519 8352.9467
90 304.24026 -1068.4941 0 -151.13319 8218.1594
100 301.9683 -1061.6332 0 -151.12284 8244.1277
Loop time of 0.88372 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.820597 (92.8571)
Neigh time (%) = 0.0170572 (1.93016)
Comm time (%) = 0.0299263 (3.3864)
Outpt time (%) = 0.000454426 (0.0514219)
Other time (%) = 0.0156853 (1.77492)
Nlocal: 5832 ave 5850 max 5813 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 10571 ave 10590 max 10553 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 545762 ave 548069 max 543643 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 2183047
Ave neighs/atom = 93.5805
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.18624e+03
Fix MSST e0 = to be -1.51123e+02
Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 5.52772 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
Loop time of 1.15112 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.834059 (72.4563)
Neigh time (%) = 0.0344771 (2.99509)
Comm time (%) = 0.0392016 (3.40552)
Outpt time (%) = 0.00405097 (0.351916)
Other time (%) = 0.239331 (20.7912)
Nlocal: 5832 ave 5874 max 5803 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 10563.8 ave 10588 max 10526 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 545708 ave 550787 max 542668 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 2182834
Ave neighs/atom = 93.5714
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (3 May 2014)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
1 by 1 by 1 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 21.4036 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
3 -61506.574 0 0 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 2196.3697 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.969872 on 1 procs for 3 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5583555 -61506.5743242
Force two-norm initial, final = 17.893 9.98801
Force max component initial, final = 0.757547 0.314107
Final line search alpha, max atom move = 0.000178805 5.61639e-05
Iterations, force evaluations = 3 25
Pair time (%) = 0.747406 (77.0623)
Bond time (%) = 0.000653505 (0.0673806)
Kspce time (%) = 0.218625 (22.5416)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00222945 (0.229871)
Outpt time (%) = 0 (0)
Other time (%) = 0.000958443 (0.0988216)
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10804 ave 10804 max 10804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 596960 ave 596960 max 596960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.19392e+06 ave 1.19392e+06 max 1.19392e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
Memory usage per processor = 20.9138 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
3 -60263.869 1242.7057 298 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 6988.0868 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58834.736 1260.2404 302.20481 -60094.977 213.89563 0 0 0 6132.6243 -20255.127 -46186.37 21262.808 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58828.252 1242.7057 298 -60070.958 437.82815 0 0 0 6455.2967 -20778.873 -46185.21 20113.98 22.5907 22.359 23.4708 0 0 0 11855.229
103 -58827.642 1235.2387 296.20942 -60062.881 453.5865 0 0 0 6411.1525 -20743.952 -46183.668 18788.656 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 5.86221 on 1 procs for 100 steps with 1400 atoms
Pair time (%) = 4.88784 (83.3788)
Bond time (%) = 0.00446033 (0.0760863)
Kspce time (%) = 0.840367 (14.3353)
Neigh time (%) = 0.0973861 (1.66125)
Comm time (%) = 0.01776 (0.302958)
Outpt time (%) = 0.000123978 (0.00211486)
Other time (%) = 0.0142703 (0.243429)
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10843 ave 10843 max 10843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 595351 ave 595351 max 595351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.1907e+06 ave 1.1907e+06 max 1.1907e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1190702
Ave neighs/atom = 850.501
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (3 May 2014)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
2 by 1 by 2 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 10.9549 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
3 -61506.574 0 0 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 2196.3697 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.288323 on 4 procs for 3 steps with 1400 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5583555 -61506.5743242
Force two-norm initial, final = 17.893 9.98801
Force max component initial, final = 0.757547 0.314107
Final line search alpha, max atom move = 0.000178805 5.61639e-05
Iterations, force evaluations = 3 25
Pair time (%) = 0.19587 (67.9344)
Bond time (%) = 0.000175655 (0.060923)
Kspce time (%) = 0.0835239 (28.9689)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00802237 (2.78243)
Outpt time (%) = 0 (0)
Other time (%) = 0.000730693 (0.253429)
Nlocal: 350 ave 399 max 305 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6602 ave 6647 max 6553 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 149240 ave 170954 max 129384 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 298480 ave 340157 max 260160 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:195)
Memory usage per processor = 10.7173 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
3 -60263.869 1242.7057 298 -61506.574 192.23343 0 0 0 5462.762 -20966.52 -46195.05 6988.0868 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58834.736 1260.2404 302.20481 -60094.977 213.89563 0 0 0 6132.6243 -20255.127 -46186.37 21262.808 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58828.252 1242.7057 298 -60070.958 437.82815 0 0 0 6455.2967 -20778.873 -46185.21 20113.98 22.5907 22.359 23.4708 0 0 0 11855.229
103 -58827.642 1235.2387 296.20942 -60062.881 453.5865 0 0 0 6411.1525 -20743.952 -46183.668 18788.656 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 1.67162 on 4 procs for 100 steps with 1400 atoms
Pair time (%) = 1.28323 (76.7654)
Bond time (%) = 0.00121307 (0.0725687)
Kspce time (%) = 0.22219 (13.2919)
Neigh time (%) = 0.0252143 (1.50837)
Comm time (%) = 0.123892 (7.4115)
Outpt time (%) = 0.000187218 (0.0111998)
Other time (%) = 0.0156981 (0.939097)
Nlocal: 350 ave 356 max 341 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 6638.5 ave 6656 max 6627 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 148838 ave 151622 max 145706 min
Histogram: 1 0 0 0 1 0 1 0 0 1
FullNghs: 297676 ave 302447 max 289666 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 1190702
Ave neighs/atom = 850.501
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
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
40 settings made for type
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 temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
#dump 1 all custom 5000 dump.nemd id type x y z
#dump 2 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
#dump_modify 3 pad 5
thermo 1000
run 50000
Memory usage per processor = 2.06269 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1132807 0.27905278 0 1.3853755 6.5147704 189.52855
2000 1.0443617 0.2588631 0 1.2966975 5.8123077 189.52855
3000 0.99740048 0.30663122 0 1.2977979 6.7893948 189.52855
4000 1.0452154 0.2549558 0 1.2936386 5.9682721 189.52855
5000 1.0446171 0.24804329 0 1.2861316 6.0510081 189.52855
6000 0.99414736 0.27672942 0 1.2646634 6.1314117 189.52855
7000 0.98222339 0.25264497 0 1.2287295 5.835047 189.52855
8000 1.0949044 0.21576814 0 1.3038294 5.491461 189.52855
9000 1.0926686 0.24221385 0 1.3280532 6.3130763 189.52855
10000 1.076097 0.2855754 0 1.3549468 5.8734258 189.52855
11000 0.99180114 0.32327904 0 1.3088814 6.7664177 189.52855
12000 0.92157563 0.3649801 0 1.2807959 7.1346057 189.52855
13000 1.0357975 0.24757954 0 1.2769033 5.1431799 189.52855
14000 1.0007104 0.23333402 0 1.22779 5.7856096 189.52855
15000 0.99137134 0.24780673 0 1.232982 6.1361025 189.52855
16000 0.94735806 0.285215 0 1.2266521 6.5489235 189.52855
17000 0.92947519 0.35111458 0 1.2747806 6.8906691 189.52855
18000 0.93468492 0.30314528 0 1.2319884 6.7846869 189.52855
19000 0.97664561 0.22133285 0 1.1918744 5.1668518 189.52855
20000 0.92288444 0.24361535 0 1.1607318 5.8575076 189.52855
21000 0.95982212 0.23711835 0 1.1909416 6.1133698 189.52855
22000 0.94710657 0.30873344 0 1.2499206 6.7011709 189.52855
23000 0.95315902 0.25917016 0 1.2063719 6.436954 189.52855
24000 0.92248708 0.25883982 0 1.1755614 6.7367986 189.52855
25000 0.90317019 0.26834925 0 1.1658746 5.8271823 189.52855
26000 0.91432206 0.29952864 0 1.2081362 7.2639988 189.52855
27000 1.0070883 0.25437551 0 1.2551695 5.9319042 189.52855
28000 0.90757676 0.33894646 0 1.2408509 6.5341369 189.52855
29000 0.93635654 0.27447038 0 1.2049747 5.7410459 189.52855
30000 1.0260914 0.26547724 0 1.2851555 6.7175944 189.52855
31000 1.0885528 0.22068838 0 1.3024377 5.9614548 189.52855
32000 0.99983894 0.26432646 0 1.2579164 5.6537115 189.52855
33000 0.98254278 0.25012552 0 1.2265274 6.00352 189.52855
34000 1.0461448 0.239846 0 1.2794524 5.8594944 189.52855
35000 1.0600085 0.32706153 0 1.3804449 7.1757696 189.52855
36000 1.0293724 0.37370741 0 1.3966463 7.1818303 189.52855
37000 0.99724062 0.35645069 0 1.3474586 7.3712517 189.52855
38000 1.1355196 0.23285267 0 1.3612752 5.9101916 189.52855
39000 1.0750755 0.31068535 0 1.3790417 6.7523098 189.52855
40000 1.0269017 0.38361397 0 1.4040975 7.532356 189.52855
41000 0.98265149 0.34340216 0 1.3199121 6.9652101 189.52855
42000 0.95262128 0.36420847 0 1.3108759 7.5380723 189.52855
43000 1.0124646 0.25137287 0 1.2575095 6.6275506 189.52855
44000 0.95142407 0.29804153 0 1.2435192 5.9780096 189.52855
45000 0.99724723 0.19281581 0 1.1838302 5.4332418 189.52855
46000 0.90112949 0.29935892 0 1.1948564 7.0600659 189.52855
47000 0.8786086 0.34312007 0 1.2162374 6.4678979 189.52855
48000 1.0516991 0.17931414 0 1.2244401 5.5158284 189.52855
49000 0.98386816 0.26044721 0 1.2381662 5.8913908 189.52855
50000 1.0316312 0.19654107 0 1.2217246 5.2461518 189.52855
Loop time of 1.10994 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.192406 (17.3349)
Neigh time (%) = 0.139588 (12.5762)
Comm time (%) = 0.0557146 (5.01961)
Outpt time (%) = 0.000450134 (0.0405549)
Other time (%) = 0.721779 (65.0287)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 351 ave 351 max 351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 351
Ave neighs/atom = 2.19375
Neighbor list builds = 5281
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
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
40 settings made for type
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 temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
#dump 1 all custom 5000 dump.nemd id type x y z
#dump 2 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
#dump_modify 3 pad 5
thermo 1000
run 50000
Memory usage per processor = 2.06108 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.124295 0.28924371 0 1.4065119 7.0530596 189.52855
2000 0.95544082 0.41610026 0 1.3655696 8.2906389 189.52855
3000 1.0379332 0.3006166 0 1.3320627 6.6571959 189.52855
4000 1.0384606 0.21868978 0 1.25066 5.5810527 189.52855
5000 0.94117133 0.28986466 0 1.2251537 6.7004134 189.52855
6000 0.8855088 0.29250925 0 1.1724836 6.0234641 189.52855
7000 0.89371735 0.22907448 0 1.1172061 6.0996491 189.52855
8000 0.91424769 0.21379978 0 1.1223334 5.3165508 189.52855
9000 0.90042293 0.21884136 0 1.1136366 5.488714 189.52855
10000 0.85048519 0.25030732 0 1.095477 5.6995459 189.52855
11000 0.84698813 0.26740545 0 1.1090999 6.0227022 189.52855
12000 0.84154976 0.27476871 0 1.1110588 6.1957407 189.52855
13000 0.95858623 0.24922085 0 1.2018159 6.1788034 189.52855
14000 1.0214286 0.21791039 0 1.2329551 5.4418702 189.52855
15000 1.0398737 0.2633112 0 1.2966857 6.4069155 189.52855
16000 1.0064086 0.32204447 0 1.322163 6.9037595 189.52855
17000 0.95972629 0.32803912 0 1.2817671 6.816773 189.52855
18000 0.97474673 0.27514532 0 1.2437999 6.5619061 189.52855
19000 0.98058523 0.29730787 0 1.2717644 6.3947579 189.52855
20000 1.0096005 0.29191846 0 1.2952089 6.5005373 189.52855
21000 1.0340906 0.30603597 0 1.3336635 6.6365016 189.52855
22000 1.0986576 0.25246406 0 1.3442551 6.3254116 189.52855
23000 1.0118481 0.31753984 0 1.3230639 6.0921359 189.52855
24000 1.0766759 0.20245452 0 1.2724012 5.4505434 189.52855
25000 1.1081144 0.1941749 0 1.2953635 5.4769844 189.52855
26000 1.0100198 0.29200311 0 1.2957102 6.4496868 189.52855
27000 1.0780229 0.22518995 0 1.2964752 5.4742933 189.52855
28000 0.95411135 0.30374431 0 1.2518925 6.4759593 189.52855
29000 0.89919125 0.33340443 0 1.2269757 7.2806173 189.52855
30000 1.0252498 0.21740235 0 1.2362443 6.0225096 189.52855
31000 0.94842379 0.29574176 0 1.2382379 6.6857537 189.52855
32000 0.98564692 0.28884608 0 1.2683327 5.8893159 189.52855
33000 1.0203197 0.25128893 0 1.2652316 6.3876672 189.52855
34000 0.92927072 0.35791559 0 1.2813784 6.9518532 189.52855
35000 1.0595999 0.2526221 0 1.3055995 6.3468891 189.52855
36000 1.0080572 0.3373598 0 1.3391167 6.8836622 189.52855
37000 1.0371553 0.39107985 0 1.421753 7.8264775 189.52855
38000 1.1399348 0.32003125 0 1.4528415 6.7472192 189.52855
39000 1.1719539 0.28244065 0 1.4470698 6.1962707 189.52855
40000 1.160549 0.2692168 0 1.4225124 6.4898037 189.52855
41000 1.082068 0.31445471 0 1.3897598 7.1045082 189.52855
42000 1.1200126 0.24056295 0 1.3535754 6.1401582 189.52855
43000 1.1131393 0.25879245 0 1.3649747 5.6653752 189.52855
44000 1.0584865 0.28294496 0 1.3348159 6.7007718 189.52855
45000 1.1250306 0.22801778 0 1.346017 5.5953791 189.52855
46000 1.0799948 0.25829243 0 1.3315373 6.2101875 189.52855
47000 1.0466019 0.30437314 0 1.3444338 6.5602361 189.52855
48000 0.99707221 0.2760815 0 1.266922 6.3946457 189.52855
49000 0.96261953 0.29992833 0 1.2565315 6.7358834 189.52855
50000 0.91044957 0.33413644 0 1.2388957 6.7732395 189.52855
Loop time of 0.905642 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.0493886 (5.45344)
Neigh time (%) = 0.0384813 (4.24906)
Comm time (%) = 0.366813 (40.5031)
Outpt time (%) = 0.000886261 (0.0978601)
Other time (%) = 0.450073 (49.6966)
Nlocal: 40 ave 42 max 38 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 36.25 ave 42 max 34 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 91 ave 103 max 84 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 364
Ave neighs/atom = 2.275
Neighbor list builds = 5274
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# 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 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 100 dump.obstacle
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 2.06342 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
3000 1 -0.52004751 0 0.16655848 1.4177739 1324.489
4000 1 -0.50683869 0 0.17976729 1.4851498 1370.896
5000 1 -0.49074513 0 0.19586085 1.2870129 1411.5513
6000 1 -0.45051896 0 0.23608702 1.2173953 1441.7581
7000 1 -0.44428914 0 0.24231685 1.2136189 1451.7268
8000 1 -0.41943736 0 0.26716862 1.0476856 1463.0805
9000 1 -0.42143857 0 0.26516741 1.1040812 1449.7584
10000 1 -0.40181705 0 0.28478893 0.97148485 1448.5974
11000 1 -0.4088962 0 0.27770978 1.1761219 1440.3567
12000 1 -0.38630717 0 0.30029881 1.0593811 1444.9934
13000 1 -0.37152911 0 0.31507687 0.98075952 1448.0726
14000 1 -0.37370096 0 0.31290502 1.0046443 1449.4749
15000 1 -0.39915937 0 0.28744662 1.0240313 1452.3583
16000 1 -0.37562636 0 0.31097963 1.0053468 1452.3514
17000 1 -0.35736161 0 0.32924437 1.070682 1452.898
18000 1 -0.38767402 0 0.29893196 1.0418661 1456.1288
19000 1 -0.38489181 0 0.30171417 1.0361798 1446.8804
20000 1 -0.39521864 0 0.29138735 1.0754044 1447.4619
21000 1 -0.37845983 0 0.30814615 1.0072922 1453.8721
22000 1 -0.40926684 0 0.27733914 1.0929362 1452.8181
23000 1 -0.3586683 0 0.32793768 1.006092 1459.6104
24000 1 -0.38908821 0 0.29751777 0.95291948 1464.8522
25000 1 -0.38890426 0 0.29770172 0.95284427 1455.9361
Loop time of 1.70272 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.496648 (29.1678)
Neigh time (%) = 0.140946 (8.27769)
Comm time (%) = 0.0254805 (1.49646)
Outpt time (%) = 0.000277758 (0.0163125)
Other time (%) = 1.03937 (61.0417)
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1624 ave 1624 max 1624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1624
Ave neighs/atom = 2.11183
Neighbor list builds = 1642
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
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 group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# 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 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 100 dump.obstacle
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 2.05581 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
3000 1 -0.49062349 0 0.1959825 1.5239344 1322.2627
4000 1 -0.50104941 0 0.18555657 1.4605776 1367.6505
5000 1 -0.4655479 0 0.22105808 1.3317864 1406.9197
6000 1 -0.50936502 0 0.17724096 1.2130158 1424.3621
7000 1 -0.44959207 0 0.23701391 1.1070391 1443.1
8000 1 -0.42617261 0 0.26043338 1.2005043 1444.8955
9000 1 -0.41192389 0 0.2746821 1.0022569 1450.9691
10000 1 -0.40940409 0 0.27720189 0.98653582 1447.7805
11000 1 -0.4093125 0 0.27729348 1.0625786 1446.6852
12000 1 -0.41948268 0 0.26712331 1.1166793 1449.6135
13000 1 -0.38874722 0 0.29785877 0.99617473 1456.1633
14000 1 -0.40067763 0 0.28592835 0.98191459 1454.6009
15000 1 -0.39026612 0 0.29633987 1.0245506 1452.7783
16000 1 -0.39139643 0 0.29520955 1.0281029 1451.2662
17000 1 -0.37821271 0 0.30839327 1.0108601 1454.1047
18000 1 -0.37382372 0 0.31278227 0.93743647 1457.2083
19000 1 -0.3737367 0 0.31286928 1.0333603 1458.6131
20000 1 -0.37232139 0 0.31428459 1.0471568 1448.6511
21000 1 -0.40114891 0 0.28545707 1.0045402 1455.5644
22000 1 -0.36552339 0 0.32108259 0.99841802 1459.4723
23000 1 -0.35573934 0 0.33086665 0.89283563 1460.8941
24000 1 -0.3608262 0 0.32577978 1.0097641 1453.0004
25000 1 -0.36649381 0 0.32011217 0.98366691 1451.5444
Loop time of 0.843615 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.125471 (14.873)
Neigh time (%) = 0.0379742 (4.50136)
Comm time (%) = 0.221488 (26.2546)
Outpt time (%) = 0.000505328 (0.0599003)
Other time (%) = 0.458177 (54.3111)
Nlocal: 192.25 ave 242 max 159 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 43 ave 45 max 39 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 414 ave 588 max 284 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 1656
Ave neighs/atom = 2.15345
Neighbor list builds = 1641
Dangerous builds = 1

