From 723da5079ab7db024145c01f5efeffc419bc869c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 15 May 2015 19:27:25 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13470 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/balance/log.balance.8Aug14.linux.1 | 187 ------- examples/balance/log.balance.8Aug14.linux.4 | 187 ------- .../log.balance.bond.fast.21Jan15.linux.1 | 203 ------- .../log.balance.bond.fast.21Jan15.linux.4 | 203 ------- .../log.balance.bond.slow.21Jan15.linux.1 | 502 ------------------ .../log.balance.bond.slow.21Jan15.linux.4 | 502 ------------------ examples/body/log.body.1Feb14.linux.1 | 71 --- examples/body/log.body.1Feb14.linux.4 | 71 --- examples/colloid/log.colloid.1Feb14.linux.1 | 131 ----- examples/colloid/log.colloid.1Feb14.linux.4 | 131 ----- examples/comb/log.comb.Cu.1Feb14.linux.1 | 76 --- examples/comb/log.comb.Cu.1Feb14.linux.4 | 76 --- .../comb/log.comb.Cu2O.elastic.1Feb14.linux.1 | 316 ----------- .../comb/log.comb.Cu2O.elastic.1Feb14.linux.4 | 316 ----------- examples/comb/log.comb.HfO2.1Feb14.linux.1 | 185 ------- examples/comb/log.comb.HfO2.1Feb14.linux.4 | 185 ------- examples/comb/log.comb.Si.1Feb14.linux.1 | 76 --- examples/comb/log.comb.Si.1Feb14.linux.4 | 76 --- .../comb/log.comb.Si.elastic.1Feb14.linux.1 | 274 ---------- .../comb/log.comb.Si.elastic.1Feb14.linux.4 | 274 ---------- examples/comb/log.comb3.1Feb14.linux.1 | 73 --- examples/comb/log.comb3.1Feb14.linux.4 | 73 --- examples/crack/log.crack.1Feb14.linux.1 | 138 ----- examples/crack/log.crack.1Feb14.linux.4 | 138 ----- examples/dipole/log.dipole.1Feb14.linux.1 | 89 ---- examples/dipole/log.dipole.1Feb14.linux.4 | 89 ---- examples/dreiding/log.dreiding.1Feb14.linux.1 | 106 ---- examples/dreiding/log.dreiding.1Feb14.linux.4 | 106 ---- examples/eim/log.eim.1Feb14.linux.1 | 72 --- examples/eim/log.eim.1Feb14.linux.4 | 72 --- .../log.ellipse.gayberne.1Feb14.linux.1 | 163 ------ .../log.ellipse.gayberne.1Feb14.linux.4 | 163 ------ .../log.ellipse.resquared.1Feb14.linux.1 | 160 ------ .../log.ellipse.resquared.1Feb14.linux.4 | 160 ------ examples/flow/log.flow.couette.1Feb14.linux.1 | 130 ----- examples/flow/log.flow.couette.1Feb14.linux.4 | 130 ----- examples/flow/log.flow.pois.1Feb14.linux.1 | 130 ----- examples/flow/log.flow.pois.1Feb14.linux.4 | 130 ----- examples/friction/log.friction.1Feb14.linux.1 | 149 ------ examples/friction/log.friction.1Feb14.linux.4 | 149 ------ .../log.hugoniostat.1Feb14.linux.1 | 90 ---- .../log.hugoniostat.1Feb14.linux.4 | 90 ---- examples/indent/log.indent.1Feb14.linux.1 | 179 ------- examples/indent/log.indent.1Feb14.linux.4 | 179 ------- examples/indent/log.indent.min.1Feb14.linux.1 | 404 -------------- examples/indent/log.indent.min.1Feb14.linux.4 | 405 -------------- examples/meam/log.meam.1Feb14.linux.1 | 67 --- examples/meam/log.meam.1Feb14.linux.4 | 67 --- examples/meam/log.meam.shear.1Feb14.linux.1 | 172 ------ examples/meam/log.meam.shear.1Feb14.linux.4 | 172 ------ examples/melt/log.melt.1Feb14.linux.1 | 63 --- examples/melt/log.melt.1Feb14.linux.4 | 63 --- examples/micelle/log.micelle.1Feb14.linux.1 | 215 -------- examples/micelle/log.micelle.1Feb14.linux.4 | 215 -------- examples/min/log.min.1Feb14.linux.1 | 118 ---- examples/min/log.min.1Feb14.linux.4 | 118 ---- examples/min/log.min.box.1Feb14.linux.1 | 356 ------------- examples/min/log.min.box.1Feb14.linux.4 | 356 ------------- examples/msst/log.msst.1Feb14.linux.1 | 138 ----- examples/msst/log.msst.1Feb14.linux.4 | 138 ----- examples/nb3b/log.nb3b.1Feb14.linux.1 | 144 ----- examples/nb3b/log.nb3b.1Feb14.linux.4 | 144 ----- examples/nemd/log.nemd.1Feb14.linux.1 | 115 ---- examples/nemd/log.nemd.1Feb14.linux.4 | 115 ---- examples/obstacle/log.obstacle.1Feb14.linux.1 | 140 ----- examples/obstacle/log.obstacle.1Feb14.linux.4 | 140 ----- examples/peptide/log.peptide.1Feb14.linux.1 | 177 ------ examples/peptide/log.peptide.1Feb14.linux.4 | 177 ------ examples/peri/log.peri.1Feb14.linux.1 | 90 ---- examples/peri/log.peri.1Feb14.linux.4 | 90 ---- examples/pour/log.pour.1Feb14.linux.1 | 147 ----- examples/pour/log.pour.1Feb14.linux.4 | 147 ----- examples/pour/log.pour.2d.1Feb14.linux.1 | 100 ---- examples/pour/log.pour.2d.1Feb14.linux.4 | 100 ---- .../pour/log.pour.2d.molecule.1Feb14.linux.1 | 113 ---- .../pour/log.pour.2d.molecule.1Feb14.linux.4 | 113 ---- examples/qeq/log.qeq.buck.8Sep14.linux.1 | 85 --- examples/qeq/log.qeq.buck.8Sep14.linux.4 | 85 --- examples/qeq/log.qeq.reaxc.8Sep14.linux.1 | 89 ---- examples/qeq/log.qeq.reaxc.8Sep14.linux.4 | 89 ---- examples/reax/log.reax.rdx.1Feb14.linux.1 | 85 --- examples/reax/log.reax.rdx.1Feb14.linux.4 | 85 --- examples/reax/log.reax.tatb.1Feb14.linux.1 | 81 --- examples/reax/log.reax.tatb.1Feb14.linux.4 | 81 --- examples/reax/log.reaxc.rdx.1Feb14.linux.1 | 88 --- examples/reax/log.reaxc.rdx.1Feb14.linux.4 | 88 --- examples/reax/log.reaxc.tatb.1Feb14.linux.1 | 86 --- examples/reax/log.reaxc.tatb.1Feb14.linux.4 | 86 --- examples/rigid/log.rigid.1Feb14.linux.1 | 314 ----------- examples/rigid/log.rigid.1Feb14.linux.4 | 314 ----------- examples/rigid/log.rigid.poems.1Feb14.linux.1 | 317 ----------- examples/rigid/log.rigid.poems.1Feb14.linux.4 | 317 ----------- .../rigid/log.rigid.poems2.1Feb14.linux.1 | 321 ----------- .../rigid/log.rigid.poems2.1Feb14.linux.4 | 321 ----------- examples/rigid/log.rigid.tnr.1Feb14.linux.1 | 401 -------------- examples/rigid/log.rigid.tnr.1Feb14.linux.4 | 401 -------------- examples/shear/log.shear.1Feb14.linux.1 | 168 ------ examples/shear/log.shear.1Feb14.linux.4 | 168 ------ examples/shear/log.shear.void.1Feb14.linux.1 | 169 ------ examples/shear/log.shear.void.1Feb14.linux.4 | 169 ------ examples/snap/log.snap.5Sep14.linux.1 | 116 ---- examples/snap/log.snap.5Sep14.linux.4 | 116 ---- examples/srd/log.srd.mixture.1Feb14.linux.1 | 232 -------- examples/srd/log.srd.mixture.1Feb14.linux.4 | 232 -------- examples/srd/log.srd.pure.1Feb14.linux.1 | 148 ------ examples/srd/log.srd.pure.1Feb14.linux.4 | 148 ------ .../streitz/log.streitz.ewald.19Feb15.linux.1 | 111 ---- .../streitz/log.streitz.ewald.19Feb15.linux.4 | 107 ---- .../streitz/log.streitz.wolf.19Feb15.linux.1 | 100 ---- .../streitz/log.streitz.wolf.19Feb15.linux.4 | 100 ---- 110 files changed, 17937 deletions(-) delete mode 100644 examples/balance/log.balance.8Aug14.linux.1 delete mode 100644 examples/balance/log.balance.8Aug14.linux.4 delete mode 100644 examples/balance/log.balance.bond.fast.21Jan15.linux.1 delete mode 100644 examples/balance/log.balance.bond.fast.21Jan15.linux.4 delete mode 100644 examples/balance/log.balance.bond.slow.21Jan15.linux.1 delete mode 100644 examples/balance/log.balance.bond.slow.21Jan15.linux.4 delete mode 100644 examples/body/log.body.1Feb14.linux.1 delete mode 100644 examples/body/log.body.1Feb14.linux.4 delete mode 100644 examples/colloid/log.colloid.1Feb14.linux.1 delete mode 100644 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examples/srd/log.srd.pure.1Feb14.linux.4 delete mode 100644 examples/streitz/log.streitz.ewald.19Feb15.linux.1 delete mode 100644 examples/streitz/log.streitz.ewald.19Feb15.linux.4 delete mode 100644 examples/streitz/log.streitz.wolf.19Feb15.linux.1 delete mode 100644 examples/streitz/log.streitz.wolf.19Feb15.linux.4 diff --git a/examples/balance/log.balance.8Aug14.linux.1 b/examples/balance/log.balance.8Aug14.linux.1 deleted file mode 100644 index fc1a321ee9..0000000000 --- a/examples/balance/log.balance.8Aug14.linux.1 +++ /dev/null @@ -1,187 +0,0 @@ -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 diff --git a/examples/balance/log.balance.8Aug14.linux.4 b/examples/balance/log.balance.8Aug14.linux.4 deleted file mode 100644 index 1de3bbeeb0..0000000000 --- a/examples/balance/log.balance.8Aug14.linux.4 +++ /dev/null @@ -1,187 +0,0 @@ -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 diff --git a/examples/balance/log.balance.bond.fast.21Jan15.linux.1 b/examples/balance/log.balance.bond.fast.21Jan15.linux.1 deleted file mode 100644 index 6c7ea17e6e..0000000000 --- a/examples/balance/log.balance.bond.fast.21Jan15.linux.1 +++ /dev/null @@ -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) - 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 diff --git a/examples/balance/log.balance.bond.fast.21Jan15.linux.4 b/examples/balance/log.balance.bond.fast.21Jan15.linux.4 deleted file mode 100644 index 17e4309693..0000000000 --- a/examples/balance/log.balance.bond.fast.21Jan15.linux.4 +++ /dev/null @@ -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 diff --git a/examples/balance/log.balance.bond.slow.21Jan15.linux.1 b/examples/balance/log.balance.bond.slow.21Jan15.linux.1 deleted file mode 100644 index 340c1e0417..0000000000 --- a/examples/balance/log.balance.bond.slow.21Jan15.linux.1 +++ /dev/null @@ -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 - 2800 0.34604747 0 0.066174138 1 1 - 2900 0.3444791 0 0.036590652 1 1 - 3000 0.34721342 0 -0.023793368 1 1 - 3100 0.33404314 0 -0.08374223 1 1 - 3200 0.33019355 0 -0.12715599 1 1 - 3300 0.33515177 0 -0.12217394 1 1 - 3400 0.33628481 0 -0.070877624 1 1 - 3500 0.34257038 0 -0.021612062 1 1 - 3600 0.32838009 0 0.030131228 1 1 - 3700 0.34462142 0 0.074586378 1 1 - 3800 0.30891825 0 0.10605673 1 1 - 3900 0.33847951 0 0.13956139 1 1 - 4000 0.32952079 0 0.12688129 1 1 - 4100 0.32646772 0 0.081089042 1 1 - 4200 0.35399503 0 0.013422873 1 1 - 4300 0.33154914 0 -0.050919508 1 1 - 4400 0.34113556 0 -0.083171 1 1 - 4500 0.32651708 0 -0.1063133 1 1 - 4600 0.34359609 0 -0.1076395 1 1 - 4700 0.34973537 0 -0.088231606 1 1 - 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 - 5400 0.33288012 0 0.078356448 1 1 - 5500 0.35142492 0 0.036958063 1 1 - 5600 0.35125368 0 -0.041371343 1 1 - 5700 0.34547744 0 -0.096450846 1 1 - 5800 0.30939887 0 -0.12356656 1 1 - 5900 0.32315628 0 -0.11338676 1 1 - 6000 0.34117485 0 -0.066198961 1 1 - 6100 0.35298043 0 -0.016172816 1 1 - 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 - 7000 0.35357865 0 -0.067248959 1 1 - 7100 0.33556885 0 -0.10983726 1 1 - 7200 0.33531101 0 -0.112179 1 1 - 7300 0.35742607 0 -0.078405267 1 1 - 7400 0.34577559 0 -0.01985432 1 1 - 7500 0.3498641 0 0.052289439 1 1 - 7600 0.33773715 0 0.092939035 1 1 - 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 - 9400 0.36140305 0 0.021427642 1 1 - 9500 0.34273562 0 -0.034064202 1 1 - 9600 0.33867054 0 -0.089076906 1 1 - 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 - 11400 0.34610624 0 0.03440148 1 1 - 11500 0.3415612 0 0.1041929 1 1 - 11600 0.34040042 0 0.13215705 1 1 - 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 - 12400 0.3321344 0 -0.11266575 1 1 - 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 - 13100 0.3422918 0 0.11978905 1 1 - 13200 0.33055236 0 0.062620483 1 1 - 13300 0.34652207 0 0.0043833459 1 1 - 13400 0.33574661 0 -0.04691024 1 1 - 13500 0.33940837 0 -0.074241604 1 1 - 13600 0.32093414 0 -0.1078027 1 1 - 13700 0.34336597 0 -0.10544097 1 1 - 13800 0.35806461 0 -0.072531559 1 1 - 13900 0.35209713 0 -0.018851408 1 1 - 14000 0.35702629 0 0.061046366 1 1 - 14100 0.33234093 0 0.094086465 1 1 - 14200 0.3459466 0 0.12186656 1 1 - 14300 0.3327428 0 0.11396572 1 1 - 14400 0.32409443 0 0.10658903 1 1 - 14500 0.35022184 0 0.083558031 1 1 - 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 - 15100 0.33647529 0 -0.055652929 1 1 - 15200 0.35328398 0 -0.020236536 1 1 - 15300 0.34252669 0 0.026434179 1 1 - 15400 0.34409435 0 0.094410599 1 1 - 15500 0.32288994 0 0.12034455 1 1 - 15600 0.32109689 0 0.13645185 1 1 - 15700 0.33681572 0 0.098607746 1 1 - 15800 0.33635195 0 0.05570715 1 1 - 15900 0.34289757 0 0.013849092 1 1 - 16000 0.34225547 0 -0.035597548 1 1 - 16100 0.33660991 0 -0.076931881 1 1 - 16200 0.32802152 0 -0.12765884 1 1 - 16300 0.3469374 0 -0.10785455 1 1 - 16400 0.34053641 0 -0.070259853 1 1 - 16500 0.34610591 0 -0.014315306 1 1 - 16600 0.35109001 0 0.041251169 1 1 - 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 - 17400 0.34540936 0 -0.093994174 1 1 - 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 - 22200 0.34750227 0 0.0056917695 1 1 - 22300 0.34766017 0 -0.0027090483 1 1 - 22400 0.33426062 0 -0.023196063 1 1 - 22500 0.34174625 0 -0.025019717 1 1 - 22600 0.3356145 0 -0.029707418 1 1 - 22700 0.3362653 0 -0.035815733 1 1 - 22800 0.33973405 0 -0.0024705835 1 1 - 22900 0.33813085 0 0.0077527467 1 1 - 23000 0.33339981 0 0.028340744 1 1 - 23100 0.34079832 0 0.018521302 1 1 - 23200 0.33074548 0 0.032378405 1 1 - 23300 0.32965664 0 0.035989589 1 1 - 23400 0.30927749 0 0.024581106 1 1 - 23500 0.32890632 0 0.01092479 1 1 - 23600 0.34137438 0 0.0094839745 1 1 - 23700 0.34512638 0 -0.012392771 1 1 - 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 diff --git a/examples/balance/log.balance.bond.slow.21Jan15.linux.4 b/examples/balance/log.balance.bond.slow.21Jan15.linux.4 deleted file mode 100644 index 974e07abcc..0000000000 --- a/examples/balance/log.balance.bond.slow.21Jan15.linux.4 +++ /dev/null @@ -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 - 400 0.34078347 0 -0.020825841 1.0304709 1.0083102 - 500 0.35201095 0 -0.062637506 1.0193906 1.0083102 - 600 0.34014717 0 -0.11122965 1.0415512 1.0083102 - 700 0.3323524 0 -0.11598015 1.0193906 1.0083102 - 800 0.35116047 0 -0.096162395 1.0083102 1.0193906 - 900 0.35695352 0 -0.01385176 1.0526316 1.0193906 - 1000 0.36986539 0 0.056772858 1.0083102 1.0083102 - 1100 0.34584644 0 0.084941323 1.0193906 1.0083102 - 1200 0.31921435 0 0.10545078 1.0415512 1.0193906 - 1300 0.32952819 0 0.124902 1.0083102 1.0083102 - 1400 0.34497365 0 0.12662081 1.0193906 1.0083102 - 1500 0.33429243 0 0.096230972 1.0526316 1.0193906 - 1600 0.33765387 0 0.025800542 1.0304709 1.0083102 - 1700 0.35134464 0 -0.04422593 1.0415512 1.0083102 - 1800 0.35003859 0 -0.096745576 1.0304709 1.0193906 - 1900 0.33839618 0 -0.095465943 1.0193906 1.0083102 - 2000 0.33732078 0 -0.094652802 1.0083102 1.0083102 - 2100 0.34552238 0 -0.076729261 1.0304709 1.0083102 - 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 - 2800 0.34604747 0 0.066174138 1.0083102 1.0083102 - 2900 0.3444791 0 0.036590652 1.0193906 1.0193906 - 3000 0.34721342 0 -0.023793368 1.0193906 1.0083102 - 3100 0.33404314 0 -0.08374223 1.0415512 1.0083102 - 3200 0.33019355 0 -0.12715599 1.0083102 1.0083102 - 3300 0.33515177 0 -0.12217394 1.0193906 1.0083102 - 3400 0.33628481 0 -0.070877624 1.0193906 1.0083102 - 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 - 4000 0.32952079 0 0.12688129 1.0193906 1.0304709 - 4100 0.32646772 0 0.081089042 1.0304709 1.0193906 - 4200 0.35399503 0 0.013422873 1.0083102 1.0083102 - 4300 0.33154914 0 -0.050919508 1.0083102 1.0193906 - 4400 0.34113556 0 -0.083171 1.0415512 1.0083102 - 4500 0.32651708 0 -0.1063133 1.0193906 1.0083102 - 4600 0.34359609 0 -0.1076395 1.0083102 1.0193906 - 4700 0.34973537 0 -0.088231606 1.0415512 1.0083102 - 4800 0.35198515 0 -0.020901044 1.0415512 1.0083102 - 4900 0.35187284 0 0.043645941 1.0193906 1.0083102 - 5000 0.34887336 0 0.095698609 1.0193906 1.0083102 - 5100 0.30308163 0 0.11649328 1.0083102 1.0083102 - 5200 0.32401285 0 0.12072411 1.0193906 1.0083102 - 5300 0.33025072 0 0.10933161 1.0304709 1.0083102 - 5400 0.33288012 0 0.078356448 1.0083102 1.0193906 - 5500 0.35142492 0 0.036958063 1.0193906 1.0083102 - 5600 0.35125368 0 -0.041371343 1.0304709 1.0083102 - 5700 0.34547744 0 -0.096450846 1.0637119 1.0083102 - 5800 0.30939887 0 -0.12356656 1.0083102 1.0083102 - 5900 0.32315628 0 -0.11338676 1.0193906 1.0304709 - 6000 0.34117485 0 -0.066198961 1.0193906 1.0193906 - 6100 0.35298043 0 -0.016172816 1.0304709 1.0193906 - 6200 0.35130653 0 0.027660468 1.0415512 1.0083102 - 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 - 7000 0.35357865 0 -0.067248959 1.0304709 1.0083102 - 7100 0.33556885 0 -0.10983726 1.0193906 1.0083102 - 7200 0.33531101 0 -0.112179 1.0304709 1.0083102 - 7300 0.35742607 0 -0.078405267 1.0304709 1.0193906 - 7400 0.34577559 0 -0.01985432 1.0193906 1.0083102 - 7500 0.3498641 0 0.052289439 1.0526316 1.0083102 - 7600 0.33773715 0 0.092939035 1.0083102 1.0193906 - 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 - 8000 0.33451798 0 0.077993125 1.0304709 1.0083102 - 8100 0.35188371 0 0.019929977 1.0193906 1.0193906 - 8200 0.33645742 0 -0.039302079 1.0193906 1.0193906 - 8300 0.3415632 0 -0.098067982 1.0304709 1.0083102 - 8400 0.30619282 0 -0.12952879 1.0193906 1.0193906 - 8500 0.34446484 0 -0.098084709 1.0083102 1.0083102 - 8600 0.33761673 0 -0.07069818 1.0193906 1.0083102 - 8700 0.34495452 0 -0.022458056 1.0193906 1.0083102 - 8800 0.33502983 0 0.027742411 1.0304709 1.0083102 - 8900 0.35418591 0 0.092390134 1.0083102 1.0193906 - 9000 0.31648387 0 0.12467398 1.0193906 1.0193906 - 9100 0.33994825 0 0.14460327 1.0193906 1.0193906 - 9200 0.33822571 0 0.11273284 1.0193906 1.0083102 - 9300 0.33260773 0 0.060063671 1.0083102 1.0193906 - 9400 0.36140305 0 0.021427642 1.0193906 1.0083102 - 9500 0.34273562 0 -0.034064202 1.0193906 1.0083102 - 9600 0.33867054 0 -0.089076906 1.0193906 1.0083102 - 9700 0.32088235 0 -0.12027075 1.0193906 1.0083102 - 9800 0.3320823 0 -0.11602794 1.0415512 1.0193906 - 9900 0.33916442 0 -0.080281044 1.0083102 1.0083102 - 10000 0.34852268 0 -0.01000914 1.0193906 1.0193906 - 10100 0.32955942 0 0.04258493 1.0083102 1.0083102 - 10200 0.34487898 0 0.086971308 1.0304709 1.0083102 - 10300 0.32325593 0 0.11558149 1.0304709 1.0193906 - 10400 0.30927871 0 0.12239437 1.0083102 1.0083102 - 10500 0.33176799 0 0.12285937 1.0193906 1.0083102 - 10600 0.35120027 0 0.084897432 1.0083102 1.0083102 - 10700 0.33129697 0 0.0053089279 1.0193906 1.0193906 - 10800 0.36028769 0 -0.04280715 1.0193906 1.0083102 - 10900 0.35552287 0 -0.084955999 1.0193906 1.0304709 - 11000 0.3406024 0 -0.096554577 1.0083102 