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LAMMPS (1 Feb 2014)
# 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
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
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 temp 275.0 275.0 100.0 tchain 1
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 image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
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 = 22.9109 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.9759 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 1.9636 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
---------------- Step 150 ----- CPU = 2.9816 (sec) ----------------
TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26717.2584 E_long = -33907.2812 Press = -333.1895
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50856e-07
8 1.08 6.58343e-08
10 1.111 5.55349e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388184
---------------- Step 200 ----- CPU = 3.9551 (sec) ----------------
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
---------------- Step 250 ----- CPU = 4.9818 (sec) ----------------
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5411
E_coul = 26713.8466 E_long = -33908.7226 Press = -188.8083
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50137e-06
8 1.08 2.09323e-06
10 1.111 5.64331e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.67992e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 6.0094 (sec) ----------------
TotEng = -5251.4349 KinEng = 1123.6255 Temp = 279.2934
PotEng = -6375.0604 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4556
E_coul = 26745.4104 E_long = -33909.1249 Press = -469.5456
Loop time of 6.00943 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 4.59488 (76.4612)
Bond time (%) = 0.0122511 (0.203865)
Kspce time (%) = 0.654233 (10.8868)
Neigh time (%) = 0.642603 (10.6932)
Comm time (%) = 0.0338275 (0.562907)
Outpt time (%) = 0.000135899 (0.00226142)
Other time (%) = 0.0715001 (1.1898)
FFT time (% of Kspce) = 0.0813602 (12.436)
FFT Gflps 3d (1d only) = 2.02205 3.15151
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: 708028 ave 708028 max 708028 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
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 temp 275.0 275.0 100.0 tchain 1
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 image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
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 = 10.3307 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.2818 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 0.5690 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
---------------- Step 150 ----- CPU = 0.8614 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50856e-07
8 1.08 6.58343e-08
10 1.111 5.55349e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388184
---------------- Step 200 ----- CPU = 1.1337 (sec) ----------------
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3869
---------------- Step 250 ----- CPU = 1.4284 (sec) ----------------
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8075
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50139e-06
8 1.08 2.09322e-06
10 1.111 5.6433e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.6799e-06
31 104.52 0.000806335
---------------- Step 300 ----- CPU = 1.7292 (sec) ----------------
TotEng = -5251.4350 KinEng = 1123.6255 Temp = 279.2935
PotEng = -6375.0605 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4558
E_coul = 26745.4101 E_long = -33909.1248 Press = -469.5428
Loop time of 1.72924 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 1.18646 (68.6113)
Bond time (%) = 0.0033986 (0.196537)
Kspce time (%) = 0.24268 (14.0339)
Neigh time (%) = 0.165521 (9.5719)
Comm time (%) = 0.0693463 (4.01021)
Outpt time (%) = 0.000285089 (0.0164864)
Other time (%) = 0.0615544 (3.55962)
FFT time (% of Kspce) = 0.0323979 (13.35)
FFT Gflps 3d (1d only) = 5.07792 11.9536
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: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

90
examples/peri/log.peri.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 24.2469 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358398e+28 4532421.1 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
1000 1.2341036e+28 3219688.2 0 8.9417102e+08 1.596857e+14 3.7196039e-06
Loop time of 19.4915 on 1 procs for 1000 steps with 3487 atoms
Pair time (%) = 18.802 (96.4629)
Neigh time (%) = 0.572242 (2.93586)
Comm time (%) = 0.00180793 (0.00927548)
Outpt time (%) = 0.000235081 (0.00120607)
Other time (%) = 0.115146 (0.59075)
Nlocal: 3487 ave 3487 max 3487 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: 567135 ave 567135 max 567135 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

90
examples/peri/log.peri.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 18.744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.3 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358398e+28 4532419.8 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
1000 1.2341036e+28 3219727.8 0 8.9417105e+08 1.596857e+14 3.7196039e-06
Loop time of 5.56029 on 4 procs for 1000 steps with 3487 atoms
Pair time (%) = 4.77191 (85.8212)
Neigh time (%) = 0.146942 (2.64271)
Comm time (%) = 0.597594 (10.7475)
Outpt time (%) = 0.000327229 (0.00588511)
Other time (%) = 0.0435197 (0.782687)
Nlocal: 871.75 ave 910 max 835 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 1343.25 ave 1380 max 1305 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 141784 ave 170146 max 116083 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

147
examples/pour/log.pour.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 MPI 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/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
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
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 8.27911 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1522.1986 68.863683 6600
8000 1206 1387.2223 64.067846 6600
9000 1206 1265.901 51.727094 6600
10000 1608 1460.2854 48.630285 6600
11000 1608 1310.6204 52.851955 6600
12000 1608 1128.6198 46.139167 6600
13000 2010 1178.8622 50.202317 6600
14000 2010 1187.0109 39.476651 6600
15000 2010 989.72713 38.740987 6600
16000 2412 1120.2349 40.342828 6600
17000 2412 1075.0554 39.589605 6600
18000 2412 855.00318 40.858609 6600
19000 2814 950.88458 41.511679 6600
20000 2814 923.42023 36.068246 6600
21000 2814 794.06955 41.150212 6600
22000 2814 548.02348 35.370804 6600
23000 3000 463.81576 37.573817 6600
24000 3000 336.43523 25.743644 6600
25000 3000 234.89941 20.298489 6600
Loop time of 9.30611 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 5.33047 (57.2792)
Neigh time (%) = 1.05786 (11.3674)
Comm time (%) = 0.251292 (2.70029)
Outpt time (%) = 0.000475883 (0.00511366)
Other time (%) = 2.66602 (28.648)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 671 ave 671 max 671 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13616 ave 13616 max 13616 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13616
Ave neighs/atom = 4.53867
Neighbor list builds = 1149
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 9.07965 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 234.89941 20.298489 6600
26000 3000 82.315315 21.537116 6600
27000 3000 108.89519 11.940364 6600
28000 3000 200.16687 11.301946 6600
29000 3000 349.26838 15.094407 6600
30000 3000 569.81999 18.792925 6600
31000 3000 898.94346 28.160958 6600
32000 3000 1240.4814 33.875237 6600
33000 3000 1731.5017 41.915333 6600
34000 3000 2295.7732 48.265714 6600
35000 3000 2886.4882 61.48829 6600
36000 3000 3662.1785 79.477977 6600
37000 3000 4508.9506 87.503245 6600
38000 3000 5487.5698 105.18573 6600
39000 3000 6502.5504 107.5985 6600
40000 3000 7472.1021 126.10799 6600
41000 3000 8747.8718 152.09945 6600
42000 3000 10083.088 151.89644 6600
43000 3000 11433.111 170.87026 6600
44000 3000 12876.825 194.58992 6600
45000 3000 14274.884 189.94299 6600
46000 3000 15664.174 225.06085 6600
47000 3000 17213.88 222.67736 6600
48000 3000 18826.294 240.96943 6600
49000 3000 20558.693 264.45506 6600
50000 3000 22270.716 276.57672 6600
Loop time of 18.1762 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 11.5992 (63.8153)
Neigh time (%) = 1.71333 (9.42624)
Comm time (%) = 0.540144 (2.97171)
Outpt time (%) = 0.000629663 (0.00346421)
Other time (%) = 4.32291 (23.7833)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 760 ave 760 max 760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14151 ave 14151 max 14151 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14151
Ave neighs/atom = 4.717
Neighbor list builds = 873
Dangerous builds = 0

147
examples/pour/log.pour.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 MPI 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/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
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
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 1000 dump.pour
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 8.15424 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1521.8348 69.010381 6600
8000 1206 1391.0761 64.407585 6600
9000 1206 1264.9766 50.327155 6600
10000 1608 1463.0633 49.89601 6600
11000 1608 1316.7149 52.402835 6600
12000 1608 1114.153 46.872522 6600
13000 2010 1205.8869 51.481237 6600
14000 2010 1185.8628 42.191907 6600
15000 2010 972.77031 43.899414 6600
16000 2412 1104.0835 40.181571 6600
17000 2412 1071.8592 41.109972 6600
18000 2412 855.89199 38.898224 6600
19000 2814 974.59266 41.798845 6600
20000 2814 949.73588 41.312762 6600
21000 2814 785.75949 39.506434 6600
22000 2814 568.33487 35.152281 6600
23000 3000 469.29459 37.172088 6600
24000 3000 335.08614 25.096975 6600
25000 3000 235.38783 16.956807 6600
Loop time of 2.9825 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 1.36805 (45.8694)
Neigh time (%) = 0.27838 (9.33378)
Comm time (%) = 0.419477 (14.0646)
Outpt time (%) = 0.000649214 (0.0217675)
Other time (%) = 0.915936 (30.7104)
Nlocal: 750 ave 767 max 740 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 389 ave 399 max 379 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3555.75 ave 3653 max 3498 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 14223
Ave neighs/atom = 4.741
Neighbor list builds = 1151
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 8.928 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 235.38783 16.956807 6600
26000 3000 86.095398 21.734167 6600
27000 3000 105.34548 13.070765 6600
28000 3000 194.48452 12.668302 6600
29000 3000 338.66556 14.53448 6600
30000 3000 561.95176 20.01635 6600
31000 3000 863.55789 28.935939 6600
32000 3000 1245.8566 31.126919 6600
33000 3000 1747.0561 43.002491 6600
34000 3000 2297.4715 52.916382 6600
35000 3000 2979.0692 60.599758 6600
36000 3000 3668.5934 70.783571 6600
37000 3000 4550.9061 84.848649 6600
38000 3000 5458.0534 96.028867 6600
39000 3000 6461.8152 108.41301 6600
40000 3000 7504.9659 119.17697 6600
41000 3000 8622.1932 129.66834 6600
42000 3000 9729.2779 150.83916 6600
43000 3000 11006.529 161.20608 6600
44000 3000 12332.682 172.45763 6600
45000 3000 13532.399 168.86419 6600
46000 3000 14872.632 194.18978 6600
47000 3000 16262.818 209.10627 6600
48000 3000 17620.467 204.85493 6600
49000 3000 19038.858 242.63587 6600
50000 3000 20554.586 248.70106 6600
Loop time of 5.60379 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 3.03686 (54.193)
Neigh time (%) = 0.445322 (7.94679)
Comm time (%) = 0.673944 (12.0266)
Outpt time (%) = 0.000772476 (0.0137849)
Other time (%) = 1.44689 (25.8198)
Nlocal: 750 ave 766 max 736 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 402.75 ave 414 max 392 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 3675.25 ave 3716 max 3594 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 14701
Ave neighs/atom = 4.90033
Neighbor list builds = 859
Dangerous builds = 0

100
examples/pour/log.pour.2d.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) 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 = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
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 range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 8.39742 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550227 5000
10000 896 1632.2116 76.952268 5000
11000 896 1594.7057 65.263337 5000
12000 896 1539.5424 56.179956 5000
13000 1000 1502.7779 61.791119 5000
14000 1000 1264.0565 50.885098 5000
15000 1000 1028.8287 48.271488 5000
16000 1000 742.47431 43.031382 5000
17000 1000 466.70958 35.374711 5000
18000 1000 311.97604 30.342738 5000
19000 1000 217.15209 31.325292 5000
20000 1000 53.963502 21.545193 5000
21000 1000 20.574937 12.436765 5000
22000 1000 14.952026 8.8587603 5000
23000 1000 12.308193 7.3973013 5000
24000 1000 11.398735 5.1815744 5000
25000 1000 10.066348 4.0359674 5000
Loop time of 2.91316 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.21785 (41.8051)
Neigh time (%) = 0.312445 (10.7253)
Comm time (%) = 0.0109541 (0.376022)
Outpt time (%) = 0.000334263 (0.0114742)
Other time (%) = 1.37158 (47.0821)
Nlocal: 1000 ave 1000 max 1000 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: 2362 ave 2362 max 2362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2362
Ave neighs/atom = 2.362
Neighbor list builds = 2038
Dangerous builds = 0

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examples/pour/log.pour.2d.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) 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 = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
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 range 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 250 dump.pour
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Memory usage per processor = 8.36296 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550227 5000
10000 896 1631.0865 79.644395 5000
11000 896 1592.1233 66.618058 5000
12000 896 1538.0168 62.305427 5000
13000 1000 1504.7663 60.453118 5000
14000 1000 1258.4278 56.953463 5000
15000 1000 1051.3757 49.481041 5000
16000 1000 745.26845 46.064462 5000
17000 1000 461.4175 44.190391 5000
18000 1000 321.52252 32.000638 5000
19000 1000 219.94195 27.786071 5000
20000 1000 47.588667 19.150667 5000
21000 1000 22.265142 13.29654 5000
22000 1000 16.795774 9.1519062 5000
23000 1000 14.227042 7.3286667 5000
24000 1000 10.712738 5.4385743 5000
25000 1000 9.180883 3.4376108 5000
Loop time of 0.936714 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 0.304334 (32.4896)
Neigh time (%) = 0.0807448 (8.62001)
Comm time (%) = 0.0846794 (9.04005)
Outpt time (%) = 0.000462651 (0.0493909)
Other time (%) = 0.466493 (49.801)
Nlocal: 250 ave 260 max 230 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 17.5 ave 24 max 12 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 598.25 ave 630 max 546 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 2393
Ave neighs/atom = 2.393
Neighbor list builds = 2035
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
communicate single vel yes cutoff 2.5
fix prop all property/atom mol
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) 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 = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Memory usage per processor = 8.8613 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 208.5324 0.0022531902 5000
2000 130 395.40215 0.0022531902 5000
3000 130 647.2719 0.0022531902 5000
4000 260 1159.1081 0.0026224951 5000
5000 260 1718.8157 0.0026515989 5000
6000 260 2031.535 10.691958 5000
7000 390 2065.2783 21.015337 5000
8000 390 1911.4694 10.935944 5000
9000 390 1884.4332 7.8649255 5000
10000 520 2109.7343 6.3162072 5000
11000 520 2055.0964 9.2024202 5000
12000 520 1737.7978 3.8651428 5000
13000 650 1827.8021 5.4025759 5000
14000 650 1714.9891 5.1408637 5000
15000 650 1460.3591 1.9883146 5000
16000 780 1656.7752 2.6070722 5000
17000 780 1487.906 2.9690473 5000
18000 780 1508.32 2.4036266 5000
19000 910 1508.0974 5.3892045 5000
20000 910 1310.8002 4.8125827 5000
21000 910 1044.281 2.4533982 5000
22000 1040 1188.4887 1.8312293 5000
23000 1040 1405.6437 2.4849983 5000
24000 1040 1287.8333 2.4405773 5000
25000 1170 1190.5047 2.8533518 5000
Loop time of 3.16526 on 1 procs for 25000 steps with 1170 atoms
Pair time (%) = 0.829346 (26.2015)
Neigh time (%) = 0.207036 (6.54087)
Comm time (%) = 0.0133698 (0.422392)
Outpt time (%) = 0.000298738 (0.00943804)
Other time (%) = 2.11521 (66.8258)
Nlocal: 1170 ave 1170 max 1170 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: 1707 ave 1707 max 1707 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1707
Ave neighs/atom = 1.45897
Neighbor list builds = 1751
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
communicate single vel yes cutoff 2.5
fix prop all property/atom mol
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) 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 = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Memory usage per processor = 8.82364 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 208.5324 0.0022531902 5000
2000 130 395.40215 0.0022531902 5000
3000 130 647.2719 0.0022531902 5000
4000 260 1159.1081 0.0026224951 5000
5000 260 1718.8157 0.0026515989 5000
6000 260 2031.535 10.691958 5000
7000 390 2065.2783 21.015337 5000
8000 390 1911.4694 10.935944 5000
9000 390 1884.4332 7.8649255 5000
10000 520 2109.7343 6.3162072 5000
11000 520 2055.0964 9.2024202 5000
12000 520 1737.7978 3.8651428 5000
13000 650 1835.9412 5.4696261 5000
14000 650 1705.5968 4.6127934 5000
15000 650 1458.6093 2.3324994 5000
16000 780 1663.1206 3.4762842 5000
17000 780 1448.6268 2.5272414 5000
18000 780 1439.06 2.3644535 5000
19000 910 1353.2736 3.4079237 5000
20000 910 1303.0395 4.7540237 5000
21000 910 1037.3662 2.6725377 5000
22000 1040 1225.3222 2.0920106 5000
23000 1040 1306.8689 2.4710217 5000
24000 1040 1304.5309 2.5544338 5000
25000 1170 1181.4033 4.5232994 5000
Loop time of 1.24255 on 4 procs for 25000 steps with 1170 atoms
Pair time (%) = 0.219425 (17.6592)
Neigh time (%) = 0.0621997 (5.00579)
Comm time (%) = 0.0965945 (7.77386)
Outpt time (%) = 0.000469327 (0.0377711)
Other time (%) = 0.863865 (69.5234)
Nlocal: 292.5 ave 312 max 278 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 44.5 ave 60 max 28 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 427.5 ave 451 max 399 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 1710
Ave neighs/atom = 1.46154
Neighbor list builds = 1769
Dangerous builds = 0

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LAMMPS (5 Sep 2014)
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 1
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
fix 2 all qeq/dynamic 1 10 1.0e-2 100 param.qeq2
run 10
Ewald initialization ...
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 1696 10 4630
kxmax kymax kzmax = 9 9 10
Memory usage per processor = 11.8158 Mbytes
Step PotEng q1 q2 qtot
0 -15435.276 0.85155361 -0.4257768 1.9326762e-12
1 -15435.28 0.85155361 -0.4257768 1.9326762e-12
2 -15435.356 0.85155361 -0.4257768 1.9326762e-12
3 -15435.5 0.85155361 -0.4257768 1.9326762e-12
4 -15435.714 0.85155361 -0.4257768 1.9326762e-12
5 -15437.489 0.85191124 -0.42595562 1.4210855e-12
6 -15439.474 0.8523022 -0.4261511 1.1937118e-12
7 -15444.065 0.85330143 -0.42665072 1.5347723e-12
8 -15445.582 0.85354575 -0.42677288 1.4210855e-12
9 -15447.225 0.8538033 -0.42690165 1.6484591e-12
10 -15450.727 0.85448844 -0.42724422 1.6484591e-12
Loop time of 0.551397 on 1 procs for 10 steps with 1200 atoms
Pair time (%) = 0.190656 (34.5769)
Kspce time (%) = 0.293027 (53.1427)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000636339 (0.115405)
Outpt time (%) = 0.000331879 (0.0601887)
Other time (%) = 0.0667453 (12.1048)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8100 ave 8100 max 8100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 367600 ave 367600 max 367600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 367600
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0

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examples/qeq/log.qeq.buck.8Sep14.linux.4
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LAMMPS (5 Sep 2014)
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
400 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
800 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot
thermo 1
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
fix 2 all qeq/dynamic 1 10 1.0e-2 100 param.qeq2
run 10
Ewald initialization ...
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 1696 10 4630
kxmax kymax kzmax = 9 9 10
Memory usage per processor = 7.02304 Mbytes
Step PotEng q1 q2 qtot
0 -15435.276 0.85155361 -0.4257768 -2.8421709e-13
1 -15435.28 0.85155361 -0.4257768 -2.8421709e-13
2 -15435.356 0.85155361 -0.4257768 -2.8421709e-13
3 -15435.5 0.85155361 -0.4257768 -2.8421709e-13
4 -15435.714 0.85155361 -0.4257768 -2.8421709e-13
5 -15437.489 0.85191124 -0.42595562 -1.1368684e-13
6 -15439.474 0.8523022 -0.4261511 -1.7053026e-13
7 -15444.065 0.85330143 -0.42665072 -1.7053026e-13
8 -15445.582 0.85354575 -0.42677288 -2.2737368e-13
9 -15447.225 0.8538033 -0.42690165 -2.2737368e-13
10 -15450.727 0.85448844 -0.42724422 0
Loop time of 0.144642 on 4 procs for 10 steps with 1200 atoms
Pair time (%) = 0.0504071 (34.8495)
Kspce time (%) = 0.0739903 (51.154)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00123513 (0.85392)
Outpt time (%) = 0.00030756 (0.212635)
Other time (%) = 0.018702 (12.9299)
Nlocal: 300 ave 300 max 300 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4875 ave 4880 max 4870 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 91900 ave 93081 max 90719 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 367600
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0

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examples/qeq/log.qeq.reaxc.8Sep14.linux.1
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LAMMPS (5 Sep 2014)
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Memory usage per processor = 15.3036 Mbytes
Step PotEng q1 q2 q3 qtot
0 -10226.557 0.095633908 -0.15658752 -0.091167326 3.1086245e-15
1 -10225.583 0.095556852 -0.15641218 -0.091155329 -3.5527137e-15
2 -10222.838 0.095491107 -0.15626315 -0.091144387 4.6629367e-15
3 -10218.529 0.095435139 -0.15613752 -0.091133515 4.8849813e-15
4 -10212.978 0.095388552 -0.15603364 -0.091123602 -1.110223e-15
5 -10206.591 0.095347264 -0.15594222 -0.091114022 -4.8849813e-15
6 -10199.824 0.095311447 -0.15586364 -0.091104787 2.6645353e-15
7 -10193.143 0.095275939 -0.15578522 -0.091096298 -8.8817842e-16
8 -10186.982 0.095240774 -0.15570734 -0.091088152 3.1086245e-15
9 -10181.712 0.095199169 -0.15561444 -0.091079454 0
10 -10177.608 0.09515654 -0.15551833 -0.091071711 -3.1086245e-15
Loop time of 0.028862 on 1 procs for 10 steps with 105 atoms
Pair time (%) = 0.023474 (81.3318)
Neigh time (%) = 0 (0)
Comm time (%) = 4.72069e-05 (0.163561)
Outpt time (%) = 0.000179768 (0.622852)
Other time (%) = 0.00516105 (17.8818)
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.5429
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