1.0083102 - 11100 0.33041202 0 -0.10703492 1.0304709 1.0083102 - 11200 0.32442686 0 -0.084328121 1.0304709 1.0083102 - 11300 0.35952468 0 -0.020191965 1.0304709 1.0193906 - 11400 0.34610624 0 0.03440148 1.0193906 1.0083102 - 11500 0.3415612 0 0.1041929 1.0193906 1.0193906 - 11600 0.34040042 0 0.13215705 1.0304709 1.0193906 - 11700 0.33555094 0 0.12738686 1.0083102 1.0304709 - 11800 0.3458647 0 0.10963398 1.0193906 1.0193906 - 11900 0.33836678 0 0.067253864 1.0193906 1.0193906 - 12000 0.34853314 0 0.03201448 1.0193906 1.0083102 - 12100 0.34600048 0 -0.034833402 1.0304709 1.0083102 - 12200 0.33145631 0 -0.09865675 1.0193906 1.0193906 - 12300 0.32848884 0 -0.1248489 1.0193906 1.0193906 - 12400 0.3321344 0 -0.11266575 1.0083102 1.0083102 - 12500 0.32622305 0 -0.061634993 1.0304709 1.0193906 - 12600 0.36213537 0 -0.0090593315 1.0526316 1.0083102 - 12700 0.34673866 0 0.036734645 1.0193906 1.0083102 - 12800 0.34606618 0 0.086267678 1.0193906 1.0083102 - 12900 0.34271431 0 0.12415522 1.0304709 1.0083102 - 13000 0.31993287 0 0.13879926 1.0193906 1.0193906 - 13100 0.3422918 0 0.11978905 1.0083102 1.0083102 - 13200 0.33055236 0 0.062620483 1.0193906 1.0083102 - 13300 0.34652207 0 0.0043833459 1.0304709 1.0083102 - 13400 0.33574661 0 -0.04691024 1.0304709 1.0083102 - 13500 0.33940837 0 -0.074241604 1.0304709 1.0193906 - 13600 0.32093414 0 -0.1078027 1.0193906 1.0083102 - 13700 0.34336597 0 -0.10544097 1.0193906 1.0083102 - 13800 0.35806461 0 -0.072531559 1.0193906 1.0083102 - 13900 0.35209713 0 -0.018851408 1.0083102 1.0083102 - 14000 0.35702629 0 0.061046366 1.0083102 1.0083102 - 14100 0.33234093 0 0.094086465 1.0083102 1.0083102 - 14200 0.3459466 0 0.12186656 1.0193906 1.0083102 - 14300 0.3327428 0 0.11396572 1.0193906 1.0083102 - 14400 0.32409443 0 0.10658903 1.0193906 1.0193906 - 14500 0.35022184 0 0.083558031 1.0083102 1.0193906 - 14600 0.34823843 0 0.024605569 1.0083102 1.0083102 - 14700 0.35298973 0 -0.040418888 1.0193906 1.0083102 - 14800 0.33679845 0 -0.10067728 1.0193906 1.0083102 - 14900 0.32790966 0 -0.10925568 1.0193906 1.0083102 - 15000 0.34208495 0 -0.09568004 1.0193906 1.0083102 - 15100 0.33647529 0 -0.055652929 1.0083102 1.0083102 - 15200 0.35328398 0 -0.020236536 1.0193906 1.0193906 - 15300 0.34252669 0 0.026434179 1.0083102 1.0193906 - 15400 0.34409435 0 0.094410599 1.0304709 1.0083102 - 15500 0.32288994 0 0.12034455 1.0415512 1.0083102 - 15600 0.32109689 0 0.13645185 1.0193906 1.0083102 - 15700 0.33681572 0 0.098607746 1.0415512 1.0083102 - 15800 0.33635195 0 0.05570715 1.0193906 1.0193906 - 15900 0.34289757 0 0.013849092 1.0304709 1.0083102 - 16000 0.34225547 0 -0.035597548 1.0304709 1.0083102 - 16100 0.33660991 0 -0.076931881 1.0193906 1.0193906 - 16200 0.32802152 0 -0.12765884 1.0083102 1.0083102 - 16300 0.3469374 0 -0.10785455 1.0083102 1.0083102 - 16400 0.34053641 0 -0.070259853 1.0193906 1.0083102 - 16500 0.34610591 0 -0.014315306 1.0193906 1.0083102 - 16600 0.35109001 0 0.041251169 1.0304709 1.0083102 - 16700 0.34336905 0 0.077996627 1.0193906 1.0083102 - 16800 0.33277414 0 0.11053634 1.0083102 1.0083102 - 16900 0.32183338 0 0.11680626 1.0193906 1.0083102 - 17000 0.34044352 0 0.10806555 1.0193906 1.0083102 - 17100 0.32967873 0 0.067759786 1.0304709 1.0304709 - 17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102 - 17300 0.35619435 0 -0.04215545 1.0193906 1.0083102 - 17400 0.34540936 0 -0.093994174 1.0193906 1.0193906 - 17500 0.33193585 0 -0.098831315 1.0083102 1.0193906 - 17600 0.3544756 0 -0.085660403 1.0193906 1.0083102 - 17700 0.34505209 0 -0.069640515 1.0304709 1.0083102 - 17800 0.36291124 0 -0.0063088133 1.0083102 1.0193906 - 17900 0.34255705 0 0.046794555 1.0304709 1.0193906 - 18000 0.34163238 0 0.11767705 1.0193906 1.0193906 - 18100 0.3466445 0 0.1351712 1.0415512 1.0193906 - 18200 0.33037668 0 0.12703659 1.0083102 1.0083102 - 18300 0.33677404 0 0.10956306 1.0083102 1.0304709 - 18400 0.34978954 0 0.087193072 1.0193906 1.0083102 - 18500 0.33354363 0 0.051095814 1.0526316 1.0193906 - 18600 0.34651729 0 0.0056245561 1.0304709 1.0193906 - 18700 0.32622232 0 -0.047319269 1.0083102 1.0193906 - 18800 0.32978847 0 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1.0083102 1.0193906 - 26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906 - 26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906 - 26600 0.33063188 0 -0.020378601 1.0083102 1.0193906 - 26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906 - 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 - 27400 0.32310744 0 0.024110945 1.0415512 1.0083102 - 27500 0.33115619 0 0.0025776713 1.0304709 1.0083102 - 27600 0.33295887 0 -0.010710764 1.0304709 1.0193906 - 27700 0.32968876 0 -0.0064595905 1.0193906 1.0083102 - 27800 0.34064581 0 -0.0086519116 1.0193906 1.0083102 - 27900 0.33559187 0 -0.0055753593 1.0083102 1.0083102 - 28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102 - 28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102 - 28200 0.35532383 0 0.013646951 1.0304709 1.0083102 - 28300 0.31507942 0 0.026532255 1.0415512 1.0193906 - 28400 0.32711006 0 0.033214981 1.0193906 1.0083102 - 28500 0.34472462 0 0.028050837 1.0304709 1.0193906 - 28600 0.33708059 0 0.019115676 1.0083102 1.0083102 - 28700 0.34478087 0 0.023743689 1.0304709 1.0083102 - 28800 0.34546686 0 0.0081772997 1.0304709 1.0083102 - 28900 0.34004886 0 0.017771865 1.0415512 1.0193906 - 29000 0.33604232 0 -0.010505671 1.0304709 1.0193906 - 29100 0.33541374 0 -0.016273261 1.0083102 1.0083102 - 29200 0.34347489 0 -0.010002306 1.0083102 1.0083102 - 29300 0.34083904 0 0.0089701784 1.0193906 1.0193906 - 29400 0.34846892 0 0.020765104 1.0083102 1.0083102 - 29500 0.3416255 0 0.022650856 1.0304709 1.0083102 - 29600 0.33725496 0 0.020693083 1.0193906 1.0193906 - 29700 0.34480638 0 0.024317128 1.0304709 1.0083102 - 29800 0.31459471 0 0.023097895 1.0083102 1.0083102 - 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 - 30300 