89
examples/qeq/log.qeq.reaxc.8Sep14.linux.4
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LAMMPS (5 Sep 2014)
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Memory usage per processor = 11.1055 Mbytes
Step PotEng q1 q2 q3 qtot
0 -10226.557 0.095633887 -0.15658751 -0.091167271 -1.110223e-15
1 -10225.583 0.095556773 -0.15641189 -0.09115546 -4.4408921e-16
2 -10222.838 0.095491109 -0.15626315 -0.091144385 -1.3322676e-15
3 -10218.529 0.095435154 -0.15613758 -0.091133492 -4.4408921e-16
4 -10212.978 0.095388557 -0.15603363 -0.091123632 -1.7763568e-15
5 -10206.591 0.095347386 -0.15594266 -0.091113837 1.110223e-15
6 -10199.824 0.095311782 -0.1558644 -0.09110485 -1.110223e-15
7 -10193.143 0.095275616 -0.15578453 -0.091096188 -4.4408921e-16
8 -10186.982 0.09524102 -0.15570787 -0.091088227 -1.3322676e-15
9 -10181.712 0.095199505 -0.15561531 -0.09107938 4.4408921e-16
10 -10177.608 0.095156459 -0.15551826 -0.091071551 3.9968029e-15
Loop time of 0.0162442 on 4 procs for 10 steps with 105 atoms
Pair time (%) = 0.0100933 (62.1349)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00139159 (8.56667)
Outpt time (%) = 0.000339925 (2.09259)
Other time (%) = 0.00441939 (27.2059)
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.0571
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

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examples/reax/log.reax.rdx.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Memory usage per processor = 2.21676 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.8843
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
20 516.83079 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107972 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574159
30 467.2641 -1940.978 -1913.1215 -35957.488 -2755.021 -6.9179958 0.049322445 0 78.853174 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861769
40 647.45542 -1951.1994 -1912.6006 -5883.714 -2798.3556 17.33481 0.15102863 0 63.235118 0.18070929 -54.59896 0 17.325008 -12.052278 883.01668 -164.21335 0 96.777423
50 716.38085 -1949.4707 -1906.7628 5473.2048 -2800.931 9.2056931 0.1541327 0 85.37148 3.2986104 -78.253597 0 34.86177 -8.5531232 882.01439 -193.8522 0 117.21316
60 1175.2706 -1975.961 -1905.8958 -1939.4802 -2726.5818 -11.651983 0.24296785 0 48.320653 7.1799711 -75.363637 0 16.520124 -4.8869434 844.75415 -194.23296 0 119.73842
70 1156.7 -1975.3463 -1906.3882 24628.243 -2880.5226 25.652536 0.26894314 0 83.724875 7.1049199 -68.70095 0 24.750741 -8.6338272 911.20093 -183.41949 0 113.22771
80 840.23792 -1955.4773 -1905.3855 -17731.433 -2755.7299 -8.0168345 0.13867988 0 86.147409 2.2387302 -76.945849 0 23.595809 -7.2609612 853.63488 -167.88294 0 94.603642
90 365.79009 -1926.4058 -1904.5988 898.4147 -2842.1833 47.368255 0.23109012 0 92.288131 0.38031335 -61.361504 0 18.476365 -12.255471 900.24235 -186.48053 0 116.88854
100 801.32068 -1953.4184 -1905.6467 -2417.7238 -2802.725 4.6677502 0.18046561 0 76.730118 5.4177141 -77.102576 0 24.997222 -7.7554226 898.67346 -196.89124 0 120.38907
Loop time of 0.413409 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.411733 (99.5945)
Neigh time (%) = 0.000702143 (0.169842)
Comm time (%) = 0.000522852 (0.126473)
Outpt time (%) = 0.000288248 (0.0697247)
Other time (%) = 0.000163078 (0.0394472)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1106 ave 1106 max 1106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1106
Ave neighs/atom = 52.6667
Neighbor list builds = 10
Dangerous builds = 0

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examples/reax/log.reax.rdx.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Memory usage per processor = 2.43839 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88429
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51149
20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107974 0.073134189 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
30 467.26409 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179961 0.049322431 0 78.853175 0.13604389 -51.653632 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861771
40 647.45569 -1951.1994 -1912.6005 -5883.7069 -2798.3557 17.334815 0.15102853 0 63.235128 0.18070898 -54.598942 0 17.325005 -12.052278 883.01681 -164.21333 0 96.77741
50 716.38166 -1949.473 -1906.765 5473.1746 -2800.931 9.205706 0.15413271 0 85.371465 3.2986143 -78.253598 0 34.861779 -8.5531229 882.0144 -193.85134 0 117.21005
60 1175.2704 -1975.9608 -1905.8956 -1939.4947 -2726.5814 -11.65205 0.24296778 0 48.320632 7.1799754 -75.363634 0 16.520121 -4.8869383 844.75394 -194.2328 0 119.73838
70 1156.7034 -1975.3496 -1906.3913 24628.204 -2880.5226 25.652517 0.26894307 0 83.724905 7.1048781 -68.700983 0 24.750747 -8.6338357 911.20075 -183.40571 0 113.21084
80 840.23678 -1955.4782 -1905.3864 -17731.413 -2755.7299 -8.0168177 0.13867967 0 86.147442 2.2387235 -76.945834 0 23.595799 -7.2609676 853.63482 -167.88302 0 94.602852
90 365.78801 -1926.4068 -1904.5999 898.3745 -2842.1832 47.368114 0.23109 0 92.288102 0.38031195 -61.361481 0 18.476353 -12.25546 900.24227 -186.48059 0 116.88762
100 801.3241 -1953.4184 -1905.6465 -2417.969 -2802.7245 4.667552 0.18046595 0 76.729919 5.4177255 -77.102568 0 24.997105 -7.7553985 898.67327 -196.8912 0 120.38931
Loop time of 0.52537 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.332517 (63.2919)
Neigh time (%) = 0.000204384 (0.0389029)
Comm time (%) = 0.192075 (36.56)
Outpt time (%) = 0.000397444 (0.0756502)
Other time (%) = 0.000176191 (0.0335366)
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 301.25 ave 827 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1205
Ave neighs/atom = 57.381
Neighbor list builds = 10
Dangerous builds = 0

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examples/reax/log.reax.tatb.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 6.71066 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
5 0.63682726 -44767.817 -44767.09 8391.1654 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3993 0 6388.8594
10 2.4306905 -44769.41 -44766.635 11717.27 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0893 0 6381.8126
15 5.0590385 -44772.631 -44766.856 17125.213 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28964 -1566.5961 252.97781 -654.93836 18835.335 -8719.2621 0 6370.4157
20 8.0678464 -44775.934 -44766.723 24620.53 -61088.791 490.4235 4.7193467 0 1565.5541 20.415031 -260.38514 -1574.1001 253.39804 -654.26838 18815.312 -8703.4032 0 6355.1922
25 10.975525 -44777.233 -44764.703 34381.132 -61068.889 490.53155 4.7164093 0 1566.5715 20.169755 -251.23112 -1582.8552 253.88696 -653.46042 18790.855 -8683.8775 0 6336.3489
Loop time of 5.79205 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 5.73756 (99.0593)
Neigh time (%) = 0.0503938 (0.870052)
Comm time (%) = 0.00252128 (0.0435299)
Outpt time (%) = 0.000276804 (0.00477903)
Other time (%) = 0.0012958 (0.0223721)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds = 0

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examples/reax/log.reax.tatb.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 3.32016 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.023
5 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.8607
10 2.4306932 -44769.412 -44766.637 11717.214 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.1085 0 6381.8302
15 5.0590454 -44772.631 -44766.856 17124.962 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3321 0 6370.4856
20 8.0678552 -44775.923 -44766.712 24620.829 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39805 -654.26837 18815.312 -8703.3072 0 6355.1072
25 10.975535 -44777.231 -44764.7 34381.277 -61068.889 490.53152 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88697 -653.46042 18790.855 -8683.8355 0 6336.3093
Loop time of 2.49995 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 2.42923 (97.1708)
Neigh time (%) = 0.0110765 (0.443066)
Comm time (%) = 0.0582517 (2.33011)
Outpt time (%) = 0.000575066 (0.023003)
Other time (%) = 0.000825465 (0.0330192)
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds = 0

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examples/reax/log.reaxc.rdx.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Memory usage per processor = 13.5445 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79962 0 168.88427
10 1288.6115 -1989.6644 -1912.8422 -19456.351 -2734.6769 -15.607219 0.20177961 0 54.629555 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43321 0 107.75935
20 538.95844 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.907833 0.077926684 0 81.610046 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69268 0 89.316919
30 463.09509 -1933.5765 -1905.9685 -33255.505 -2749.8591 -8.0154611 0.027628698 0 81.627409 0.11972389 -50.262271 0 20.820317 -9.6327034 851.88721 -149.49498 0 79.20571
40 885.49513 -1958.9125 -1906.1227 -4814.654 -2795.644 9.1506168 0.13747487 0 70.948047 0.24360542 -57.862691 0 19.076512 -11.141212 873.73895 -159.99391 0 92.434069
50 861.16162 -1954.4602 -1903.121 -1896.7715 -2784.845 3.8269557 0.15793308 0 79.851627 3.349211 -78.066131 0 32.628923 -7.9565308 872.81849 -190.98571 0 114.76
60 1167.7833 -1971.8435 -1902.2247 -3482.8295 -2705.864 -17.121533 0.22749088 0 44.507695 7.8560068 -74.789008 0 16.256504 -4.6046686 835.83079 -188.33691 0 114.19415
70 1439.9922 -1989.3026 -1903.4557 23845.829 -2890.7894 31.958655 0.26671714 0 85.758299 3.1804114 -71.002957 0 24.357196 -10.311281 905.86803 -175.38497 0 106.7967
80 502.39806 -1930.7551 -1900.804 -20356.294 -2703.8118 -18.66249 0.11286116 0 99.803602 2.0329432 -76.171314 0 19.236971 -6.2786743 826.47466 -166.0314 0 92.539547
90 749.08048 -1946.9839 -1902.3266 17798.53 -2863.7581 42.068713 0.24338045 0 96.181555 0.96183463 -69.955449 0 24.615403 -11.582762 903.68851 -190.13823 0 120.69122
100 1109.6933 -1968.5879 -1902.4322 -4490.3588 -2755.8988 -7.1225497 0.21757669 0 61.806016 7.0826283 -75.645461 0 20.115364 -6.2372642 863.56468 -198.56954 0 122.09943
Loop time of 0.266744 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.24718 (92.6655)
Neigh time (%) = 0.00907397 (3.40175)
Comm time (%) = 0.00053072 (0.198962)
Outpt time (%) = 0.000216246 (0.0810686)
Other time (%) = 0.00974345 (3.65274)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

88
examples/reax/log.reaxc.rdx.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Memory usage per processor = 11.5757 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95822 -1942.7037 -1910.5731 -10725.635 -2803.7394 7.9078291 0.077926697 0 81.610051 0.22951943 -57.557107 0 30.331207 -10.178049 878.9901 -159.68963 0 89.313877
30 463.09523 -1933.5765 -1905.9685 -33255.535 -2749.859 -8.0154756 0.027628846 0 81.627404 0.11972406 -50.262287 0 20.820307 -9.6327017 851.88715 -149.49499 0 79.205722
40 885.49345 -1958.9125 -1906.1228 -4814.6579 -2795.6439 9.1506373 0.1374749 0 70.948017 0.24360495 -57.862671 0 19.076505 -11.141215 873.73891 -159.99392 0 92.434084
50 861.16061 -1954.4602 -1903.1211 -1896.7508 -2784.8451 3.8270211 0.15793303 0 79.851614 3.3492088 -78.06613 0 32.628946 -7.9565395 872.81855 -190.98572 0 114.76
60 1167.7828 -1971.8434 -1902.2247 -3482.8488 -2705.8638 -17.121551 0.227491 0 44.507677 7.8559987 -74.789014 0 16.256493 -4.6046659 835.83066 -188.33693 0 114.19417
70 1439.9917 -1989.3026 -1903.4558 23846.315 -2890.7893 31.958613 0.26671709 0 85.75826 3.1804345 -71.002976 0 24.357232 -10.311269 905.86798 -175.385 0 106.79673
80 502.39502 -1930.755 -1900.8041 -20356.14 -2703.813 -18.662112 0.11286018 0 99.803696 2.0329323 -76.171277 0 19.237208 -6.2787216 826.47527 -166.03126 0 92.539416
90 749.07195 -1946.9842 -1902.3273 17798.308 -2863.7576 42.068592 0.24338053 0 96.18133 0.9618479 -69.955394 0 24.615347 -11.58276 903.68813 -190.13817 0 120.69115
100 1109.687 -1968.5881 -1902.4328 -4490.0888 -2755.9001 -7.1221876 0.21757676 0 61.805736 7.082699 -75.645404 0 20.115587 -6.2372974 863.56536 -198.56966 0 122.09956
Loop time of 0.225687 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.173643 (76.9395)
Neigh time (%) = 0.0053342 (2.36353)
Comm time (%) = 0.00461483 (2.04479)
Outpt time (%) = 0.000434995 (0.192742)
Other time (%) = 0.0416606 (18.4594)
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

86
examples/reax/log.reaxc.tatb.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Memory usage per processor = 168.657 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278
5 0.61603967 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.3525552 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139
15 4.9013321 -44766.36 -44760.764 17716.956 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2549 0 6370.4211
20 7.829462 -44769.686 -44760.747 25205.546 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5195 0 6355.2708
25 10.697905 -44772.904 -44760.691 34232.775 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3691 0 6336.8499
Loop time of 3.55415 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 2.75234 (77.4401)
Neigh time (%) = 0.404833 (11.3904)
Comm time (%) = 0.00249434 (0.0701809)
Outpt time (%) = 0.000215769 (0.00607089)
Other time (%) = 0.394269 (11.0932)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

86
examples/reax/log.reaxc.tatb.1Feb14.linux.4
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LAMMPS (1 Feb 2014)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
fix 4 all reax/c/bonds 5 bonds.reaxc
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Memory usage per processor = 110.859 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44760.998 -44760.998 7827.7868 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277
5 0.61603967 -44761.698 -44760.994 8934.6345 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.352555 -44763.227 -44760.541 12288.585 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9755 0 6381.7133
15 4.9013276 -44766.36 -44760.764 17717.042 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2303 0 6370.3965
20 7.8294571 -44769.686 -44760.747 25205.564 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5115 0 6355.2627
25 10.697903 -44772.904 -44760.691 34232.722 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3809 0 6336.8616
Loop time of 2.12304 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 1.72134 (81.0791)
Neigh time (%) = 0.225867 (10.6388)
Comm time (%) = 0.00605559 (0.285232)
Outpt time (%) = 0.00259632 (0.122292)
Other time (%) = 0.16718 (7.87454)
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation

314
examples/rigid/log.rigid.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
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 9 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
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.86288 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 -7.9722845e-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 1.2554428 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 7.846062 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 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 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 -0.00022115871 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 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 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 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550094 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 -0.00024984565 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 0.127403 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00816727 (6.41058)
Neigh time (%) = 0.0309787 (24.3155)
Comm time (%) = 0.00888801 (6.97629)
Outpt time (%) = 0.00162864 (1.27833)
Other time (%) = 0.0777404 (61.0193)
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

314
examples/rigid/log.rigid.1Feb14.linux.4
View File

@ -1,314 +0,0 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
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 9 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
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.8248 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 -7.9722856e-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 1.2554428 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 7.846062 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 -0.070934367 0 5269.4889 12.025288
3750 16737.731 0.20706557 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 -0.00022115871 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 -0.00039690662 0 5269.5189 12.011706
8500 16738.481 -0.0034646802 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 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 -0.00037652439 0 5269.5216 12.011692
9550 16738.493 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589893 0 5269.4979 12.062708
9750 16738.013 0.13550084 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270547 0 5269.5237 11.395098
9900 16738.489 -0.00024984575 0 5269.5242 11.395084
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.173009 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00257808 (1.49014)
Neigh time (%) = 0.0103006 (5.95377)
Comm time (%) = 0.0810853 (46.8676)
Outpt time (%) = 0.00332773 (1.92344)
Other time (%) = 0.0757175 (43.765)
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