0.33375921 0 0.0010991235 1.0083102 1.0193906 - 30400 0.35008944 0 -0.0027316177 1.0415512 1.0083102 - 30500 0.33279729 0 -0.0035788551 1.0193906 1.0193906 - 30600 0.33868746 0 -0.0016249482 1.0083102 1.0193906 - 30700 0.33597034 0 -0.0014524001 1.0193906 1.0193906 - 30800 0.3227257 0 0.016353457 1.0415512 1.0193906 - 30900 0.32676516 0 0.027396654 1.0193906 1.0083102 - 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 diff --git a/examples/body/log.body.1Feb14.linux.1 b/examples/body/log.body.1Feb14.linux.1 deleted file mode 100644 index d937db215f..0000000000 --- a/examples/body/log.body.1Feb14.linux.1 +++ /dev/null @@ -1,71 +0,0 @@ -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 diff --git a/examples/body/log.body.1Feb14.linux.4 b/examples/body/log.body.1Feb14.linux.4 deleted file mode 100644 index bf51e6b354..0000000000 --- a/examples/body/log.body.1Feb14.linux.4 +++ /dev/null @@ -1,71 +0,0 @@ -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 diff --git a/examples/colloid/log.colloid.1Feb14.linux.1 b/examples/colloid/log.colloid.1Feb14.linux.1 deleted file mode 100644 index ab05a97851..0000000000 --- a/examples/colloid/log.colloid.1Feb14.linux.1 +++ /dev/null @@ -1,131 +0,0 @@ -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 - diff --git a/examples/colloid/log.colloid.1Feb14.linux.4 b/examples/colloid/log.colloid.1Feb14.linux.4 deleted file mode 100644 index 85a4b6fedf..0000000000 --- a/examples/colloid/log.colloid.1Feb14.linux.4 +++ /dev/null @@ -1,131 +0,0 @@ -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 - diff --git a/examples/comb/log.comb.Cu.1Feb14.linux.1 b/examples/comb/log.comb.Cu.1Feb14.linux.1 deleted file mode 100644 index 6e328fcb91..0000000000 --- a/examples/comb/log.comb.Cu.1Feb14.linux.1 +++ /dev/null @@ -1,76 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Cu.1Feb14.linux.4 b/examples/comb/log.comb.Cu.1Feb14.linux.4 deleted file mode 100644 index 4ee0d43d29..0000000000 --- a/examples/comb/log.comb.Cu.1Feb14.linux.4 +++ /dev/null @@ -1,76 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 b/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 deleted file mode 100644 index 2818739e21..0000000000 --- a/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.1 +++ /dev/null @@ -1,316 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 b/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 deleted file mode 100644 index 3e71d6c1c4..0000000000 --- a/examples/comb/log.comb.Cu2O.elastic.1Feb14.linux.4 +++ /dev/null @@ -1,316 +0,0 @@ -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 diff --git a/examples/comb/log.comb.HfO2.1Feb14.linux.1 b/examples/comb/log.comb.HfO2.1Feb14.linux.1 deleted file mode 100644 index 25b2c38b35..0000000000 --- a/examples/comb/log.comb.HfO2.1Feb14.linux.1 +++ /dev/null @@ -1,185 +0,0 @@ -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 diff --git a/examples/comb/log.comb.HfO2.1Feb14.linux.4 b/examples/comb/log.comb.HfO2.1Feb14.linux.4 deleted file mode 100644 index 3c2650300c..0000000000 --- a/examples/comb/log.comb.HfO2.1Feb14.linux.4 +++ /dev/null @@ -1,185 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Si.1Feb14.linux.1 b/examples/comb/log.comb.Si.1Feb14.linux.1 deleted file mode 100644 index 22f31468e4..0000000000 --- a/examples/comb/log.comb.Si.1Feb14.linux.1 +++ /dev/null @@ -1,76 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Si.1Feb14.linux.4 b/examples/comb/log.comb.Si.1Feb14.linux.4 deleted file mode 100644 index 859af60766..0000000000 --- a/examples/comb/log.comb.Si.1Feb14.linux.4 +++ /dev/null @@ -1,76 +0,0 @@ -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 diff --git a/examples/comb/log.comb.Si.elastic.1Feb14.linux.1 b/examples/comb/log.comb.Si.elastic.1Feb14.linux.1 deleted file mode 100644 index 19c17143a0..0000000000 --- a/examples/comb/log.comb.Si.elastic.1Feb14.linux.1 +++ /dev/null @@ -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 diff --git a/examples/comb/log.comb.Si.elastic.1Feb14.linux.4 b/examples/comb/log.comb.Si.elastic.1Feb14.linux.4 deleted file mode 100644 index 0923be479a..0000000000 --- a/examples/comb/log.comb.Si.elastic.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/comb/log.comb3.1Feb14.linux.1 b/examples/comb/log.comb3.1Feb14.linux.1 deleted file mode 100644 index 29ab477696..0000000000 --- a/examples/comb/log.comb3.1Feb14.linux.1 +++ /dev/null @@ -1,73 +0,0 @@ -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 diff --git a/examples/comb/log.comb3.1Feb14.linux.4 b/examples/comb/log.comb3.1Feb14.linux.4 deleted file mode 100644 index 688abd6d1d..0000000000 --- a/examples/comb/log.comb3.1Feb14.linux.4 +++ /dev/null @@ -1,73 +0,0 @@ -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 diff --git a/examples/crack/log.crack.1Feb14.linux.1 b/examples/crack/log.crack.1Feb14.linux.1 deleted file mode 100644 index aaae9648e3..0000000000 --- a/examples/crack/log.crack.1Feb14.linux.1 +++ /dev/null @@ -1,138 +0,0 @@ -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 diff --git a/examples/crack/log.crack.1Feb14.linux.4 b/examples/crack/log.crack.1Feb14.linux.4 deleted file mode 100644 index 9e20ca6ddb..0000000000 --- a/examples/crack/log.crack.1Feb14.linux.4 +++ /dev/null @@ -1,138 +0,0 @@ -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 diff --git a/examples/dipole/log.dipole.1Feb14.linux.1 b/examples/dipole/log.dipole.1Feb14.linux.1 deleted file mode 100644 index 8db4c7791c..0000000000 --- a/examples/dipole/log.dipole.1Feb14.linux.1 +++ /dev/null @@ -1,89 +0,0 @@ -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 diff --git a/examples/dipole/log.dipole.1Feb14.linux.4 b/examples/dipole/log.dipole.1Feb14.linux.4 deleted file mode 100644 index ad5701640c..0000000000 --- a/examples/dipole/log.dipole.1Feb14.linux.4 +++ /dev/null @@ -1,89 +0,0 @@ -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 diff --git a/examples/dreiding/log.dreiding.1Feb14.linux.1 b/examples/dreiding/log.dreiding.1Feb14.linux.1 deleted file mode 100644 index 21691d94fa..0000000000 --- a/examples/dreiding/log.dreiding.1Feb14.linux.1 +++ /dev/null @@ -1,106 +0,0 @@ -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 - diff --git a/examples/dreiding/log.dreiding.1Feb14.linux.4 b/examples/dreiding/log.dreiding.1Feb14.linux.4 deleted file mode 100644 index 83b0b6fc0f..0000000000 --- a/examples/dreiding/log.dreiding.1Feb14.linux.4 +++ /dev/null @@ -1,106 +0,0 @@ -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 - diff --git a/examples/eim/log.eim.1Feb14.linux.1 b/examples/eim/log.eim.1Feb14.linux.1 deleted file mode 100644 index 7f8a42c96f..0000000000 --- a/examples/eim/log.eim.1Feb14.linux.1 +++ /dev/null @@ -1,72 +0,0 @@ -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 diff --git a/examples/eim/log.eim.1Feb14.linux.4 b/examples/eim/log.eim.1Feb14.linux.4 deleted file mode 100644 index 03e206e99e..0000000000 --- a/examples/eim/log.eim.1Feb14.linux.4 +++ /dev/null @@ -1,72 +0,0 @@ -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 diff --git a/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1 b/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1 deleted file mode 100644 index b97b1ab635..0000000000 --- a/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.1 +++ /dev/null @@ -1,163 +0,0 @@ -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 - diff --git a/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.4 b/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.4 deleted file mode 100644 index 80d3a006ef..0000000000 --- a/examples/ellipse/log.ellipse.gayberne.1Feb14.linux.4 +++ /dev/null @@ -1,163 +0,0 @@ -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 - diff --git a/examples/ellipse/log.ellipse.resquared.1Feb14.linux.1 b/examples/ellipse/log.ellipse.resquared.1Feb14.linux.1 deleted file mode 100644 index 0fec468629..0000000000 --- a/examples/ellipse/log.ellipse.resquared.1Feb14.linux.1 +++ /dev/null @@ -1,160 +0,0 @@ -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 diff --git a/examples/ellipse/log.ellipse.resquared.1Feb14.linux.4 b/examples/ellipse/log.ellipse.resquared.1Feb14.linux.4 deleted file mode 100644 index 3fc11060ee..0000000000 --- a/examples/ellipse/log.ellipse.resquared.1Feb14.linux.4 +++ /dev/null @@ -1,160 +0,0 @@ -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 diff --git a/examples/flow/log.flow.couette.1Feb14.linux.1 b/examples/flow/log.flow.couette.1Feb14.linux.1 deleted file mode 100644 index a15eb598b4..0000000000 --- a/examples/flow/log.flow.couette.1Feb14.linux.1 +++ /dev/null @@ -1,130 +0,0 @@ -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 diff --git a/examples/flow/log.flow.couette.1Feb14.linux.4 b/examples/flow/log.flow.couette.1Feb14.linux.4 deleted file mode 100644 index 4ed2ecfc39..0000000000 --- a/examples/flow/log.flow.couette.1Feb14.linux.4 +++ /dev/null @@ -1,130 +0,0 @@ -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 diff --git a/examples/flow/log.flow.pois.1Feb14.linux.1 b/examples/flow/log.flow.pois.1Feb14.linux.1 deleted file mode 100644 index bad13d6498..0000000000 --- a/examples/flow/log.flow.pois.1Feb14.linux.1 +++ /dev/null @@ -1,130 +0,0 @@ -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 diff --git a/examples/flow/log.flow.pois.1Feb14.linux.4 b/examples/flow/log.flow.pois.1Feb14.linux.4 deleted file mode 100644 index 2d8feab652..0000000000 --- a/examples/flow/log.flow.pois.1Feb14.linux.4 +++ /dev/null @@ -1,130 +0,0 @@ -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 diff --git a/examples/friction/log.friction.1Feb14.linux.1 b/examples/friction/log.friction.1Feb14.linux.1 deleted file mode 100644 index 107e79d7ff..0000000000 --- a/examples/friction/log.friction.1Feb14.linux.1 +++ /dev/null @@ -1,149 +0,0 @@ -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 diff --git a/examples/friction/log.friction.1Feb14.linux.4 b/examples/friction/log.friction.1Feb14.linux.4 deleted file mode 100644 index 81ddbbc2af..0000000000 --- a/examples/friction/log.friction.1Feb14.linux.4 +++ /dev/null @@ -1,149 +0,0 @@ -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 diff --git a/examples/hugoniostat/log.hugoniostat.1Feb14.linux.1 b/examples/hugoniostat/log.hugoniostat.1Feb14.linux.1 deleted file mode 100644 index 246a2d3f59..0000000000 --- a/examples/hugoniostat/log.hugoniostat.1Feb14.linux.1 +++ /dev/null @@ -1,90 +0,0 @@ -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 diff --git a/examples/hugoniostat/log.hugoniostat.1Feb14.linux.4 b/examples/hugoniostat/log.hugoniostat.1Feb14.linux.4 deleted file mode 100644 index 7739b7e17a..0000000000 --- a/examples/hugoniostat/log.hugoniostat.1Feb14.linux.4 +++ /dev/null @@ -1,90 +0,0 @@ -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 diff --git a/examples/indent/log.indent.1Feb14.linux.1 b/examples/indent/log.indent.1Feb14.linux.1 deleted file mode 100644 index bd04dbc254..0000000000 --- a/examples/indent/log.indent.1Feb14.linux.1 +++ /dev/null @@ -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) - 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 diff --git a/examples/indent/log.indent.1Feb14.linux.4 b/examples/indent/log.indent.1Feb14.linux.4 deleted file mode 100644 index 45aca9093d..0000000000 --- a/examples/indent/log.indent.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/indent/log.indent.min.1Feb14.linux.1 b/examples/indent/log.indent.min.1Feb14.linux.1 deleted file mode 100644 index 51b0cbe029..0000000000 --- a/examples/indent/log.indent.min.1Feb14.linux.1 +++ /dev/null @@ -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 diff --git a/examples/indent/log.indent.min.1Feb14.linux.4 b/examples/indent/log.indent.min.1Feb14.linux.4 deleted file mode 100644 index 7f14a43c83..0000000000 --- a/examples/indent/log.indent.min.