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@ -1,317 +0,0 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
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 9 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.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.93979 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 7.4384278
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 -0.86699139
1200 21815.003 45.317413 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064079
1300 20780.781 217.36508 0 3680.8286 6.0538613
1350 20558.971 254.36484 0 3680.8601 -3.6773928
1400 21485.029 99.812897 0 3680.6511 -16.185475
1450 21771.107 52.159622 0 3680.6775 -2.4756668
1500 21520.948 93.50391 0 3680.3286 2.1023576
1550 21351.418 121.68135 0 3680.2511 5.5159926
1600 20778.805 216.92181 0 3680.0559 15.089192
1650 21477.637 100.21848 0 3679.8247 -1.1045589
1700 18501.336 596.47967 0 3680.0357 -15.679718
1750 18563.641 587.34804 0 3681.2882 33.532242
1800 19110.182 494.82394 0 3679.8543 18.024056
1850 21364.187 119.23612 0 3679.9339 2.5290785
1900 20146.615 322.15055 0 3679.9197 5.7314455
1950 20692.672 231.25319 0 3680.0319 4.2977815
2000 20943.904 189.11228 0 3679.7629 -22.6447
2050 19667.984 401.84213 0 3679.8394 3.6248494
2100 20280.339 299.77895 0 3679.8354 7.480669
2150 19181.64 483.55835 0 3680.4983 22.624694
2200 21300.479 130.65196 0 3680.7318 4.7093384
2250 20486.287 266.74857 0 3681.1297 -8.6495123
2300 18651.575 572.50504 0 3681.1009 -5.261082
2350 21514.238 95.495372 0 3681.2017 -9.3698609
2400 21465.082 103.76223 0 3681.2758 -29.530492
2450 20102.547 331.8625 0 3682.2869 35.630207
2500 20766.689 221.28369 0 3682.3986 -12.4229
2550 20456.257 272.87511 0 3682.2513 -22.515235
2600 21464.354 104.88637 0 3682.2788 -10.110008
2650 20885.777 201.39511 0 3682.358 5.0268371
2700 18576.387 586.63809 0 3682.7026 22.269183
2750 21023.584 178.26789 0 3682.1985 -8.8172166
2800 21363.884 121.51908 0 3682.1664 -6.913586
2850 17264.155 805.16849 0 3682.5276 29.921611
2900 19751.146 390.19286 0 3682.0506 8.8575471
2950 21171.167 153.48579 0 3682.0136 1.9171651
3000 18698.646 565.2524 0 3681.6934 -16.611709
3050 19756.096 389.49951 0 3682.1822 0.79771573
3100 20716.934 229.53125 0 3682.3536 18.675629
3150 21107.033 164.26375 0 3682.1026 6.292817
3200 21194.557 149.62327 0 3682.0495 0.40762301
3250 19019.061 511.83944 0 3681.683 -1.0191767
3300 19904.232 364.91979 0 3682.2917 1.580824
3350 19383.048 452.00672 0 3682.5146 8.9939778
3400 18629.871 577.12591 0 3682.1044 19.393397
3450 20366.419 287.55662 0 3681.9598 6.7676479
3500 20957.937 189.21014 0 3682.1996 9.17515
3550 21807.252 47.635006 0 3682.1771 2.2490841
3600 21690.617 67.029898 0 3682.1327 -1.4725416
3650 21600.202 82.085085 0 3682.1188 -3.9470263
3700 19902.074 365.09934 0 3682.1117 3.5789954
3750 20669.825 237.14074 0 3682.1116 -7.992071
3800 20226.287 311.40404 0 3682.4519 -11.829103
3850 20713.814 230.18758 0 3682.4899 -11.37713
3900 19621.738 411.85323 0 3682.1428 -0.86016858
3950 20828.921 210.87742 0 3682.3643 -1.7978283
4000 21734.525 60.230547 0 3682.6513 3.0013342
4050 19859.621 371.8688 0 3681.8056 19.53421
4100 20748.845 224.82927 0 3682.9701 -0.67873587
4150 19578.269 420.02964 0 3683.0745 4.448634
4200 19142.314 492.92862 0 3683.3143 7.5300212
4250 20189.963 318.02141 0 3683.0152 2.2489634
4300 20569.793 254.7842 0 3683.0831 2.014004
4350 21505.248 99.029749 0 3683.2377 -1.8448103
4400 21795.012 50.799563 0 3683.3016 -3.3446933
4450 21630.638 78.27653 0 3683.3829 0.97935456
4500 20485.622 268.77758 0 3683.0479 9.0931688
4550 21328.202 128.77982 0 3683.4802 6.9392514
4600 20425.456 279.4671 0 3683.7097 14.657178
4650 21734.316 61.575892 0 3683.9619 -6.1228621
4700 20377.517 287.77871 0 3684.0315 -10.350636
4750 21765.762 56.481378 0 3684.1084 -13.686961
4800 21064.967 173.07588 0 3683.9038 -3.5246286
4850 21496.739 100.96272 0 3683.7525 3.4134893
4900 21387.734 118.85944 0 3683.4818 2.7545377
4950 21606.598 82.305575 0 3683.4052 2.7661083
5000 20813.389 211.50552 0 3680.4037 -1.99709
5050 21258.837 140.0257 0 3683.1652 -4.6011608
5100 18840.1 543.32464 0 3683.3413 31.178048
5150 22005.655 16.168882 0 3683.778 -4.3729594
5200 20808.086 215.87951 0 3683.8939 7.4410336
5250 18679.669 570.83153 0 3684.1098 14.191478
5300 19753.173 391.94671 0 3684.1422 -8.5241508
5350 21608.313 82.705694 0 3684.0912 -3.6094817
5400 21488.174 102.68409 0 3684.0464 4.2600964
5450 17518.356 764.26875 0 3683.9947 -0.12243804
5500 21696.071 68.069788 0 3684.0816 -1.5476526
5550 18502.148 599.7684 0 3683.4597 37.379976
5600 18128.267 662.17376 0 3683.5516 16.554047
5650 18537.13 594.3189 0 3683.8406 12.05774
5700 20851.723 208.91824 0 3684.2053 -4.3830301
5750 20941.372 194.08984 0 3684.3185 -0.1943864
5800 20194.472 318.72727 0 3684.4726 5.154744
5850 20856.188 208.56814 0 3684.5994 3.2314482
5900 21125.245 164.07233 0 3684.9465 -0.33002911
5950 20138.458 328.54345 0 3684.9532 10.557313
6000 20981.486 188.51066 0 3685.4249 -9.0163197
6050 20822.112 215.14903 0 3685.5011 -18.139995
6100 20076.859 339.70008 0 3685.8432 -3.0307257
6150 19953.615 360.46342 0 3686.066 8.3344429
6200 20903.384 202.40101 0 3686.2984 -0.39424049
6250 21134.826 163.89116 0 3686.3621 -4.1668704
6300 21258.213 143.90658 0 3686.9422 -7.391516
6350 20373.797 291.10416 0 3686.7369 -14.895748
6400 19051.752 510.8571 0 3686.1491 -0.078518196
6450 19649.32 412.61991 0 3687.5065 -1.5921483
6500 20142.923 330.66911 0 3687.8229 6.8022912
6550 19574.327 424.60137 0 3686.9891 11.82743
6600 16105.355 1002.7817 0 3687.0076 17.558797
6650 21537.744 97.953562 0 3687.5775 2.735191
6700 16808.381 887.46461 0 3688.8614 -9.3638392
6750 16391.199 958.16942 0 3690.0359 24.040757
6800 19891.18 371.95843 0 3687.1551 -25.326616
6850 19344.505 464.12314 0 3688.2073 -16.88882
6900 21489.989 106.09106 0 3687.7559 -2.7741331
6950 19023.694 517.19865 0 3687.8143 12.795625
7000 21072.663 175.47912 0 3687.5897 -4.6260178
7050 19697.946 404.85665 0 3687.8476 0.96426982
7100 20684.854 240.16243 0 3687.638 -6.9283531
7150 20888.947 205.87412 0 3687.3653 2.4592293
7200 20709.233 235.52341 0 3687.0622 1.8850608
7250 20644.676 246.05983 0 3686.8391 -1.9432958
7300 19940.501 363.58269 0 3686.9996 8.7916219
7350 20904.854 202.70884 0 3686.8511 1.1932912
7400 19794.615 388.44762 0 3687.5502 4.2494869
7450 20398.713 287.96541 0 3687.7509 1.9565661
7500 14969.907 1195.4664 0 3690.451 61.49775
7550 20048.243 346.41733 0 3687.7911 8.8637262
7600 13724.843 1400.6649 0 3688.1386 -28.102927
7650 17323.581 800.37606 0 3687.6396 17.015401
7700 20781.624 224.2726 0 3687.8767 2.5260419
7750 19629.33 416.31516 0 3687.8702 18.39744
7800 20804.173 220.99571 0 3688.3579 11.409891
7850 20756.856 228.60421 0 3688.0803 -33.84006
7900 21716.444 68.965593 0 3688.3729 -12.291272
7950 19610.154 419.14133 0 3687.5002 1.7759679
8000 18622.409 585.42868 0 3689.1635 26.686729
8050 19777.369 392.63726 0 3688.8654 -22.209128
8100 16497.521 939.24542 0 3688.8322 -42.367659
8150 19446.13 444.3108 0 3685.3324 32.613169
8200 20411.209 286.5915 0 3688.4597 -5.2887315
8250 14328.544 1302.6847 0 3690.7753 15.143982
8300 21405.234 121.47682 0 3689.0157 -4.6378296
8350 15481.055 1109.2428 0 3689.4186 57.85088
8400 14139.682 1332.356 0 3688.9697 -0.1974486
8450 15623.736 1084.5594 0 3688.5155 37.668188
8500 18872.571 543.29677 0 3688.7253 -11.622477
8550 18568.346 594.15647 0 3688.8809 -0.53198127
8600 18857.924 546.26599 0 3689.2533 6.9976522
8650 20422.926 285.18311 0 3689.0041 -2.1124395
8700 15904.428 1038.6394 0 3689.3774 11.108432
8750 17585.096 758.32272 0 3689.172 -13.175342
8800 19561.883 429.1997 0 3689.5135 31.379344
8850 21083.378 174.46783 0 3688.3642 -1.405537
8900 21922.179 35.258703 0 3688.9551 0.92994553
8950 15270.836 1145.5748 0 3690.714 59.72214
9000 21236.73 149.52929 0 3688.9843 3.6894217
9050 20391.028 289.54828 0 3688.053 -12.318301
9100 19963.6 361.58733 0 3688.854 -1.6201635
9150 20852.5 213.26173 0 3688.6783 3.4781812
9200 17559.276 763.58389 0 3690.13 23.653055
9250 20719.763 235.38861 0 3688.6825 -7.2385902
9300 20210.461 320.16875 0 3688.5789 0.71513298
9350 20589.665 256.39159 0 3688.0025 11.766742
9400 21888.845 39.743204 0 3687.884 0.2325157
9450 19995.034 355.22797 0 3687.7336 -30.801824
9500 20562.534 260.81379 0 3687.9028 7.6818244
9550 20724.259 233.42976 0 3687.4729 2.5906906
9600 21156.272 161.92778 0 3687.9731 -3.6794578
9650 15407.774 1117.1504 0 3685.1127 10.296536
9700 20086.616 339.94203 0 3687.7114 6.85039
9750 21017.639 184.92766 0 3687.8675 -4.924906
9800 17788.545 723.17057 0 3687.928 19.866063
9850 21918.073 35.503859 0 3688.516 -1.9119993
9900 17765.237 727.83046 0 3688.7033 19.055502
9950 21306.635 137.72864 0 3688.8345 -5.5977574
10000 21575.787 92.853786 0 3688.8182 -4.0094168
Loop time of 3.5147 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.153219 (4.35937)
Neigh time (%) = 0.0883856 (2.51474)
Comm time (%) = 0.00992155 (0.282288)
Outpt time (%) = 0.00212979 (0.0605968)
Other time (%) = 3.26104 (92.783)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 56 ave 56 max 56 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 750 ave 750 max 750 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 750
Ave neighs/atom = 9.25926
Neighbor list builds = 990
Dangerous builds = 927
Please see the log.cite file for references relevant to this simulation

317
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@ -1,317 +0,0 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
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 9 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.poems
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Memory usage per processor = 1.90126 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 -0.86699149
1200 21815.003 45.317415 0 3681.1512 1.5988314
1250 18655.437 572.41453 0 3681.654 10.064078
1300 20780.781 217.36506 0 3680.8286 6.0538616
1350 20558.971 254.36482 0 3680.8601 -3.6773956
1400 21485.029 99.812922 0 3680.6511 -16.185473
1450 21771.107 52.159608 0 3680.6775 -2.4756674
1500 21520.948 93.503928 0 3680.3286 2.1023577
1550 21351.418 121.68138 0 3680.2511 5.515995
1600 20778.805 216.92177 0 3680.0559 15.089187
1650 21477.638 100.21835 0 3679.8247 -1.1045756
1700 18501.339 596.47913 0 3680.0357 -15.679677
1750 18563.642 587.34787 0 3681.2882 33.532207
1800 19110.186 494.82333 0 3679.8543 18.024046
1850 21364.191 119.23538 0 3679.9339 2.5291119
1900 20146.628 322.14841 0 3679.9197 5.7313081
1950 20692.671 231.25336 0 3680.0319 4.2977737
2000 20943.904 189.11227 0 3679.7629 -22.645146
2050 19668.063 401.82894 0 3679.8394 3.6252006
2100 20280.448 299.76054 0 3679.8353 7.4807993
2150 19181.869 483.52061 0 3680.4987 22.620257
2200 21300.14 130.70883 0 3680.7322 4.710318
2250 20486.992 266.63125 0 3681.1299 -8.6453582
2300 18653.249 572.22692 0 3681.1018 -5.2639533
2350 21513.474 95.623043 0 3681.2021 -9.3615923
2400 21466.352 103.55115 0 3681.2765 -29.563489
2450 20099.92 332.30226 0 3682.2888 35.75288
2500 20764.233 221.69469 0 3682.4003 -12.472324
2550 20434.265 276.55013 0 3682.261 -22.406554
2600 21466.593 104.51528 0 3682.2808 -10.076416
2650 20808.645 214.25423 0 3682.3618 5.1518496
2700 18565.645 588.3715 0 3682.6457 22.26312
2750 20753.062 223.37556 0 3682.2193 -7.8155982
2800 20986.776 184.39985 0 3682.1958 -7.0608776
2850 16721.211 895.59298 0 3682.4615 33.619161
2900 19294.24 466.43871 0 3682.1454 8.0033435
2950 20471.71 270.09532 0 3682.047 2.5545202
3000 20609.248 247.27073 0 3682.1453 -1.8817723
3050 18576.568 586.31423 0 3682.4089 -1.7806882
3100 19790.767 383.54865 0 3682.0099 -6.0384293
3150 20941.678 191.88039 0 3682.16 4.7195299
3200 20187.734 317.22178 0 3681.8441 7.1381064
3250 19982.327 351.80543 0 3682.1932 -10.356822
3300 19720.165 395.60482 0 3682.299 12.415019
3350 20008.047 347.27468 0 3681.9491 5.0458582
3400 20411.522 280.16521 0 3682.0855 -7.1769483
3450 20046.145 341.27051 0 3682.2947 0.22584972
3500 17937.429 692.9726 0 3682.544 16.131523
3550 18771.683 553.86993 0 3682.4837 -1.5944448
3600 19901.288 364.81878 0 3681.7001 -24.39551
3650 20746.323 224.83374 0 3682.5543 -7.6981313
3700 21681.686 68.935986 0 3682.5503 -5.7316854
3750 21130.966 160.34639 0 3682.174 2.5404231
3800 19573.729 419.87434 0 3682.1625 10.483835
3850 19672.797 403.73028 0 3682.5297 7.9092657
3900 19429.209 444.39996 0 3682.6014 4.6871663
3950 18794.538 550.12554 0 3682.5485 -3.4850598
4000 18356.499 622.71257 0 3682.1291 21.961288
4050 18499.159 599.5728 0 3682.7659 9.7197804
4100 18893.082 533.58148 0 3682.4285 7.1537738
4150 18555.438 590.46012 0 3683.0331 -5.9854705
4200 20095.772 332.86056 0 3682.1558 6.0048046
4250 21395.629 117.09714 0 3683.0352 -12.849296
4300 20642.157 242.80387 0 3683.1634 -7.1285142
4350 16782.008 886.90013 0 3683.9014 59.279202
4400 21722.722 63.477041 0 3683.9307 -6.7708918
4450 21483.705 103.77396 0 3684.3914 -14.801558
4500 18637.223 577.90593 0 3684.1097 -5.399645
4550 21501.072 101.01026 0 3684.5223 -0.2687012
4600 21419.25 114.67746 0 3684.5525 -5.1248351
4650 19532.212 428.88221 0 3684.251 -13.937733
4700 19108.648 500.22789 0 3685.0025 0.72814013
4750 21304.939 134.30984 0 3685.133 -10.419682
4800 21011.564 183.12003 0 3685.0474 -0.21596054
4850 21288.378 137.28914 0 3685.3522 -3.783224
4900 20238.761 312.44314 0 3685.57 -0.89650269
4950 20973.64 190.4195 0 3686.0262 2.3977528
5000 20982.662 188.75492 0 3685.8652 -10.898981
5050 20287.196 304.79028 0 3685.9895 7.9988821
5100 20161.046 325.98224 0 3686.1566 11.304549
5150 20768.1 224.94586 0 3686.2959 -11.679983
5200 20550.091 261.40569 0 3686.4209 -3.8503144
5250 20274.307 307.08369 0 3686.1349 3.2350203
5300 21107.734 168.31547 0 3686.2711 -2.7299125
5350 21575.088 90.511714 0 3686.3597 -23.416041
5400 19335.208 463.98466 0 3686.5193 1.1686111
5450 20334.202 297.13584 0 3686.1696 7.9612042
5500 18596.894 586.39323 0 3685.8756 19.42362
5550 16402.199 953.72484 0 3687.4247 -7.6804149
5600 19716.462 400.17421 0 3686.2512 0.73274328
5650 19794.552 387.60203 0 3686.694 7.4829917
5700 21404.995 119.38491 0 3686.884 1.1256427
5750 21737.498 64.038982 0 3686.9553 0.66497166
5800 21196.338 153.70183 0 3686.4248 -4.0562788
5850 18817.877 550.28735 0 3686.6001 15.517346
5900 20855.92 210.47881 0 3686.4654 -6.7252193
5950 18187.477 655.72108 0 3686.9673 -5.840425
6000 21574.226 91.415225 0 3687.1196 -4.1947877
6050 20647.597 245.36705 0 3686.6333 -4.2710188
6100 20195.663 320.68953 0 3686.6333 1.9183471
6150 19569.943 425.30544 0 3686.9627 -2.0191803
6200 21009.348 185.15969 0 3686.7176 -1.5383241
6250 21311.107 135.08699 0 3686.9382 -8.4198399
6300 18617.034 583.66046 0 3686.4994 11.716969
6350 19818.978 382.62883 0 3685.7919 4.9679172
6400 21403.509 119.46416 0 3686.7156 -1.3369474
6450 16394.437 955.35248 0 3687.7587 22.900909
6500 15570.429 1095.0835 0 3690.155 -24.50813
6550 20905.847 202.70205 0 3687.0099 -5.4533991
6600 20419.664 282.65592 0 3685.9333 -1.0348411
6650 16008.949 1023.4924 0 3691.6506 48.451181
6700 18929.104 531.79459 0 3686.6452 8.487112
6750 20317.67 301.1228 0 3687.4011 -9.6972866
6800 21238.238 147.54216 0 3687.2486 -4.457873
6850 19469.334 441.11845 0 3686.0075 29.322933
6900 20880.087 207.70983 0 3687.7244 -4.1197403
6950 20864.561 210.00891 0 3687.4358 -9.4014401
7000 21701.899 70.744638 0 3687.7278 2.6762921
7050 18936.455 531.70563 0 3687.7815 29.134314
7100 21418.983 118.08942 0 3687.9199 0.64845095
7150 21271.75 142.65664 0 3687.9482 -6.1860835
7200 21584.017 90.531714 0 3687.8679 -15.915843
7250 20478.212 274.65055 0 3687.6858 3.5293379
7300 20787.975 223.07914 0 3687.7416 8.3746157
7350 21169.849 159.84727 0 3688.1554 4.806229
7400 18050.739 679.46766 0 3687.9242 0.1356599
7450 21759.344 61.894907 0 3688.4523 -6.0686382
7500 20115.323 334.36139 0 3686.9153 -3.9834726
7550 21513.687 103.04204 0 3688.6565 -3.6546291
7600 20396.612 289.44922 0 3688.8845 8.3149013
7650 19954.93 363.06299 0 3688.8846 6.7857536
7700 20579.453 259.44475 0 3689.3535 -13.300779
7750 21435.784 117.44734 0 3690.078 -3.5454036
7800 19676.963 410.82634 0 3690.3202 16.17995
7850 22001.763 23.427845 0 3690.3883 -3.2253193
7900 21367.244 128.97238 0 3690.1797 -10.139451
7950 21835.619 51.102569 0 3690.3723 -6.9113133
8000 21081.866 176.87472 0 3690.519 -3.400648
8050 17587.847 759.00567 0 3690.3134 42.149831
8100 20622.874 253.16935 0 3690.3149 -1.0529121
8150 18826.468 552.8081 0 3690.5528 -26.78369
8200 19639.531 417.23576 0 3690.491 11.18475
8250 18736.82 568.57113 0 3691.3744 6.4120512
8300 21628.735 86.117146 0 3690.9062 -15.136564
8350 21300.133 140.75663 0 3690.7788 -1.3028295
8400 20100.75 340.28553 0 3690.4105 2.3621868
8450 20330.628 301.64835 0 3690.0863 -6.9035421
8500 21379.743 126.87873 0 3690.1693 -0.67103323
8550 21693.455 74.592469 0 3690.1683 -6.6175553
8600 20824.252 219.41263 0 3690.1212 1.7682173
8650 20289.679 308.59538 0 3690.2085 11.354028
8700 21803.688 56.071063 0 3690.0191 -2.6145414
8750 21111.316 171.22439 0 3689.777 6.7898851
8800 20775.535 227.17109 0 3689.7603 9.4162984
8850 19043.442 515.72721 0 3689.6343 5.3736614
8900 21157.163 163.34868 0 3689.5426 1.4354174
8950 20978.891 192.95509 0 3689.437 0.96560879
9000 21292.787 140.85118 0 3689.6489 -8.9387525
9050 20239.076 316.1505 0 3689.3299 8.0442974
9100 19869.892 377.60414 0 3689.2529 -7.7929877
9150 21454.531 113.72022 0 3689.4753 -13.322839
9200 17967.414 695.13611 0 3689.705 5.5120587
9250 20511.881 271.10991 0 3689.7567 7.4880289
9300 19920.611 369.49427 0 3689.5961 20.373053
9350 20461.102 279.43877 0 3689.6224 10.339057
9400 20099.827 339.51057 0 3689.4817 6.7892922
9450 19918.317 369.41224 0 3689.1318 10.326641
9500 21020.607 186.56179 0 3689.9963 7.3622937
9550 21179.796 160.20422 0 3690.1702 -1.0782427
9600 21518.982 104.08914 0 3690.5861 -5.3790399
9650 21206.19 156.4724 0 3690.8374 1.6109043
9700 21452.317 115.4785 0 3690.8646 -6.2719599
9750 19577.709 427.73595 0 3690.6875 -5.943044
9800 15600.07 1090.9222 0 3690.9338 12.384319
9850 18256.931 647.85044 0 3690.6723 3.3325276
9900 20351.693 298.44268 0 3690.3914 1.2947227
9950 21085.505 176.1557 0 3690.4065 -6.3748251
10000 18801.541 557.05356 0 3690.6438 -8.7522263
Loop time of 3.73648 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0408831 (1.09416)
Neigh time (%) = 0.026132 (0.699376)
Comm time (%) = 0.239869 (6.41966)
Outpt time (%) = 0.00523436 (0.140088)
Other time (%) = 3.42436 (91.6467)
Nlocal: 20.25 ave 79 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 46.25 ave 68 max 12 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 181.5 ave 722 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 726
Ave neighs/atom = 8.96296
Neighbor list builds = 990
Dangerous builds = 920
Please see the log.cite file for references relevant to this simulation