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/meam/log.meam.1Feb14.linux.1 b/examples/meam/log.meam.1Feb14.linux.1 deleted file mode 100644 index 802805ffe0..0000000000 --- a/examples/meam/log.meam.1Feb14.linux.1 +++ /dev/null @@ -1,67 +0,0 @@ -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 diff --git a/examples/meam/log.meam.1Feb14.linux.4 b/examples/meam/log.meam.1Feb14.linux.4 deleted file mode 100644 index 4752971afb..0000000000 --- a/examples/meam/log.meam.1Feb14.linux.4 +++ /dev/null @@ -1,67 +0,0 @@ -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 diff --git a/examples/meam/log.meam.shear.1Feb14.linux.1 b/examples/meam/log.meam.shear.1Feb14.linux.1 deleted file mode 100644 index 55c09b7605..0000000000 --- a/examples/meam/log.meam.shear.1Feb14.linux.1 +++ /dev/null @@ -1,172 +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) - 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 diff --git a/examples/meam/log.meam.shear.1Feb14.linux.4 b/examples/meam/log.meam.shear.1Feb14.linux.4 deleted file mode 100644 index 1c6ed02573..0000000000 --- a/examples/meam/log.meam.shear.1Feb14.linux.4 +++ /dev/null @@ -1,172 +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 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 diff --git a/examples/melt/log.melt.1Feb14.linux.1 b/examples/melt/log.melt.1Feb14.linux.1 deleted file mode 100644 index 9eb6f59881..0000000000 --- a/examples/melt/log.melt.1Feb14.linux.1 +++ /dev/null @@ -1,63 +0,0 @@ -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 diff --git a/examples/melt/log.melt.1Feb14.linux.4 b/examples/melt/log.melt.1Feb14.linux.4 deleted file mode 100644 index 27a0eff37f..0000000000 --- a/examples/melt/log.melt.1Feb14.linux.4 +++ /dev/null @@ -1,63 +0,0 @@ -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 diff --git a/examples/micelle/log.micelle.1Feb14.linux.1 b/examples/micelle/log.micelle.1Feb14.linux.1 deleted file mode 100644 index 75290e9668..0000000000 --- a/examples/micelle/log.micelle.1Feb14.linux.1 +++ /dev/null @@ -1,215 +0,0 @@ -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 diff --git a/examples/micelle/log.micelle.1Feb14.linux.4 b/examples/micelle/log.micelle.1Feb14.linux.4 deleted file mode 100644 index baba789cbe..0000000000 --- a/examples/micelle/log.micelle.1Feb14.linux.4 +++ /dev/null @@ -1,215 +0,0 @@ -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 diff --git a/examples/min/log.min.1Feb14.linux.1 b/examples/min/log.min.1Feb14.linux.1 deleted file mode 100644 index 97b1c1f5b6..0000000000 --- a/examples/min/log.min.1Feb14.linux.1 +++ /dev/null @@ -1,118 +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) - 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 diff --git a/examples/min/log.min.1Feb14.linux.4 b/examples/min/log.min.1Feb14.linux.4 deleted file mode 100644 index 12458c6323..0000000000 --- a/examples/min/log.min.1Feb14.linux.4 +++ /dev/null @@ -1,118 +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 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 diff --git a/examples/min/log.min.box.1Feb14.linux.1 b/examples/min/log.min.box.1Feb14.linux.1 deleted file mode 100644 index 6b21fac428..0000000000 --- a/examples/min/log.min.box.1Feb14.linux.1 +++ /dev/null @@ -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) - 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 diff --git a/examples/min/log.min.box.1Feb14.linux.4 b/examples/min/log.min.box.1Feb14.linux.4 deleted file mode 100644 index 9c55a1967b..0000000000 --- a/examples/min/log.min.box.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/msst/log.msst.1Feb14.linux.1 b/examples/msst/log.msst.1Feb14.linux.1 deleted file mode 100644 index b37b9dc648..0000000000 --- a/examples/msst/log.msst.1Feb14.linux.1 +++ /dev/null @@ -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 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 diff --git a/examples/msst/log.msst.1Feb14.linux.4 b/examples/msst/log.msst.1Feb14.linux.4 deleted file mode 100644 index b6441e9163..0000000000 --- a/examples/msst/log.msst.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/nb3b/log.nb3b.1Feb14.linux.1 b/examples/nb3b/log.nb3b.1Feb14.linux.1 deleted file mode 100644 index 4cb66af140..0000000000 --- a/examples/nb3b/log.nb3b.1Feb14.linux.1 +++ /dev/null @@ -1,144 +0,0 @@ -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 diff --git a/examples/nb3b/log.nb3b.1Feb14.linux.4 b/examples/nb3b/log.nb3b.1Feb14.linux.4 deleted file mode 100644 index 5234a25047..0000000000 --- a/examples/nb3b/log.nb3b.1Feb14.linux.4 +++ /dev/null @@ -1,144 +0,0 @@ -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 diff --git a/examples/nemd/log.nemd.1Feb14.linux.1 b/examples/nemd/log.nemd.1Feb14.linux.1 deleted file mode 100644 index f27eb71016..0000000000 --- a/examples/nemd/log.nemd.1Feb14.linux.1 +++ /dev/null @@ -1,115 +0,0 @@ -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 diff --git a/examples/nemd/log.nemd.1Feb14.linux.4 b/examples/nemd/log.nemd.1Feb14.linux.4 deleted file mode 100644 index 301959b81d..0000000000 --- a/examples/nemd/log.nemd.1Feb14.linux.4 +++ /dev/null @@ -1,115 +0,0 @@ -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 diff --git a/examples/obstacle/log.obstacle.1Feb14.linux.1 b/examples/obstacle/log.obstacle.1Feb14.linux.1 deleted file mode 100644 index 43029158b4..0000000000 --- a/examples/obstacle/log.obstacle.1Feb14.linux.1 +++ /dev/null @@ -1,140 +0,0 @@ -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 diff --git a/examples/obstacle/log.obstacle.1Feb14.linux.4 b/examples/obstacle/log.obstacle.1Feb14.linux.4 deleted file mode 100644 index 537b0826d8..0000000000 --- a/examples/obstacle/log.obstacle.1Feb14.linux.4 +++ /dev/null @@ -1,140 +0,0 @@ -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 diff --git a/examples/peptide/log.peptide.1Feb14.linux.1 b/examples/peptide/log.peptide.1Feb14.linux.1 deleted file