321
examples/rigid/log.rigid.poems2.1Feb14.linux.1
View File

@ -1,321 +0,0 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
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 9 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.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:245)
Memory usage per processor = 2.2859 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444672
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47584 0 3765.6103 -17.923459
1500 19223.688 204.15169 0 3764.0939 -1.613454
1550 18147.996 404.12676 0 3764.8668 8.4194769
1600 18615.043 317.42464 0 3764.6548 -2.328898
1650 20120.654 38.887941 0 3764.935 -8.7620212
1700 19450.906 162.98296 0 3765.0025 2.3254683
1750 19374.633 177.37942 0 3765.2744 8.9328782
1800 19424.403 167.93976 0 3765.0514 0.081237835
1850 17936.373 442.81943 0 3764.3699 6.6007243
1900 19982.597 64.405942 0 3764.8868 -2.953039
1950 16216.047 761.87633 0 3764.848 13.993767
2000 18584.36 322.1319 0 3763.68 7.1655723
2050 20107.967 41.025515 0 3764.723 -0.31095875
2100 20002.359 60.588285 0 3764.7288 -6.7919218
2150 16949.463 626.65155 0 3765.4411 3.5099746
2200 20010.951 58.808709 0 3764.5403 -10.862337
2250 18982.724 247.0099 0 3762.3292 -0.53785372
2300 18401.404 354.86011 0 3762.5276 1.0917872
2350 19390.477 172.95029 0 3763.7793 -3.3527625
2400 16082.495 786.07427 0 3764.3141 -16.195237
2450 18871.033 268.63511 0 3763.2709 11.187102
2500 19687.13 117.79738 0 3763.5622 4.3929264
2550 18873.431 268.30382 0 3763.3836 -5.6531376
2600 17014.989 612.51599 0 3763.44 6.3265978
2650 18779.234 286.24534 0 3763.8812 2.3814839
2700 19733.494 108.84054 0 3763.1912 -0.28455721
2750 19487.299 154.68388 0 3763.4429 -1.5938513
2800 18419.252 351.12627 0 3762.0988 20.847774
2850 18788.886 283.58089 0 3763.0043 3.0280372
2900 20110.801 39.005938 0 3763.2284 0.0030136934
2950 15582.268 877.76573 0 3763.3708 16.827059
3000 17927.524 442.93443 0 3762.8463 4.0702273
3050 19054.272 234.78929 0 3763.3582 7.6784952
3100 19318.656 185.86832 0 3763.3972 3.4909968
3150 19336.244 182.13325 0 3762.9192 -19.24283
3200 18983.457 247.36835 0 3762.8233 -5.7526831
3250 19674.232 119.66794 0 3763.0442 1.9423166
3300 16157.209 769.95841 0 3762.0342 2.80189
3350 19030.029 239.07461 0 3763.1541 7.0444034
3400 15352.517 920.23705 0 3763.2957 26.469475
3450 19113.998 223.38478 0 3763.0139 5.4622379
3500 15355.047 921.10005 0 3764.6272 12.744088
3550 18453.302 345.84221 0 3763.1203 4.3303151
3600 15805.132 835.73363 0 3762.6098 -19.192108
3650 19366.655 176.75046 0 3763.168 3.6029674
3700 17926.815 443.58998 0 3763.3705 6.3106911
3750 18145.089 402.96409 0 3763.1657 -1.4495144
3800 17128.054 590.66146 0 3762.5233 1.3740587
3850 19650.661 123.98432 0 3762.9956 -3.6403709
3900 13651.635 1236.4269 0 3764.5075 1.8197344
3950 19607.542 131.80571 0 3762.8321 -5.2300693
4000 15976.222 803.9711 0 3762.5308 5.8844711
4050 17251.262 568.38221 0 3763.0604 -27.565001
4100 18718.869 296.1222 0 3762.5795 0.24957933
4150 18981.941 247.56533 0 3762.7396 8.9334676
4200 18058.249 418.65815 0 3762.7784 -9.7406053
4250 17840.27 458.9852 0 3762.7389 -1.2566229
4300 16801.487 651.25038 0 3762.6368 20.311604
4350 19284.648 191.5548 0 3762.786 3.8849247
4400 18089.637 412.4593 0 3762.392 -0.16156227
4450 18109.553 409.19646 0 3762.8174 -6.6744782
4500 18559.157 325.84529 0 3762.7262 -3.7834397
4550 19417.817 167.1903 0 3763.0824 -1.9438809
4600 19940.102 70.544215 0 3763.1558 -6.5714777
4650 17531.219 516.03395 0 3762.5561 16.825376
4700 18330.28 368.15762 0 3762.6539 -5.8154827
4750 18059.26 418.88115 0 3763.1886 6.9154907
4800 18230.172 387.09769 0 3763.0554 -5.8764301
4850 15352.316 920.35111 0 3763.3726 -14.150721
4900 17901.178 447.18401 0 3762.217 12.995669
4950 17096.795 596.75363 0 3762.8268 6.9584988
5000 18233.348 386.97511 0 3763.521 -8.6953829
5050 19238.643 200.76564 0 3763.4773 -0.95923788
5100 18851.592 272.21836 0 3763.2539 6.6015785
5150 17618.203 500.9924 0 3763.6226 6.4089848
5200 19510.809 150.29265 0 3763.4053 -1.138488
5250 17991.038 431.73878 0 3763.4124 0.9206177
5300 16496.992 709.42568 0 3764.4241 8.328767
5350 16683.15 674.66196 0 3764.1342 -12.119189
5400 19197.624 208.27759 0 3763.3932 1.8895925
5450 16776.936 656.25236 0 3763.0923 8.3324322
5500 18314.437 372.39317 0 3763.9556 0.87158511
5550 18678.675 304.31808 0 3763.3319 8.1494425
5600 18772.959 286.93218 0 3763.406 -1.3023432
5650 15494.947 894.36223 0 3763.7968 -10.336527
5700 18507.481 336.45923 0 3763.7704 -3.8746687
5750 17082.667 600.40729 0 3763.8641 42.148906
5800 19845.873 88.449333 0 3763.611 1.7380604
5850 17992.679 431.95872 0 3763.9363 -12.928704
5900 19680.707 119.00911 0 3763.5844 -0.79613571
5950 19914.393 75.816066 0 3763.6667 5.5342994
6000 19142.271 218.80112 0 3763.6661 7.4018805
6050 17025.724 611.14107 0 3764.053 -6.1043602
6100 18966.612 250.76138 0 3763.0969 1.1322144
6150 17451.81 531.32734 0 3763.144 -6.5894955
6200 16334.478 739.3296 0 3764.233 -27.518822
6250 18790.228 283.56338 0 3763.2353 -7.8911412
6300 18163.654 399.45237 0 3763.092 -0.20584174
6350 18674.03 305.36153 0 3763.5151 -10.44952
6400 19677.482 119.8165 0 3763.7947 4.767842
6450 19606.353 133.20697 0 3764.0132 3.1402747
6500 18685.174 303.25291 0 3763.4703 1.219211
6550 18842.997 274.29542 0 3763.7394 -3.0675196
6600 18984.844 247.94633 0 3763.6582 3.2871433
6650 19270.874 194.75275 0 3763.4332 2.0520948
6700 16730.98 665.42234 0 3763.752 24.63305
6750 18240.959 385.54575 0 3763.5012 9.3542656
6800 19212.072 205.42671 0 3763.2178 -4.7707967
6850 19428.264 165.41827 0 3763.2449 -5.9896144
6900 16510.385 705.90782 0 3763.3866 -4.5120114
6950 18469.724 342.72852 0 3763.0477 1.5930349
7000 19023.531 240.06714 0 3762.9432 0.97630625
7050 19981.38 63.051871 0 3763.3075 1.1975773
7100 18884.497 266.0407 0 3763.1698 5.014732
7150 20007.363 58.305336 0 3763.3725 -3.8475432
7200 19060.008 233.74726 0 3763.3784 -7.355987
7250 19587.118 136.14609 0 3763.3902 -0.071525055
7300 18255.08 382.9175 0 3763.4878 8.3070642
7350 19840.127 89.391828 0 3763.4894 3.0925365
7400 19081.218 229.96717 0 3763.5261 -0.088491483
7450 19495.919 153.12566 0 3763.481 7.3486168
7500 18103.878 410.89471 0 3763.4647 8.253657
7550 18818.034 278.46924 0 3763.2904 -6.6529064
7600 16900.909 634.03412 0 3763.8321 24.447016
7650 19309.193 187.4356 0 3763.2121 5.0831969
7700 17040.81 608.00812 0 3763.7136 -4.5789647
7750 19420.333 167.12363 0 3763.4815 4.3678178
7800 19164.248 214.10676 0 3763.0416 0.12405627
7850 19137.03 219.31269 0 3763.2071 -6.7131335
7900 19606.78 132.67382 0 3763.5591 -4.5096484
7950 18593.444 319.64585 0 3762.8763 -4.9001288
8000 19288.423 191.51728 0 3763.4475 3.8370068
8050 19132.57 220.46289 0 3763.5314 -1.3284232
8100 17510.857 520.52922 0 3763.2806 -4.6183989
8150 18356.887 364.17504 0 3763.5986 4.3938444
8200 19553.346 142.51623 0 3763.5063 0.93248057
8250 17919.922 444.70362 0 3763.2076 7.3984984
8300 17268.822 564.38824 0 3762.3182 24.155843
8350 19389.272 172.63516 0 3763.241 5.9225389
8400 17896.652 449.19012 0 3763.3849 0.63394353
8450 18315.977 371.4271 0 3763.2746 -33.234548
8500 16047.998 796.54623 0 3768.3978 51.901492
8550 19188.248 210.03454 0 3763.4138 -1.5401941
8600 17951.392 433.85317 0 3758.185 26.657038
8650 18678.909 304.65925 0 3763.7164 -0.5735548
8700 18473.965 342.61835 0 3763.7231 -0.39588258
8750 17278.537 562.78121 0 3762.5102 16.884408
8800 19997.623 60.585822 0 3763.8494 -2.7220886
8850 17720.683 482.98842 0 3764.5963 13.298184
8900 19450.503 162.05753 0 3764.0025 -5.0266355
8950 20065.748 48.178324 0 3764.0575 -3.298456
9000 18411.075 354.70332 0 3764.1617 2.5439463
9050 19835.128 90.878715 0 3764.0505 -2.4322016
9100 19486.363 155.54042 0 3764.1261 -5.332552
9150 19203.984 207.95102 0 3764.2443 3.1640673
9200 18048.222 421.26909 0 3763.5324 23.881772
9250 19682.985 119.25528 0 3764.2524 1.533906
9300 19857.159 86.947891 0 3764.1996 -4.5024234
9350 20060.359 49.452616 0 3764.3338 -1.493574
9400 19561.395 141.85818 0 3764.3387 -3.1573118
9450 19134.008 221.07861 0 3764.4133 -0.60832086
9500 18369.624 362.74228 0 3764.5244 -0.37049085
9550 18146.354 404.01981 0 3764.4558 10.150467
9600 15002.89 991.64237 0 3769.9553 51.550272
9650 18607.005 318.66284 0 3764.4045 3.3985276
9700 18489.496 340.51647 0 3764.4972 2.941698
9750 19635.157 128.29122 0 3764.4315 -14.101437
9800 18284.554 378.61 0 3764.6385 -7.2125841
9850 17756.297 476.00442 0 3764.2076 -4.4238573
9900 18996.512 246.68301 0 3764.5557 -5.0986512
9950 19432.438 165.78467 0 3764.3843 -3.7163888
10000 19336.629 183.60921 0 3764.4664 -0.93973872
Loop time of 3.72182 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.113393 (3.0467)
Neigh time (%) = 0.0677266 (1.81972)
Comm time (%) = 0.0135663 (0.364506)
Outpt time (%) = 0.00212884 (0.0571989)
Other time (%) = 3.525 (94.7119)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69 ave 69 max 69 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 636 ave 636 max 636 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 636
Ave neighs/atom = 7.85185
Neighbor list builds = 991
Dangerous builds = 933
Please see the log.cite file for references relevant to this simulation

321
examples/rigid/log.rigid.poems2.1Feb14.linux.4
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@ -1,321 +0,0 @@
LAMMPS (1 Feb 2014)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
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 9 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.poems2
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: More than one fix poems (../fix_poems.cpp:351)
WARNING: One or more atoms are time integrated more than once (../modify.cpp:245)
Memory usage per processor = 2.24534 Mbytes
Step Temp E_pair E_mol TotEng Press
0 196.00047 3632.2347 0 3668.5311 -2.7403788
50 12167.633 1505.5478 0 3758.8133 35.125973
100 17556.978 512.66277 0 3763.9549 11.137534
150 19579.586 138.04942 0 3763.8987 -29.953971
200 19757.51 105.30542 0 3764.1036 -0.030645317
250 18218.374 390.10747 0 3763.8804 13.711001
300 19383.039 174.40688 0 3763.8586 5.7240693
350 20125.986 36.972611 0 3764.0071 1.9559205
400 18888.816 266.10975 0 3764.0386 9.6362168
450 19307.656 188.2511 0 3763.743 1.9326206
500 16331.197 738.56392 0 3762.8597 9.1715579
550 19318.722 186.16172 0 3763.7027 3.0115336
600 19455.268 161.20621 0 3764.0336 0.55208034
650 18487.011 340.03216 0 3763.5528 -8.0359122
700 17321.201 556.32471 0 3763.9545 -13.631751
750 18979.187 249.04389 0 3763.7082 -2.6072455
800 19342.456 181.85552 0 3763.7918 8.1918726
850 19070.641 232.19342 0 3763.7936 7.3148472
900 19478.873 156.65987 0 3763.8586 2.4284987
950 19912.415 76.437437 0 3763.9216 -1.4667227
1000 16003.749 802.39753 0 3766.0548 46.642188
1050 19859.583 86.64176 0 3764.3424 -2.1961943
1100 19229.575 203.61488 0 3764.6473 -10.632365
1150 18821.6 279.15861 0 3764.64 -0.89495035
1200 19392.695 173.59744 0 3764.8373 1.8508753
1250 16459.624 717.32104 0 3765.3995 33.478127
1300 19343.863 182.59043 0 3764.7874 0.75890736
1350 20019.643 57.503573 0 3764.8448 0.31444671
1400 18549.582 329.31436 0 3764.4221 10.738303
1450 15163.926 957.47586 0 3765.6103 -17.92346
1500 19223.687 204.15182 0 3764.0939 -1.613452
1550 18147.996 404.12678 0 3764.8668 8.4194792
1600 18615.043 317.42471 0 3764.6548 -2.3288881
1650 20120.654 38.887882 0 3764.935 -8.7620352
1700 19450.908 162.98242 0 3765.0025 2.3254787
1750 19374.63 177.37994 0 3765.2744 8.9328764
1800 19424.404 167.93955 0 3765.0514 0.081221207
1850 17936.104 442.8692 0 3764.3699 6.6014634
1900 19982.594 64.406495 0 3764.8868 -2.9529141
1950 16215.626 761.95548 0 3764.8491 13.995806
2000 18584.494 322.10724 0 3763.6801 7.1652003
2050 20107.964 41.026031 0 3764.723 -0.31084595
2100 20002.303 60.598606 0 3764.7288 -6.7920431
2150 16950.12 626.52975 0 3765.4408 3.5077027
2200 20010.956 58.807784 0 3764.5404 -10.861982
2250 18982.743 247.00649 0 3762.3293 -0.53838506
2300 18401.159 354.90522 0 3762.5273 1.0923853
2350 19390.592 172.92882 0 3763.7792 -3.3521232
2400 16078.693 786.77936 0 3764.3151 -16.207246
2450 18869.645 268.89132 0 3763.27 11.210758
2500 19689.703 117.31993 0 3763.5612 4.3700595
2550 18867.605 269.38371 0 3763.3847 -5.673697
2600 17024.852 610.68855 0 3763.4389 6.2927269
2650 18723.802 296.52976 0 3763.9005 2.4475504
2700 19752.355 105.40597 0 3763.2494 -0.38635488
2750 19524.414 147.78984 0 3763.4221 -1.5733395
2800 17840.968 459.3254 0 3763.2085 29.661669
2850 18887.52 265.43414 0 3763.1231 3.7534553
2900 20160.325 29.79531 0 3763.1888 2.8076367
2950 17931.673 442.25832 0 3762.9386 4.1038365
3000 19003.992 243.57426 0 3762.832 3.5213285
3050 18907.933 261.70341 0 3763.1725 6.1845639
3100 19086.668 229.05632 0 3763.6245 -1.7059047
3150 19524.328 148.10446 0 3763.7208 -13.257029
3200 19888.015 80.720451 0 3763.6863 -5.9850932
3250 18329.653 367.80596 0 3762.1862 2.5356842
3300 17774.857 472.07926 0 3763.7194 26.05786
3350 18586.91 322.11111 0 3764.1316 5.7227572
3400 18142.722 404.27409 0 3764.0373 22.972948
3450 19641.028 126.721 0 3763.9484 4.4124099
3500 19716.345 112.83226 0 3764.0073 3.0970704
3550 19750.966 106.4596 0 3764.0458 -1.2020093
3600 19385.115 174.22116 0 3764.0572 -0.30312978
3650 19806.188 96.296016 0 3764.1086 1.3884533
3700 19632.503 128.4744 0 3764.1231 5.4783086
3750 19984.029 63.34637 0 3764.0924 -7.6169503
3800 19391.726 173.11834 0 3764.1788 -5.5199774
3850 19701.864 115.6328 0 3764.1262 -4.613059
3900 19071.277 232.53842 0 3764.2563 0.60414949
3950 19543.806 144.70463 0 3763.9279 3.9673805
4000 17072.153 601.63639 0 3763.1462 14.038181
4050 19472.634 157.9704 0 3764.0138 0.075484598
4100 19458.162 160.55562 0 3763.919 1.7856979
4150 19028.89 239.83121 0 3763.6997 11.420854
4200 20109.582 39.912078 0 3763.9088 -2.4825779
4250 19501.856 151.85318 0 3763.308 4.4374703
4300 19953.632 68.83941 0 3763.9565 -1.9144758
4350 19109.358 225.03756 0 3763.8075 0.43487388
4400 19762.511 104.29295 0 3764.0171 2.7984598
4450 19722.718 111.70804 0 3764.0632 2.2845927
4500 19915.846 75.911584 0 3764.0312 4.1625614
4550 19884.847 81.607953 0 3763.987 2.0252211
4600 18612.632 317.21746 0 3764.0011 5.1726513
4650 19078.336 230.90268 0 3763.9279 5.205472
4700 19715.75 112.95427 0 3764.019 4.3237781
4750 19742.684 107.93515 0 3763.9878 2.1485577
4800 19197.053 208.91261 0 3763.9225 -2.943785
4850 19760.387 104.71117 0 3764.0421 -4.0934577
4900 17998.47 431.02848 0 3764.0784 13.811824
4950 19604.398 133.53703 0 3763.9811 -5.5636088
5000 19232.029 202.51843 0 3764.0053 -1.8269075
5050 19715.235 112.97181 0 3763.9412 1.7390053
5100 19398.744 171.53062 0 3763.8906 3.3491974
5150 19314.84 187.15985 0 3763.982 2.8628327
5200 19694.326 116.88381 0 3763.9813 0.87055141
5250 19863.902 85.505146 0 3764.0056 -0.59127781
5300 18854.279 272.69199 0 3764.2251 0.97585642
5350 20102.125 41.375281 0 3763.9911 3.4442258
5400 18613.294 317.12781 0 3764.0342 9.5393349
5450 19559.083 141.5345 0 3763.5869 3.6962703
5500 17569.068 510.18672 0 3763.7179 13.24936
5550 19270.914 194.90196 0 3763.5898 3.8986118
5600 19498.122 153.15583 0 3763.9191 -3.4776966
5650 19777.463 101.36242 0 3763.8555 -11.848632
5700 19084.468 229.69625 0 3763.8569 1.2585904
5750 18724.734 296.2904 0 3763.8337 2.6582121
5800 19386.427 173.81408 0 3763.8932 4.2211994
5850 19803.648 96.837994 0 3764.1802 1.3140639
5900 19673.781 120.82275 0 3764.1155 -2.5154465
5950 19736.953 109.09143 0 3764.0827 -2.2181212
6000 19790.274 99.158109 0 3764.0237 -3.68098
6050 19545.34 144.53706 0 3764.0444 0.39182955
6100 17986.935 433.2002 0 3764.114 10.030916
6150 19723.117 111.58597 0 3764.015 2.7481914
6200 19196.262 209.2757 0 3764.139 -4.1838898
6250 19595.664 135.40327 0 3764.2299 -4.9572417
6300 20066.143 48.26479 0 3764.2173 -2.0440702
6350 19658.915 123.66551 0 3764.2054 6.3983302
6400 16099.375 783.30808 0 3764.6738 10.626182
6450 18777.763 287.09552 0 3764.4591 -4.455207
6500 16707.737 670.37041 0 3764.3958 13.941367
6550 19762.607 104.62762 0 3764.3696 0.16306805
6600 19257.046 198.21098 0 3764.3305 -5.4407238
6650 19832.195 91.712241 0 3764.3409 -1.9458256
6700 19850.998 88.250674 0 3764.3614 5.8183659
6750 19413.067 169.26039 0 3764.2728 6.1295075
6800 19765.494 103.96165 0 3764.2383 -3.7688435
6850 16858.457 642.54223 0 3764.4787 4.5079169
6900 19982.921 63.847652 0 3764.3885 -9.1345046
6950 19913.352 76.606013 0 3764.2639 -2.5724183
7000 19224.043 204.40946 0 3764.4174 8.8267535
7050 19611.945 132.75353 0 3764.5952 -1.2121033
7100 18439.385 350.13652 0 3764.8375 -10.124288
7150 19682.442 120.04202 0 3764.9386 -3.6256683
7200 19422.224 168.10408 0 3764.8122 0.82487728
7250 18329.588 370.25204 0 3764.6202 11.648525
7300 19708.59 114.99145 0 3764.7304 0.046523759
7350 19816.323 95.213196 0 3764.9026 -0.47763944
7400 17665.439 493.59617 0 3764.9737 -0.91038002
7450 19566.729 141.55672 0 3765.0251 -5.4595222
7500 19814.753 95.678399 0 3765.077 2.7766353
7550 18372.821 362.40112 0 3764.7753 14.250033
7600 19501.443 153.75428 0 3765.1326 7.1710143
7650 19668.707 122.7639 0 3765.117 -7.9237216
7700 19679.165 120.74844 0 3765.0382 -2.2087708
7750 19318.592 187.36213 0 3764.8791 5.2470406
7800 18421.715 352.99021 0 3764.419 9.1913905
7850 18895.708 265.3653 0 3764.5705 5.549395
7900 19577.99 139.06024 0 3764.614 -9.4076317
7950 19740.609 109.09893 0 3764.7672 -9.8961255
8000 18940.832 256.98999 0 3764.5514 3.9687427
8050 18969.072 252.07733 0 3764.8685 -4.0865115
8100 18105.878 411.85769 0 3764.798 6.9985575
8150 17720.026 483.41227 0 3764.8985 -9.9691828
8200 19228.141 204.22365 0 3764.9906 4.5129102
8250 18208.089 392.95005 0 3764.8183 -1.1095191
8300 17975.092 435.94429 0 3764.665 17.753982
8350 18763.356 290.24792 0 3764.9434 2.4934075
8400 20081.591 46.079041 0 3764.8922 -1.2146918
8450 19112.458 225.50295 0 3764.847 -4.35039
8500 19307.507 189.3956 0 3764.86 5.0874862
8550 19181.088 212.75782 0 3764.8111 0.25341129
8600 18801.701 282.9206 0 3764.7171 -11.907333
8650 18881.312 268.25685 0 3764.7961 7.0176888
8700 15686.277 860.48983 0 3765.356 21.424289
8750 18618.866 316.47733 0 3764.4154 -4.6552691
8800 18339.56 368.23406 0 3764.4489 2.6401219
8850 19445.679 163.71793 0 3764.7697 -2.4895575
8900 19121.794 223.5113 0 3764.5842 -5.0630299
8950 14402.118 1099.2335 0 3766.2923 -7.4933486
9000 19175.071 213.69795 0 3764.637 -5.6657242
9050 19412.386 169.60603 0 3764.4924 -12.723782
9100 18455.972 346.68851 0 3764.4611 9.1721288
9150 19954.848 69.041959 0 3764.3841 -0.91356236
9200 19613.768 132.03036 0 3764.2097 4.9013519
9250 15254.687 939.82439 0 3764.7665 11.510878
9300 19048.696 236.62627 0 3764.1625 0.67464829
9350 18952.271 254.3769 0 3764.0568 8.2625973
9400 17082.985 600.49483 0 3764.0105 -9.9046787
9450 16757.345 660.90075 0 3764.1128 21.116304
9500 19841.884 89.284407 0 3763.7073 -0.64193305
9550 19304.212 189.00596 0 3763.86 -12.873723
9600 16227.696 759.23524 0 3764.3641 11.721944
9650 17820.924 463.01451 0 3763.1857 3.9496789
9700 19354.393 179.78068 0 3763.9275 -2.6872013
9750 13935.985 1183.7739 0 3764.5119 10.647433
9800 19587.907 136.31855 0 3763.7087 5.5549859
9850 19080.946 230.80379 0 3764.3124 -4.0577518
9900 19455.883 161.42232 0 3764.3637 -1.6117009
9950 18749.317 292.29982 0 3764.3955 3.9849608
10000 18721.798 297.49023 0 3764.4899 1.6710415
Loop time of 3.78797 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0290385 (0.766597)
Neigh time (%) = 0.0196837 (0.519638)
Comm time (%) = 0.144778 (3.82205)
Outpt time (%) = 0.0049271 (0.130072)
Other time (%) = 3.58954 (94.7616)
Nlocal: 20.25 ave 36 max 0 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 16 ave 33 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 162.75 ave 371 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 651
Ave neighs/atom = 8.03704
Neighbor list builds = 993
Dangerous builds = 949
Please see the log.cite file for references relevant to this simulation

401
examples/rigid/log.rigid.tnr.1Feb14.linux.1
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@ -1,401 +0,0 @@
LAMMPS (1 Feb 2014)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 1 by 1 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394293 0.009326014
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709636 0.0044949165 0.0038341296
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738259 0.0090537939 0.013165402
2500 1.4153808 5.9421661 7.0538718 0.00015906304 7.0607216 62.244 62.244 62.244 0.0023516208 -0.0019814985 0.00010706681
2600 1.4014223 5.9431386 7.0438807 0.0070733748 7.3484816 62.244 62.244 62.244 0.005414387 0.010055843 0.0057498949
2700 1.4138077 5.9369067 7.047377 0.0024268844 7.1518859 62.244 62.244 62.244 0.0052918441 0.0014960354 0.00049277387
2800 1.432192 5.9347676 7.0596777 0.0077670451 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113035 0.0047214114
2900 1.3938659 5.921023 7.01583 0.00537512 7.2472989 62.244 62.244 62.244 0.0020490377 0.007656609 0.0064197131
3000 1.390221 5.9205014 7.0124455 -0.0010750979 6.9661485 62.244 62.244 62.244 0.0019519824 -0.0041878903 -0.00098938592
3100 1.4205722 5.9178284 7.0336117 0.009873547 7.4587965 62.244 62.244 62.244 0.0040973363 0.012167266 0.013356039
3200 1.398418 5.9150349 7.0134173 0.0061541829 7.278435 62.244 62.244 62.244 0.0067621803 0.011952562 -0.0002521939
3300 1.4269859 5.9148726 7.0356937 0.0060623983 7.2967588 62.244 62.244 62.244 0.012956243 -2.4795615e-05 0.0052557479
3400 1.434286 5.9356705 7.0622253 0.00027314048 7.0739876 62.244 62.244 62.244 -0.00054962139 0.0052526062 -0.0038835634
3500 1.4416809 5.9228152 7.0551783 0.0083382965 7.4142505 62.244 62.244 62.244 0.0073993829 0.0030328137 0.014582693
3600 1.4136063 5.9039442 7.0142563 0.001971221 7.099143 62.244 62.244 62.244 -0.00032316217 0.003503006 0.0027338193
3700 1.433382 5.9120101 7.0378549 0.0071287089 7.3448386 62.244 62.244 62.244 0.0064768154 0.0046765426 0.010232769
3800 1.3659482 5.9032871 6.9761662 -0.0054032435 6.7434863 62.244 62.244 62.244 -0.0073942825 -0.0082831048 -0.00053234334
3900 1.3963224 5.9042995 7.0010359 0.0053310327 7.2306062 62.244 62.244 62.244 0.0081855547 0.0048807072 0.0029268363
4000 1.4125479 5.9060668 7.0155474 0.0028451204 7.1380669 62.244 62.244 62.244 0.0052588116 0.00072372172 0.0025528279
4100 1.3943956 5.9040893 6.9993123 0.0058043569 7.2492654 62.244 62.244 62.244 0.0060576276 0.002478686 0.0088767572
4200 1.4249783 5.8906355 7.0098796 0.0030213234 7.1399869 62.244 62.244 62.244 0.0061743252 -0.0020791501 0.0049687951
4300 1.3899826 5.8966344 6.9883912 0.0057294842 7.2351201 62.244 62.244 62.244 0.0049055668 0.0021899931 0.010092893
4400 1.4414357 5.8986162 7.0307867 0.0050933157 7.2501203 62.244 62.244 62.244 0.0057939021 0.0037947176 0.0056913275
4500 1.4092608 5.892298 6.9991969 0.0012247406 7.0519379 62.244 62.244 62.244 0.0042876402 0.0014588188 -0.0020722372
4600 1.3779488 5.8928773 6.9751823 0.0020733584 7.0644674 62.244 62.244 62.244 0.0029285418 -0.0031642229 0.0064557564
4700 1.4084742 5.909909 7.0161901 -0.00053850548 6.9930004 62.244 62.244 62.244 -0.0018600331 -0.0018359559 0.0020804726
4800 1.4391588 5.9150069 7.0453891 0.015310705 7.7047142 62.244 62.244 62.244 0.014756643 0.018034492 0.013140978
4900 1.4496016 5.907877 7.0464614 0.0075305556 7.3707499 62.244 62.244 62.244 0.0091920128 0.0081340187 0.0052656353
5000 1.4293045 5.9102892 7.0329313 -0.0015935867 6.9643067 62.244 62.244 62.244 -0.0049858888 0.001820566 -0.0016154373
Loop time of 6.35156 on 1 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.478212 (7.52904)
Bond time (%) = 0.222193 (3.49824)
Neigh time (%) = 1.2401 (19.5243)
Comm time (%) = 0.172963 (2.72315)
Outpt time (%) = 0.00360727 (0.0567935)
Other time (%) = 4.23449 (66.6685)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1351 ave 1351 max 1351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5255 ave 5255 max 5255 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5255
Ave neighs/atom = 0.938393
Ave special neighs/atom = 0.571429
Neighbor list builds = 766
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4293045 5.9102892 7.0329313 0.028061066 8.2413255 62.244 62.244 62.244 0.017765452 0.040562905 0.02585484
5100 1.4400998 5.9022414 7.0333627 0.0061821009 7.2995826 62.244 62.244 62.244 0.009770998 0.0030836918 0.0056916129
5200 1.4082657 5.9104139 7.0165312 0.0064210573 7.2930413 62.244 62.244 62.244 0.0080770492 0.0051169375 0.0060691852
5300 1.45649 5.8801752 7.0241701 0.0069092534 7.3217034 62.244 62.244 62.244 0.0065768895 0.0056877656 0.0084631052
5400 1.4233427 5.8824466 7.000406 0.0035507414 7.1533117 62.244 62.244 62.244 0.0033649256 -0.00080481231 0.0080921109
5500 1.4203908 5.8713513 6.9869921 0.0082802387 7.3435642 62.244 62.244 62.244 0.0073789675 0.0076306312 0.0098311173
5600 1.4100524 5.8744301 6.9819507 0.0025993542 7.0938867 62.244 62.244 62.244 -0.002226516 0.005551312 0.0044732667
5700 1.4094008 5.8740942 6.981103 0.001858876 7.0611518 62.244 62.244 62.244 -0.00080782471 -0.00061623499 0.0070006878
5800 1.4017129 5.8875092 6.9884795 0.0010380104 7.0331794 62.244 62.244 62.244 0.0043974934 -0.0033700586 0.0020865964
5900 1.3979088 5.8861057 6.9840882 0.0019969425 7.0700826 62.244 62.244 62.244 -0.002580911 0.0061245675 0.0024471709
6000 1.4274747 5.8829671 7.004172 0.00018898098 7.0123101 62.244 62.244 62.244 0.0019071211 -0.0011893793 -0.00015079887
Loop time of 1.27908 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.137631 (10.7602)
Bond time (%) = 0.0451553 (3.53029)
Neigh time (%) = 0.276716 (21.634)
Comm time (%) = 0.0356052 (2.78366)
Outpt time (%) = 0.000710726 (0.0555654)
Other time (%) = 0.783261 (61.2363)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1380 ave 1380 max 1380 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5416 ave 5416 max 5416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5416
Ave neighs/atom = 0.967143
Ave special neighs/atom = 0.571429
Neighbor list builds = 153
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.4274747 5.8829671 7.004172 -0.02124798 6.0891699 62.244 62.244 62.244 -0.0035029341 -0.035545622 -0.024695385
6100 1.4047816 5.8827162 6.9860969 0.0039973389 7.1582344 62.244 62.244 62.244 0.0038546201 0.0038745986 0.0042627978
6200 1.4013195 5.8723518 6.9730132 0.0055794243 7.21328 62.244 62.244 62.244 0.0052298684 0.006566317 0.0049420874
6300 1.4164814 5.8699858 6.982556 0.0046834632 7.18424 62.244 62.244 62.244 0.0042595662 0.0075687542 0.0022220694
6400 1.4008382 5.8754385 6.9757219 0.0057855428 7.2248648 62.244 62.244 62.244 0.011229504 0.0035917167 0.0025354077
6500 1.3961747 5.8821344 6.9787548 0.0054798914 7.2147355 62.244 62.244 62.244 0.0079746581 0.0012807952 0.007184221
6600 1.3989989 5.8839851 6.9828238 0.0078068029 7.3190083 62.244 62.244 62.244 0.0075737438 0.01001737 0.0058292953
6700 1.3944424 5.8846079 6.9798678 0.0025837202 7.0911306 62.244 62.244 62.244 0.001801077 0.0043727527 0.0015773308
6800 1.3886249 5.8876899 6.9783804 0.0083096819 7.3362204 62.244 62.244 62.244 0.0057252172 0.0080731664 0.011130662
6900 1.4128008 5.8873288 6.9970082 -0.0017879625 6.9200131 62.244 62.244 62.244 0.0032920311 -0.0044843856 -0.004171533
7000 1.4296767 5.8776376 7.0005721 0.0028980535 7.125371 62.244 62.244 62.244 0.0020944649 0.002732346 0.0038673497
Loop time of 1.30653 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.140375 (10.7442)
Bond time (%) = 0.0453455 (3.47069)
Neigh time (%) = 0.278969 (21.3519)
Comm time (%) = 0.0354125 (2.71043)
Outpt time (%) = 0.000714064 (0.0546535)
Other time (%) = 0.805712 (61.6681)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1365 ave 1365 max 1365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5888 ave 5888 max 5888 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5888
Ave neighs/atom = 1.05143
Ave special neighs/atom = 0.571429
Neighbor list builds = 151
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4296767 5.8776376 7.0005721 0.012931516 7.5574422 62.244 62.244 62.244 -0.033811545 0.071351891 0.0012542007
7100 1.4257807 5.8661379 6.9860122 0.0063203866 7.2286059 59.901999 59.901999 59.901999 0.0075682964 0.0028831604 0.0085097032
7200 1.407746 5.857124 6.962833 0.0084753318 7.2534913 57.694979 57.694979 57.694979 0.010202527 0.0094388943 0.005784574
7300 1.3925246 5.8467137 6.9404672 0.014254002 7.3803203 55.699712 55.699712 55.699712 0.010958166 0.015538449 0.01626539
7400 1.3876126 5.8261824 6.9160778 0.011565854 7.238709 53.8566 53.8566 53.8566 0.010074234 0.013288968 0.011334359
7500 1.4080244 5.8243986 6.9303263 0.013237792 7.2665719 52.200705 52.200705 52.200705 0.014684708 0.015549417 0.0094792517
7600 1.4024992 5.8202266 6.9218146 0.0087754412 7.1257639 50.677331 50.677331 50.677331 0.012762778 0.0046632388 0.0089003068
7700 1.4053227 5.79557 6.8993757 0.017894387 7.2814436 49.264862 49.264862 49.264862 0.017455799 0.011081333 0.02514603
7800 1.3626299 5.7913047 6.8615775 -0.0027715764 6.8070755 47.931898 47.931898 47.931898 -0.00096112659 -0.00022698058 -0.0071266219
7900 1.3811061 5.7611338 6.8459187 0.022417792 7.2542129 46.722152 46.722152 46.722152 0.017429453 0.023217068 0.026606854
8000 1.3909989 5.7527072 6.8452623 0.0050901754 6.9314891 45.607102 45.607102 45.607102 0.0033084213 0.0050773514 0.0068847534
Loop time of 2.1421 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.243607 (11.3723)
Bond time (%) = 0.067399 (3.1464)
Neigh time (%) = 0.578037 (26.9846)
Comm time (%) = 0.0550971 (2.5721)
Outpt time (%) = 0.000721693 (0.0336909)
Other time (%) = 1.19724 (55.8909)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1964 ave 1964 max 1964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11395 ave 11395 max 11395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 11395
Ave neighs/atom = 2.03482
Ave special neighs/atom = 0.571429
Neighbor list builds = 263
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.3909989 5.7527072 6.8452623 -0.013693646 6.6132941 45.607102 45.607102 45.607102 -0.043122633 -0.045235911 0.047277607
8100 1.3859992 5.7541236 6.8427517 0.025001526 7.2534745 44.228819 45.607102 45.607102 0.034466544 0.018726978 0.021811058
8200 1.3854121 5.741923 6.83009 0.00064570832 6.8403853 42.926629 45.607102 45.607102 0.0027453757 0.0012726672 -0.002080918
8300 1.4154816 5.7503811 6.8621661 0.0142623 7.0833894 41.760381 45.607102 45.607102 0.011045171 0.01999352 0.011748208
8400 1.3809342 5.7526615 6.8373114 0.010034961 6.9882285 40.489828 45.607102 45.607102 0.013514677 0.009127176 0.0074630301
8500 1.377763 5.7274882 6.8096473 0.010601881 6.9645838 39.345393 45.607102 45.607102 0.011511215 0.00061614599 0.019678283
8600 1.431011 5.716086 6.8400685 0.0082177641 6.9567982 38.242914 45.607102 45.607102 0.017556217 0.0072745279 -0.00017745274
8700 1.4088268 5.7023605 6.8089185 0.014325516 7.006943 37.216169 45.607102 45.607102 0.030284184 0.0090717286 0.0036206352
8800 1.4053586 5.7019319 6.8057658 0.004331614 6.8641135 36.265817 45.607102 45.607102 0.0075148755 0.012823387 -0.0073434199
8900 1.4159123 5.7005178 6.812641 0.013485111 6.9893826 35.286383 45.607102 45.607102 0.025461313 0.0051541371 0.0098398833
9000 1.4232531 5.6865082 6.8043973 0.014588857 6.9910378 34.44354 45.607102 45.607102 0.016849826 0.025113792 0.0018029545
Loop time of 2.23572 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.329728 (14.7482)
Bond time (%) = 0.0679741 (3.04037)
Neigh time (%) = 0.547063 (24.4692)
Comm time (%) = 0.0531805 (2.37867)
Outpt time (%) = 0.000710964 (0.0318003)
Other time (%) = 1.23706 (55.3317)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2374 ave 2374 max 2374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14730 ave 14730 max 14730 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14730
Ave neighs/atom = 2.63036
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39499 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.4232531 5.6865082 6.8043973 -0.045897712 6.2172112 34.44354 45.607102 45.607102 -0.13827955 -0.060145768 0.060732183
9100 1.4046189 5.689947 6.7931999 0.025063166 7.0966586 33.816926 44.777394 44.777394 0.026506621 0.026941055 0.021741822
9200 1.4514944 5.6439353 6.7840064 0.010043669 6.8992028 33.212004 43.97641 43.97641 0.013456849 0.016567864 0.00010629292
9300 1.4577939 5.655083 6.800102 0.010672001 6.9162857 32.639692 43.218605 43.218605 0.026259683 -0.0039439335 0.0097002517
9400 1.4990612 5.6382783 6.8157106 0.0044191075 6.8615643 32.121265 42.53215 42.53215 -0.0025936629 0.022212724 -0.0063617388
9500 1.4578238 5.6474926 6.7925351 0.011187763 6.9033093 31.623599 41.873184 41.873184 0.026402116 0.012016515 -0.0048553414
9600 1.4618782 5.6455953 6.7938223 0.040647445 7.17882 31.159311 41.258416 41.258416 0.030007882 0.037188739 0.054745715
9700 1.472894 5.6140659 6.7709452 0.031213864 7.0543129 30.721834 40.679146 40.679146 0.030150709 0.023805303 0.03968558
9800 1.4853035 5.5879969 6.7546233 0.019089748 6.920651 30.285846 40.101849 40.101849 -0.001882924 0.030361407 0.02879076
9900 1.4922807 5.5739043 6.7460109 0.034454036 7.033471 29.869325 39.55033 39.55033 0.037756787 0.037488603 0.028116717
10000 1.4702912 5.5609742 6.7158092 0.02974948 6.9548436 29.496685 39.056912 39.056912 0.048495581 0.026126614 0.014626246
Loop time of 2.46339 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.418965 (17.0077)
Bond time (%) = 0.0689692 (2.79977)
Neigh time (%) = 0.69069 (28.0382)
Comm time (%) = 0.0612285 (2.48554)
Outpt time (%) = 0.00073576 (0.0298677)
Other time (%) = 1.2228 (49.639)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2884 ave 2884 max 2884 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21437 ave 21437 max 21437 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21437
Ave neighs/atom = 3.82804
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 6.39881 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4702912 5.5609742 6.7158092 0.072285735 7.2966186 29.496685 39.056912 39.056912 0.0517015 0.12420995 0.040945755
10100 1.4573097 5.5587677 6.7034064 0.044500854 7.0509833 29.081982 38.507799 39.056912 0.044350384 0.023335488 0.06581669
10200 1.4979402 5.529745 6.7062968 0.020491404 6.8628393 28.761597 38.083573 39.056912 0.027897265 0.011514546 0.0220624
10300 1.5172843 5.5187731 6.7105187 0.02641776 6.9082543 28.469328 37.696576 39.056912 0.036912371 0.030960772 0.011380138
10400 1.4760818 5.5254938 6.684877 0.0091876447 6.7521031 28.14814 37.271288 39.056912 0.015300105 0.02827069 -0.016007861
10500 1.5146302 5.5026001 6.692261 0.021789385 6.8479527 27.815895 36.831359 39.056912 0.015592969 0.032547229 0.017227956
10600 1.4679788 5.4885912 6.64161 0.011753224 6.7237238 27.505044 36.419757 39.056912 0.010721153 0.010926592 0.013611926
10700 1.4667245 5.4720863 6.6241198 0.0043905713 6.6539747 27.135001 35.929779 39.056912 -0.03606819 0.013643937 0.035595967
10800 1.4647544 5.4559859 6.606472 0.036718423 6.8501768 26.80851 35.497468 39.056912 0.044497798 0.031324763 0.034332708
10900 1.4580432 5.4564769 6.6016918 0.065478135 7.0263115 26.499317 35.088061 39.056912 0.08229008 0.052793688 0.061350637
11000 1.4700915 5.4471801 6.6018582 -0.016382922 6.4976429 26.245381 34.751822 39.056912 -0.0093025128 -0.034580288 -0.005265964
Loop time of 2.65811 on 1 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.524128 (19.7181)
Bond time (%) = 0.068589 (2.58037)
Neigh time (%) = 0.759783 (28.5836)
Comm time (%) = 0.0634546 (2.38721)
Outpt time (%) = 0.000737429 (0.0277426)
Other time (%) = 1.24142 (46.7031)
Nlocal: 5600 ave 5600 max 5600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3289 ave 3289 max 3289 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 27077 ave 27077 max 27077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 27077
Ave neighs/atom = 4.83518
Ave special neighs/atom = 0.571429
Neighbor list builds = 170
Dangerous builds = 0

401
examples/rigid/log.rigid.tnr.1Feb14.linux.4
View File

@ -1,401 +0,0 @@
LAMMPS (1 Feb 2014)
# Tethered nanorods
atom_style molecular
read_data data.rigid.tnr
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
1 by 2 by 2 MPI processor grid
reading atoms ...
5600 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
1600 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
# Specify bond parameters
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
# Specify initial velocities
velocity all create 1.4 109345
# Specify rigid components
group rods type 2
4000 atoms in group rods
group tethers subtract all rods
1600 atoms in group tethers
neigh_modify exclude molecule rods delay 0 every 1
# Specify the pair potentials
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff * * 1.0 1.0 1.122
pair_coeff 2 2 1.0 1.0 2.5
# Specify output
thermo 100
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
thermo_modify flush yes lost warn
timestep 0.005
fix 1 rods rigid molecule
800 rigid bodies with 4000 atoms
fix 2 tethers nve
fix 3 all langevin 1.4 1.4 1.0 437624
run 5000
Memory usage per processor = 4.9731 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624
200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719
300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786
400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141
500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529
600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222
700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907
800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859
900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971
1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735
1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195
1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658
1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474
1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314
1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432
1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699
1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975
1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981
1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291
2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901
2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978
2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521
2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595
2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.0006382503
2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414197 0.0039571832 0.0048428539
2600 1.3876469 5.9249124 7.0148347 -0.0017777225 6.9382806 62.244 62.244 62.244 -0.00047616391 -0.0025484918 -0.0023085117
2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812868 0.0032048357
2800 1.4444643 5.9283432 7.0628925 0.0019400021 7.1464349 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.00030624082
2900 1.3902832 5.9152516 7.0072446 -0.0021662209 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403252 -0.0046971889
3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147657
3100 1.3569137 5.9171753 6.9829583 -0.0028266776 6.8612331 62.244 62.244 62.244 -0.0069507251 0.0010084389 -0.0025377465
3200 1.4004275 5.905939 7.0058998 0.0054394662 7.2401396 62.244 62.244 62.244 0.010352182 0.0057594147 0.00020680221
3300 1.3641217 5.9145275 6.985972 -0.0027212879 6.8687852 62.244 62.244 62.244 -0.00065934268 -0.0057713101 -0.0017332109
3400 1.3868722 5.9059546 6.9952684 0.0092591224 7.3939941 62.244 62.244 62.244 0.010690868 0.010752519 0.00633398
3500 1.3939168 5.8992292 6.9940762 0.0074340081 7.314207 62.244 62.244 62.244 0.010137313 0.0044252684 0.007739443
3600 1.3982508 5.921946 7.0201971 0.0056794461 7.2647712 62.244 62.244 62.244 0.0023367067 0.0080592062 0.0066424255
3700 1.4019908 5.9059956 7.0071842 0.0065915632 7.2910368 62.244 62.244 62.244 0.0049554575 0.010826968 0.0039922641
3800 1.3960735 5.9020789 6.9986199 0.0027763383 7.1181774 62.244 62.244 62.244 -0.0015907441 0.0025861872 0.0073335719
3900 1.4352827 5.8986212 7.0259589 0.0034983551 7.1766087 62.244 62.244 62.244 0.0030418441 0.0027739 0.0046793211
4000 1.4121841 5.9079029 7.0170979 0.0050462456 7.2344045 62.244 62.244 62.244 0.004554319 0.0064113582 0.0041730596
4100 1.3989603 5.9082373 7.0070457 0.00042910949 7.0255244 62.244 62.244 62.244 0.0025742152 0.0025182507 -0.0038051374
4200 1.3998831 5.8998111 6.9993443 0.0042773229 7.1835387 62.244 62.244 62.244 0.0013730326 0.0064696933 0.0049892428
4300 1.4076053 5.904453 7.0100516 0.0066772664 7.2975948 62.244 62.244 62.244 0.0073577056 0.0048125374 0.0078615562
4400 1.4161358 5.9064223 7.0187211 -0.0011881346 6.9675565 62.244 62.244 62.244 -0.0019130158 -0.003763749 0.002112361
4500 1.4292267 5.8980407 7.0206217 0.0018482653 7.1002136 62.244 62.244 62.244 0.0041030608 0.0010365485 0.00040518656
4600 1.4160092 5.9019877 7.0141871 0.0050227685 7.2304827 62.244 62.244 62.244 0.0041611202 0.005764734 0.0051424512
4700 1.37861 5.8826208 6.9654451 0.0035124303 7.116701 62.244 62.244 62.244 0.0079436662 0.00069676038 0.0018968642
4800 1.3775582 5.8917844 6.9737825 0.00067406862 7.00281 62.244 62.244 62.244 0.0010058199 0.00035582238 0.00066056358
4900 1.4215964 5.8938211 7.0104089 -0.00048994747 6.9893103 62.244 62.244 62.244 -0.00067798345 0.0053757544 -0.0061676133
5000 1.4066006 5.8998845 7.0046939 0.0033843577 7.1504345 62.244 62.244 62.244 0.011284317 -0.0049851816 0.0038539381
Loop time of 3.20721 on 4 procs for 5000 steps with 5600 atoms
Pair time (%) = 0.116136 (3.62109)
Bond time (%) = 0.0531921 (1.65852)
Neigh time (%) = 0.438128 (13.6607)
Comm time (%) = 0.246661 (7.69083)
Outpt time (%) = 0.00308365 (0.0961474)
Other time (%) = 2.35001 (73.2727)
Nlocal: 1400 ave 1889 max 911 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 650.75 ave 723 max 584 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 1275.5 ave 1907 max 726 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 5102
Ave neighs/atom = 0.911071
Ave special neighs/atom = 0.571429
Neighbor list builds = 757
Dangerous builds = 0
# Replace fix rigid and fix langevin with new ones
unfix 1
unfix 3
fix 3 tethers langevin 1.4 1.4 1.0 198450
# Test different integrators for rods
fix 1 rods rigid/nve molecule
800 rigid bodies with 4000 atoms
print "rigid/nve"
rigid/nve
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
5000 1.4066006 5.8998845 7.0046939 0.032740437 8.4145959 62.244 62.244 62.244 0.045650084 0.034743967 0.017827261
5100 1.4217949 5.8923804 7.0091242 0.0086289093 7.380711 62.244 62.244 62.244 0.0055651416 0.01368451 0.0066370762
5200 1.4108746 5.9047641 7.0129305 0.0049647851 7.2267292 62.244 62.244 62.244 0.0046376956 0.0086302594 0.0016264003
5300 1.4067621 5.8876234 6.9925597 0.0027189828 7.1096473 62.244 62.244 62.244 0.0020158207 -0.00063477598 0.0067759036
5400 1.4293632 5.8838403 7.0065285 0.0092204598 7.4035893 62.244 62.244 62.244 0.0084019091 0.0099425199 0.0093169505
5500 1.4221951 5.8868259 7.003884 0.0078308214 7.3411028 62.244 62.244 62.244 0.0073406766 0.0097916953 0.0063600922
5600 1.4031432 5.8858207 6.9879145 0.001239457 7.0412893 62.244 62.244 62.244 0.0011109965 0.0023197155 0.00028765886
5700 1.4000575 5.883162 6.9828322 0.010499133 7.4349566 62.244 62.244 62.244 0.01198025 0.012641441 0.0068757094
5800 1.3722465 5.8848443 6.9626704 -0.00035914741 6.9472044 62.244 62.244 62.244 -0.0028690389 -0.00088916453 0.0026807612
5900 1.3734578 5.8841178 6.9628953 0.0065044666 7.2429973 62.244 62.244 62.244 0.0068963214 0.0094261457 0.0031909327
6000 1.3754553 5.8937449 6.9740914 0.0035762742 7.1280965 62.244 62.244 62.244 0.0028555765 0.0033314156 0.0045418303
Loop time of 0.71103 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0324474 (4.56343)
Bond time (%) = 0.0106753 (1.50138)
Neigh time (%) = 0.100071 (14.0741)
Comm time (%) = 0.0545349 (7.66984)
Outpt time (%) = 0.000602841 (0.0847842)
Other time (%) = 0.512699 (72.1065)
Nlocal: 1400 ave 1881 max 915 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 668 ave 762 max 600 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1269 ave 1827 max 647 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5076
Ave neighs/atom = 0.906429
Ave special neighs/atom = 0.571429
Neighbor list builds = 154
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
800 rigid bodies with 4000 atoms
print "rigid/nvt"
rigid/nvt
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
6000 1.3754553 5.8937449 6.9740914 0.049674573 9.1132283 62.244 62.244 62.244 0.056393855 0.044956749 0.047673114
6100 1.3818996 5.8984681 6.9838762 0.00058645322 7.0091306 62.244 62.244 62.244 0.0029282001 -0.0010828799 -8.596054e-05
6200 1.4315931 5.8945239 7.0189637 0.0034484132 7.1674627 62.244 62.244 62.244 0.0058150828 0.00034494103 0.0041852159
6300 1.4553306 5.904541 7.0476252 0.0010038355 7.0908534 62.244 62.244 62.244 0.0018558228 -0.0024096116 0.0035652954
6400 1.4684339 5.8903917 7.0437678 0.0050340074 7.2605473 62.244 62.244 62.244 0.0081274355 0.0060258489 0.0009487377
6500 1.397466 5.8957046 6.9933393 0.0026494888 7.1074343 62.244 62.244 62.244 0.0025578255 0.0017879539 0.0036026871
6600 1.4017782 5.8966082 6.9976299 0.0059660342 7.2545454 62.244 62.244 62.244 0.0052881291 0.0059401179 0.0066698556
6700 1.4147355 5.8899121 7.001111 0.00034372887 7.015913 62.244 62.244 62.244 -0.00039811564 0.0042903128 -0.0028610106
6800 1.4026154 5.8846134 6.9862927 0.0058210004 7.2369625 62.244 62.244 62.244 0.0066928038 0.0053938331 0.0053763642
6900 1.4334896 5.8930688 7.0189981 0.00096971534 7.0607569 62.244 62.244 62.244 0.0014759985 0.005380295 -0.0039471475
7000 1.4183184 5.8899892 7.0040023 0.0065331422 7.2853391 62.244 62.244 62.244 0.0087688941 0.0045715326 0.0062589999
Loop time of 0.724545 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0333842 (4.60761)
Bond time (%) = 0.0107084 (1.47795)
Neigh time (%) = 0.0995998 (13.7465)
Comm time (%) = 0.0522026 (7.20488)
Outpt time (%) = 0.000613034 (0.0846095)
Other time (%) = 0.528037 (72.8784)
Nlocal: 1400 ave 1835 max 890 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 702.5 ave 810 max 574 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 1381.5 ave 1991 max 716 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 5526
Ave neighs/atom = 0.986786
Ave special neighs/atom = 0.571429
Neighbor list builds = 155
Dangerous builds = 0
unfix 1
compute myTemp all temp
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt iso"
rigid/npt iso
fix_modify 1 temp myTemp
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.9921 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
7000 1.4183184 5.8899892 7.0040023 0.0050486391 7.2214119 62.244 62.244 62.244 0.043816651 -0.087155941 0.058485207
7100 1.4038983 5.8814774 6.9841642 0.009993125 7.3679901 59.915655 59.915655 59.915655 0.0070735055 0.010976068 0.011929801
7200 1.4312073 5.8606903 6.984827 0.0089330912 7.2912768 57.700805 57.700805 57.700805 0.01156272 0.0074893368 0.0077472167
7300 1.4407415 5.8415009 6.9731262 0.011035789 7.313692 55.700862 55.700862 55.700862 0.010519024 0.0067474464 0.015840899
7400 1.4196359 5.8415108 6.9565587 0.0025417019 7.0274842 53.862756 53.862756 53.862756 0.0043954525 0.004824396 -0.0015947429
7500 1.4156145 5.8327435 6.9446329 0.010433473 7.2089087 52.152148 52.152148 52.152148 0.01179134 0.0055857749 0.013923305
7600 1.4180615 5.8188658 6.9326772 0.015609218 7.2939723 50.608446 50.608446 50.608446 0.0028724549 0.022210059 0.02174514
7700 1.4259294 5.8098966 6.9298877 0.0030559519 6.9948575 49.194626 49.194626 49.194626 0.0046696448 0.00055793026 0.0039402805
7800 1.411295 5.7988715 6.9073681 0.0092006473 7.0879075 47.897612 47.897612 47.897612 0.017128448 0.0054472316 0.0050262622
7900 1.4108742 5.7752582 6.8834242 0.00087414641 6.8993415 46.718678 46.718678 46.718678 0.0044372502 -0.00052897293 -0.001285838
8000 1.3910325 5.7775053 6.8700867 0.019735394 7.2031692 45.551007 45.551007 45.551007 0.012397847 0.021690086 0.02511825
Loop time of 1.04095 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0613976 (5.89824)
Bond time (%) = 0.0165009 (1.58518)
Neigh time (%) = 0.201774 (19.3837)
Comm time (%) = 0.0760022 (7.30125)
Outpt time (%) = 0.000428915 (0.0412043)
Other time (%) = 0.684844 (65.7904)
Nlocal: 1400 ave 1797 max 1000 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1040 ave 1186 max 930 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 2652 ave 3792 max 1522 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 10608
Ave neighs/atom = 1.89429
Ave special neighs/atom = 0.571429
Neighbor list builds = 262
Dangerous builds = 0
unfix 1
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/npt x"
rigid/npt x
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
8000 1.3910325 5.7775053 6.8700867 0.068684018 8.0292954 45.551007 45.551007 45.551007 0.0075744454 0.11785739 0.080620215
8100 1.4160395 5.7676429 6.8798661 0.0065100016 6.9864766 44.198871 45.551007 45.551007 0.011695272 0.0040404036 0.0037943293
8200 1.4429338 5.7597227 6.8930699 0.0044623039 6.9639774 42.886955 45.551007 45.551007 0.015037624 -0.0047943681 0.0031436559
8300 1.4413276 5.7513302 6.8834158 0.010009783 7.0380516 41.694377 45.551007 45.551007 0.014564125 0.012896809 0.0025684155
8400 1.4343217 5.7515313 6.8781141 0.0072223957 6.986466 40.489955 45.551007 45.551007 0.0091249482 0.0056233713 0.0069188677
8500 1.4136692 5.751692 6.8620534 0.0096235568 7.0024139 39.364181 45.551007 45.551007 0.011711119 0.013318118 0.0038414335
8600 1.3994641 5.7464082 6.8456122 0.025028488 7.2002905 38.246529 45.551007 45.551007 0.021265819 0.025439388 0.028380257
8700 1.4138866 5.7179769 6.8285091 0.014028521 7.021982 37.222055 45.551007 45.551007 0.019904996 0.022260772 -8.0204045e-05
8800 1.3697378 5.7168466 6.7927023 0.02231094 7.092514 36.267933 45.551007 45.551007 0.02769865 0.012576894 0.026657276
8900 1.402393 5.7128653 6.8143699 0.02837253 7.1862185 35.372046 45.551007 45.551007 0.02762235 0.040370216 0.017125023
9000 1.431654 5.6938727 6.8183602 0.016130352 7.0241345 34.430181 45.551007 45.551007 0.0088192249 0.0091663636 0.030405467
Loop time of 1.08382 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.0826703 (7.62768)
Bond time (%) = 0.0164793 (1.52048)
Neigh time (%) = 0.202493 (18.6832)
Comm time (%) = 0.0888866 (8.20123)
Outpt time (%) = 0.000417709 (0.0385405)
Other time (%) = 0.692874 (63.9288)
Nlocal: 1400 ave 1816 max 1003 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1106.75 ave 1237 max 962 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3609 ave 5743 max 1869 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 14436
Ave neighs/atom = 2.57786
Ave special neighs/atom = 0.571429
Neighbor list builds = 192
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph iso"
rigid/nph iso
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
9000 1.431654 5.6938727 6.8183602 0.01143345 6.9642163 34.430181 45.551007 45.551007 0.087625543 -0.18424224 0.13091705
9100 1.4696353 5.669441 6.8237607 0.02683122 7.1482512 33.82289 44.747564 44.747564 0.038188706 0.021753624 0.020551331
9200 1.4503489 5.6757074 6.8148788 0.021148084 7.0572895 33.223889 43.955088 43.955088 0.028893061 0.023573367 0.010977824
9300 1.4890502 5.6551355 6.8247047 0.032005229 7.1730611 32.655613 43.20326 43.20326 0.027960938 0.047252183 0.020802567
9400 1.4974788 5.6550122 6.8312016 0.022789713 7.0672131 32.118481 42.492636 42.492636 0.014186376 0.02731245 0.026870315
9500 1.4861129 5.6301004 6.7973625 0.056540979 7.3532565 31.566986 41.763011 41.763011 0.070975879 0.039997167 0.058649893
9600 1.4882551 5.6046579 6.7736025 0.013643963 6.9021339 31.120487 41.172295 41.172295 0.0054708323 0.017134071 0.018326985
9700 1.4721961 5.5861689 6.7425 0.046847392 7.1653218 30.679447 40.5888 40.5888 0.033912637 0.065035347 0.041594191
9800 1.4827559 5.5716195 6.7362449 0.032095321 7.0144242 30.268062 40.044538 40.044538 0.048655332 0.025995432 0.021635198
9900 1.476568 5.5566339 6.716399 0.037796165 7.0309954 29.862457 39.507925 39.507925 0.034991254 0.044450492 0.033946749
10000 1.4606684 5.5590139 6.7062906 0.011771017 6.8005705 29.482105 39.00472 39.00472 -0.0066083806 0.012698228 0.029223204
Loop time of 1.14607 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.107624 (9.39068)
Bond time (%) = 0.0165663 (1.44549)
Neigh time (%) = 0.246527 (21.5107)
Comm time (%) = 0.0994916 (8.68113)
Outpt time (%) = 0.000405192 (0.035355)
Other time (%) = 0.675454 (58.9367)
Nlocal: 1400 ave 1725 max 1072 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1286.75 ave 1414 max 1166 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 5461 ave 7932 max 3039 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 21844
Ave neighs/atom = 3.90071
Ave special neighs/atom = 0.571429
Neighbor list builds = 190
Dangerous builds = 0
unfix 1
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
800 rigid bodies with 4000 atoms
print "rigid/nph xy couple"
rigid/nph xy couple
run 1000
WARNING: Inconsistent image flags (../domain.cpp:645)
Memory usage per processor = 4.99592 Mbytes
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
10000 1.4606684 5.5590139 6.7062906 -0.054323908 6.2711839 29.482105 39.00472 39.00472 -0.13889514 0.022522203 -0.046598788
10100 1.4657219 5.5658034 6.7170494 0.046191264 7.078621 29.145622 38.559555 39.00472 0.041993444 0.057731099 0.038849248
10200 1.5086998 5.5537733 6.7387762 0.037571227 7.0249318 28.749452 38.035423 39.00472 0.059943553 0.01714367 0.035626459
10300 1.4942525 5.5348006 6.7084559 0.035441685 6.9720943 28.412097 37.589104 39.00472 0.058842839 0.029199467 0.01828275
10400 1.4835714 5.5161809 6.6814467 0.011614772 6.7654283 28.011918 37.059668 39.00472 0.0020323206 0.044104517 -0.011292523
10500 1.4822309 5.5103173 6.6745303 0.057714827 7.0812115 27.652821 36.584584 39.00472 0.080057627 0.041550212 0.051536644
10600 1.4815153 5.4966675 6.6603185 0.033053113 6.8888568 27.392359 36.239994 39.00472 0.042895505 0.034396997 0.021866837
10700 1.4777966 5.4994576 6.6601877 0.011268502 6.7364448 27.099624 35.852707 39.00472 0.019713922 -0.0036266081 0.017718191
10800 1.4876859 5.4727622 6.6412597 0.036949917 6.8864907 26.83719 35.505507 39.00472 0.040563603 0.044972283 0.025313864
10900 1.4960872 5.4500779 6.6251742 0.0012247499 6.6331413 26.569303 35.151093 39.00472 0.0023049747 0.01451802 -0.013148745
11000 1.4608347 5.4589178 6.6063252 -0.00321258 6.5857748 26.347448 34.857581 39.00472 0.0066852906 -0.0045030316 -0.011819999
Loop time of 1.19108 on 4 procs for 1000 steps with 5600 atoms
Pair time (%) = 0.133478 (11.2065)
Bond time (%) = 0.0166689 (1.39948)
Neigh time (%) = 0.258172 (21.6755)
Comm time (%) = 0.104376 (8.76311)
Outpt time (%) = 0.000403106 (0.0338438)
Other time (%) = 0.677981 (56.9216)
Nlocal: 1400 ave 1661 max 1127 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1414.25 ave 1494 max 1312 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 6643.25 ave 9132 max 4197 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 26573
Ave neighs/atom = 4.74518
Ave special neighs/atom = 0.571429
Neighbor list builds = 169
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI 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 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 2.37453 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02
25 220.34459 -8272.5701 0 -8233.1798 5168.6655 19547.02
50 300 -8237.7876 0 -8184.1576 13741.264 19686.493
75 292.67269 -8229.8093 0 -8177.4891 14319.387 19744.946
100 300 -8245.8191 0 -8192.189 9034.8776 19778.592
Loop time of 0.242724 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 0.227235 (93.6186)
Neigh time (%) = 0.00858116 (3.53536)
Comm time (%) = 0.00186229 (0.767244)
Outpt time (%) = 5.88894e-05 (0.0242619)
Other time (%) = 0.00498676 (2.0545)
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 100 dump.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 2.37644 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 298.53339 -8245.8191 0 -8210.2533 8056.2702 19786.12
100 300 -8260.7953 0 -8225.0549 3176.1215 19817.501
200 298.50746 -8257.8441 0 -8222.2815 1695.9804 19934.196
300 296.80999 -8250.2343 0 -8214.8739 -338.79329 20058.878
400 306.47135 -8245.2265 0 -8208.7151 9.7568356 20142.386
500 298.68843 -8240.244 0 -8204.6599 722.21355 20168.894
600 302.37622 -8230.4652 0 -8194.4417 4005.8413 20287.297
700 300 -8222.0223 0 -8186.2819 6766.8121 20413.543
800 303.21952 -8210.998 0 -8174.874 8149.6736 20518.069
900 297.74338 -8197.2403 0 -8161.7687 10760.713 20642.656
1000 300 -8180.7508 0 -8145.0104 14222.046 20768.465
1100 305.89822 -8166.6544 0 -8130.2113 18071.408 20883.281
1200 295.27459 -8152.0699 0 -8116.8924 21320.011 21009.09
1300 300 -8141.732 0 -8105.9916 22791.087 21123.905
1400 300 -8130.0647 0 -8094.3243 23517.708 21254.6
1500 300 -8125.4387 0 -8089.6983 21994.275 21364.53
1600 300 -8128.9533 0 -8093.2128 18321.801 21494.003
1700 300 -8151.4563 0 -8115.7159 11507 21608.819
1800 300 -8160.1502 0 -8124.4098 7544.7477 21732.185
1900 309.29943 -8153.7122 0 -8116.8639 8406.6165 21866.544
2000 307.15092 -8160.675 0 -8124.0826 5891.9485 21985.024
2100 308.54207 -8156.5601 0 -8119.802 4915.0348 22103.504
2200 300 -8157.4804 0 -8121.74 2411.006 22225.648
2300 300 -8162.7297 0 -8126.9893 -128.06955 22342.907
2400 300 -8166.1396 0 -8130.3991 -1504.3669 22467.494
2500 300 -8169.094 0 -8133.3536 -119.92093 22587.196
2600 304.76063 -8162.5898 0 -8126.2822 2245.7194 22722.776
2700 308.04872 -8167.1208 0 -8130.4215 77.123843 22842.478
2800 300 -8167.1381 0 -8131.3977 -2884.8582 22959.736
2900 308.65071 -8164.1796 0 -8127.4086 -7535.1379 23084.324
3000 302.42612 -8159.1684 0 -8123.139 -9971.2947 23197.918
Loop time of 7.49716 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 6.81268 (90.8701)
Neigh time (%) = 0.474639 (6.33091)
Comm time (%) = 0.0605421 (0.807533)
Outpt time (%) = 0.000495911 (0.00661464)
Other time (%) = 0.148806 (1.98483)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2104 ave 2104 max 2104 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 44986 ave 44986 max 44986 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 44986
Ave neighs/atom = 23.5282
Neighbor list builds = 221
Dangerous builds = 0

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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI 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 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 2.27477 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02
25 219.81848 -8272.1577 0 -8232.8615 5206.8057 19547.02
50 300 -8238.3413 0 -8184.7112 13308.809 19688.933
75 294.78636 -8232.2217 0 -8179.5237 13192.782 19748.176
100 300 -8248.1223 0 -8194.4923 7352.0246 19816.321
Loop time of 0.06813 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.0606876 (89.0762)
Neigh time (%) = 0.00226843 (3.32957)
Comm time (%) = 0.00331974 (4.87265)
Outpt time (%) = 7.83205e-05 (0.114957)
Other time (%) = 0.00177592 (2.60666)
Nlocal: 478 ave 490 max 466 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 1036.25 ave 1046 max 1027 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 11488 ave 11948 max 11157 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 45952
Ave neighs/atom = 24.0335
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 100 dump.shear
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 2.27477 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 302.4034 -8248.1223 0 -8212.0956 6393.6774 19845.81
100 291.62219 -8259.5645 0 -8224.8222 -1305.829 19874.353
200 293.37436 -8257.0158 0 -8222.0647 -803.21007 19965.105
300 305.94964 -8252.9337 0 -8216.4845 -1338.206 20062.042
400 309.97419 -8247.5911 0 -8210.6624 -1064.8166 20094.42
500 301.9509 -8239.3761 0 -8203.4033 794.43498 20172.617
600 302.22577 -8230.7201 0 -8194.7145 3984.6172 20265.23
700 296.33661 -8221.2208 0 -8185.9168 5407.761 20394.703
800 291.23709 -8207.8855 0 -8173.1891 10664.616 20510.74
900 297.90023 -8196.1342 0 -8160.6439 13966.21 20646.32
1000 301.54908 -8182.0178 0 -8146.0928 17938.624 20752.586
1100 309.01306 -8164.9485 0 -8128.1343 22821.748 20889.388
1200 301.9299 -8153.5108 0 -8117.5405 25613.387 21000.539
1300 300 -8143.4144 0 -8107.674 26662.495 21122.684
1400 300 -8136.3101 0 -8100.5697 26322.787 21254.6
1500 300 -8132.5702 0 -8096.8297 23577.661 21379.187
1600 300 -8129.9485 0 -8094.2081 20683.092 21497.667
1700 300 -8131.6622 0 -8095.9218 15384.841 21617.369
1800 300 -8149.3274 0 -8113.587 9702.6228 21738.292
1900 300 -8156.1594 0 -8120.419 9896.6056 21861.658
2000 300 -8162.0579 0 -8126.3174 8370.0255 21987.467
2100 300 -8164.32 0 -8128.5796 5207.4966 22105.947
2200 309.50383 -8171.5055 0 -8134.6328 263.16699 22234.198
2300 300 -8173.946 0 -8138.2056 -2861.1575 22346.571
2400 300 -8184.1165 0 -8148.3761 -6684.5831 22471.159
2500 308.09598 -8186.7631 0 -8150.0582 -8719.8136 22598.189
2600 293.95252 -8179.2012 0 -8144.1813 -8299.1668 22720.333
2700 300 -8173.1769 0 -8137.4365 -8570.4623 22831.485
2800 307.83907 -8172.8218 0 -8136.1475 -10364.571 22959.736
2900 299.48361 -8169.4289 0 -8133.75 -8567.3623 23079.438
3000 300 -8167.764 0 -8132.0236 -11479.844 23206.468
Loop time of 2.11249 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 1.79807 (85.1163)
Neigh time (%) = 0.123332 (5.83823)
Comm time (%) = 0.135713 (6.4243)
Outpt time (%) = 0.000717998 (0.0339883)
Other time (%) = 0.0546538 (2.58718)
Nlocal: 478 ave 510 max 443 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 1018.25 ave 1064 max 972 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 11225.8 ave 12344 max 10134 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 44903
Ave neighs/atom = 23.4848
Neighbor list builds = 226
Dangerous builds = 0

169
examples/shear/log.shear.void.1Feb14.linux.1
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LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI 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 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 2.35723 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
25 222.66197 -7321.4403 0 -7287.5071 562.28854 19547.02
50 300 -7292.2273 0 -7246.508 7555.5059 19688.542
75 292.67603 -7286.2016 0 -7241.5984 6825.409 19746.217
100 300 -7297.4174 0 -7251.698 1627.2455 19775.648
Loop time of 0.209278 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.195591 (93.4599)
Neigh time (%) = 0.00736594 (3.51969)
Comm time (%) = 0.001688 (0.806585)
Outpt time (%) = 6.91414e-05 (0.0330381)
Other time (%) = 0.00456381 (2.18074)
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 100 dump.shear.void
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 2.35723 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 785.80272 19779.424
100 290.32156 -7309.73 0 -7280.2463 -5960.68 19838.822
200 290.76236 -7306.4805 0 -7276.952 -7418.7514 19927.076
300 293.25821 -7304.1086 0 -7274.3267 -11009.15 20043.748
400 293.84766 -7299.0985 0 -7269.2567 -7883.11 20105.777
500 291.74499 -7299.9751 0 -7270.3468 -5633.9534 20145.528
600 303.46664 -7291.5162 0 -7260.6975 -1009.8362 20277.444
700 300 -7287.9569 0 -7257.4903 -2204.427 20399.405
800 300 -7280.4222 0 -7249.9555 -2875.1442 20520.781
900 292.92463 -7272.7361 0 -7242.9881 -1776.2948 20641.435
1000 307.93499 -7265.1866 0 -7233.9141 -1238.1504 20758.693
1100 300.17079 -7260.1229 0 -7229.6389 -1842.3017 20889.388
1200 302.06128 -7255.9277 0 -7225.2517 -1888.5899 21012.754
1300 300 -7259.2664 0 -7228.7998 -3184.8863 21119.02
1400 300 -7265.444 0 -7234.9774 -6107.2621 21252.157
1500 308.79162 -7271.0073 0 -7239.6478 -6104.8023 21369.416
1600 300 -7275.2324 0 -7244.7658 -8516.6115 21500.11
1700 309.22602 -7278.5756 0 -7247.172 -13747.711 21618.59
1800 300 -7284.3068 0 -7253.8402 -14332.302 21728.52
1900 299.75827 -7283.413 0 -7252.9709 -14457.778 21854.329
2000 297.70312 -7274.9007 0 -7244.6674 -20473.262 21986.245
2100 304.09482 -7269.8328 0 -7238.9503 -19783.936 22101.061
2200 299.66443 -7269.2566 0 -7238.8241 -16596.846 22224.427
2300 299.27231 -7268.2781 0 -7237.8853 -15841.479 22345.35
2400 300.69324 -7259.5316 0 -7228.9946 -14593.472 22471.159
2500 297.44581 -7258.0006 0 -7227.7934 -17840.459 22589.639
2600 300 -7253.3731 0 -7222.9065 -18551.141 22719.112
2700 305.12651 -7253.1648 0 -7222.1775 -20324.426 22832.706
2800 294.14063 -7249.1464 0 -7219.2748 -17535.191 22960.958
2900 307.30441 -7249.4895 0 -7218.281 -17444.188 23079.438
3000 304.44871 -7244.9559 0 -7214.0374 -15836.731 23207.69
Loop time of 6.38739 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 5.8135 (91.0153)
Neigh time (%) = 0.385951 (6.04239)
Comm time (%) = 0.0530334 (0.830282)
Outpt time (%) = 0.00047183 (0.0073869)
Other time (%) = 0.134431 (2.10463)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1879 ave 1879 max 1879 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38632 ave 38632 max 38632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38632
Ave neighs/atom = 22.6183
Neighbor list builds = 209
Dangerous builds = 0

169
examples/shear/log.shear.void.1Feb14.linux.4
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@ -1,169 +0,0 @@
LAMMPS (1 Feb 2014)
# 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 orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI 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 box
Created 1912 atoms
pair_style eam
pair_coeff * * Ni_u3.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 group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# 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
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
timestep 0.001
run 100
Memory usage per processor = 2.26255 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02
25 220.57465 -7320.4003 0 -7286.7852 832.69858 19547.02
50 300 -7292.1121 0 -7246.3928 7101.9213 19686.075
75 295.2793 -7286.9013 0 -7241.9014 5282.1114 19746.39
100 300 -7301.0026 0 -7255.2833 -1939.7714 19790.975
Loop time of 0.0608495 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.0528613 (86.8723)
Neigh time (%) = 0.00192648 (3.16598)
Comm time (%) = 0.00410181 (6.74092)
Outpt time (%) = 0.000108302 (0.177983)
Other time (%) = 0.00185156 (3.04285)
Nlocal: 427 ave 437 max 419 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 780 ave 788 max 774 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 9859.75 ave 10248 max 9544 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 39439
Ave neighs/atom = 23.0907
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 100 dump.shear.void
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
reset_timestep 0
run 3000
Memory usage per processor = 2.26255 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 299.05825 -7301.0026 0 -7270.6316 -2766.8643 19799.958
100 301.19116 -7308.1272 0 -7277.5397 -8905.8025 19851.046
200 296.34396 -7306.2167 0 -7276.1214 -9976.4707 19977.676
300 301.10727 -7303.6912 0 -7273.1122 -9863.5572 20024.08
400 303.06413 -7299.743 0 -7268.9652 -7947.839 20095.051
500 298.67442 -7297.287 0 -7266.955 -5764.8779 20168.374
600 296.13094 -7292.6877 0 -7262.614 -1786.0615 20265.23
700 305.86337 -7287.378 0 -7256.3159 -1049.7285 20413.77
800 297.25967 -7280.2104 0 -7250.0221 -1484.4549 20516.847
900 305.16151 -7272.5608 0 -7241.57 -808.36942 20629.22
1000 303.28807 -7264.3771 0 -7233.5765 -2139.5907 20763.579
1100 297.67659 -7258.2851 0 -7228.0544 -770.05741 20890.609
1200 309.60751 -7254.7626 0 -7223.3203 819.60099 20995.654
1300 300 -7251.8704 0 -7221.4038 -1919.6357 21121.462
1400 300 -7258.7732 0 -7228.3066 -5164.6854 21253.378
1500 304.51839 -7269.5164 0 -7238.5909 -8462.6306 21376.744
1600 302.30135 -7270.4656 0 -7239.7653 -10283.715 21489.117
1700 300 -7273.6082 0 -7243.1416 -11338.311 21616.147
1800 306.59272 -7269.4364 0 -7238.3003 -14218.514 21740.735
1900 306.24897 -7271.6064 0 -7240.5052 -19238.112 21854.329
2000 302.17783 -7267.1183 0 -7236.4305 -20204.467 21975.252
2100 308.30693 -7268.4528 0 -7237.1425 -25338.75 22097.397
2200 306.39487 -7266.6795 0 -7235.5635 -27066.965 22230.534
2300 300 -7262.1576 0 -7231.691 -24009.895 22351.457
2400 300 -7261.5352 0 -7231.0686 -20454.104 22478.487
2500 300.08812 -7260.6902 0 -7230.2146 -15315.132 22587.196
2600 296.32147 -7257.4049 0 -7227.3118 -13410.947 22722.776
2700 300 -7256.5862 0 -7226.1196 -15961.676 22830.263
2800 298.83111 -7256.171 0 -7225.8231 -20667.094 22960.958
2900 291.53879 -7248.9903 0 -7219.3829 -23968.563 23081.881
3000 293.96302 -7243.6435 0 -7213.79 -25021.209 23200.361
Loop time of 1.76354 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 1.51321 (85.8057)
Neigh time (%) = 0.0997625 (5.65696)
Comm time (%) = 0.100933 (5.72334)
Outpt time (%) = 0.000777066 (0.044063)
Other time (%) = 0.048848 (2.76989)
Nlocal: 427 ave 450 max 403 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 785 ave 843 max 722 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 9576.75 ave 10183 max 9094 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 38307
Ave neighs/atom = 22.428
Neighbor list builds = 215
Dangerous builds = 0

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