mode 100644 index 385e51cfd6..0000000000 --- a/examples/peptide/log.peptide.1Feb14.linux.1 +++ /dev/null @@ -1,177 +0,0 @@ -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 - diff --git a/examples/peptide/log.peptide.1Feb14.linux.4 b/examples/peptide/log.peptide.1Feb14.linux.4 deleted file mode 100644 index acff7be92d..0000000000 --- a/examples/peptide/log.peptide.1Feb14.linux.4 +++ /dev/null @@ -1,177 +0,0 @@ -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 - diff --git a/examples/peri/log.peri.1Feb14.linux.1 b/examples/peri/log.peri.1Feb14.linux.1 deleted file mode 100644 index df78c4ba4f..0000000000 --- a/examples/peri/log.peri.1Feb14.linux.1 +++ /dev/null @@ -1,90 +0,0 @@ -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 - diff --git a/examples/peri/log.peri.1Feb14.linux.4 b/examples/peri/log.peri.1Feb14.linux.4 deleted file mode 100644 index 9faeeeb893..0000000000 --- a/examples/peri/log.peri.1Feb14.linux.4 +++ /dev/null @@ -1,90 +0,0 @@ -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 - diff --git a/examples/pour/log.pour.1Feb14.linux.1 b/examples/pour/log.pour.1Feb14.linux.1 deleted file mode 100644 index d220169a42..0000000000 --- a/examples/pour/log.pour.1Feb14.linux.1 +++ /dev/null @@ -1,147 +0,0 @@ -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 diff --git a/examples/pour/log.pour.1Feb14.linux.4 b/examples/pour/log.pour.1Feb14.linux.4 deleted file mode 100644 index f80c74c064..0000000000 --- a/examples/pour/log.pour.1Feb14.linux.4 +++ /dev/null @@ -1,147 +0,0 @@ -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 diff --git a/examples/pour/log.pour.2d.1Feb14.linux.1 b/examples/pour/log.pour.2d.1Feb14.linux.1 deleted file mode 100644 index 0b9dbc49e0..0000000000 --- a/examples/pour/log.pour.2d.1Feb14.linux.1 +++ /dev/null @@ -1,100 +0,0 @@ -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 diff --git a/examples/pour/log.pour.2d.1Feb14.linux.4 b/examples/pour/log.pour.2d.1Feb14.linux.4 deleted file mode 100644 index d09147fa44..0000000000 --- a/examples/pour/log.pour.2d.1Feb14.linux.4 +++ /dev/null @@ -1,100 +0,0 @@ -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 diff --git a/examples/pour/log.pour.2d.molecule.1Feb14.linux.1 b/examples/pour/log.pour.2d.molecule.1Feb14.linux.1 deleted file mode 100644 index c81812d238..0000000000 --- a/examples/pour/log.pour.2d.molecule.1Feb14.linux.1 +++ /dev/null @@ -1,113 +0,0 @@ -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 diff --git a/examples/pour/log.pour.2d.molecule.1Feb14.linux.4 b/examples/pour/log.pour.2d.molecule.1Feb14.linux.4 deleted file mode 100644 index 57b4a68262..0000000000 --- a/examples/pour/log.pour.2d.molecule.1Feb14.linux.4 +++ /dev/null @@ -1,113 +0,0 @@ -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 diff --git a/examples/qeq/log.qeq.buck.8Sep14.linux.1 b/examples/qeq/log.qeq.buck.8Sep14.linux.1 deleted file mode 100644 index 9db9386453..0000000000 --- a/examples/qeq/log.qeq.buck.8Sep14.linux.1 +++ /dev/null @@ -1,85 +0,0 @@ -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 diff --git a/examples/qeq/log.qeq.buck.8Sep14.linux.4 b/examples/qeq/log.qeq.buck.8Sep14.linux.4 deleted file mode 100644 index 90b6190bd8..0000000000 --- a/examples/qeq/log.qeq.buck.8Sep14.linux.4 +++ /dev/null @@ -1,85 +0,0 @@ -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 diff --git a/examples/qeq/log.qeq.reaxc.8Sep14.linux.1 b/examples/qeq/log.qeq.reaxc.8Sep14.linux.1 deleted file mode 100644 index c9fa00deac..0000000000 --- a/examples/qeq/log.qeq.reaxc.8Sep14.linux.1 +++ /dev/null @@ -1,89 +0,0 @@ -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 - diff --git a/examples/qeq/log.qeq.reaxc.8Sep14.linux.4 b/examples/qeq/log.qeq.reaxc.8Sep14.linux.4 deleted file mode 100644 index cf53883f59..0000000000 --- a/examples/qeq/log.qeq.reaxc.8Sep14.linux.4 +++ /dev/null @@ -1,89 +0,0 @@ -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 - diff --git a/examples/reax/log.reax.rdx.1Feb14.linux.1 b/examples/reax/log.reax.rdx.1Feb14.linux.1 deleted file mode 100644 index fa27af0961..0000000000 --- a/examples/reax/log.reax.rdx.1Feb14.linux.1 +++ /dev/null @@ -1,85 +0,0 @@ -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 diff --git a/examples/reax/log.reax.rdx.1Feb14.linux.4 b/examples/reax/log.reax.rdx.1Feb14.linux.4 deleted file mode 100644 index 34f2f28a87..0000000000 --- a/examples/reax/log.reax.rdx.1Feb14.linux.4 +++ /dev/null @@ -1,85 +0,0 @@ -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 diff --git a/examples/reax/log.reax.tatb.1Feb14.linux.1 b/examples/reax/log.reax.tatb.1Feb14.linux.1 deleted file mode 100644 index 40024440f4..0000000000 --- a/examples/reax/log.reax.tatb.1Feb14.linux.1 +++ /dev/null @@ -1,81 +0,0 @@ -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 diff --git a/examples/reax/log.reax.tatb.1Feb14.linux.4 b/examples/reax/log.reax.tatb.1Feb14.linux.4 deleted file mode 100644 index 65ab5db54f..0000000000 --- a/examples/reax/log.reax.tatb.1Feb14.linux.4 +++ /dev/null @@ -1,81 +0,0 @@ -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 diff --git a/examples/reax/log.reaxc.rdx.1Feb14.linux.1 b/examples/reax/log.reaxc.rdx.1Feb14.linux.1 deleted file mode 100644 index 2933d4e6c8..0000000000 --- a/examples/reax/log.reaxc.rdx.1Feb14.linux.1 +++ /dev/null @@ -1,88 +0,0 @@ -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 - diff --git a/examples/reax/log.reaxc.rdx.1Feb14.linux.4 b/examples/reax/log.reaxc.rdx.1Feb14.linux.4 deleted file mode 100644 index 4455fb7cea..0000000000 --- a/examples/reax/log.reaxc.rdx.1Feb14.linux.4 +++ /dev/null @@ -1,88 +0,0 @@ -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 - diff --git a/examples/reax/log.reaxc.tatb.1Feb14.linux.1 b/examples/reax/log.reaxc.tatb.1Feb14.linux.1 deleted file mode 100644 index 92d9412703..0000000000 --- a/examples/reax/log.reaxc.tatb.1Feb14.linux.1 +++ /dev/null @@ -1,86 +0,0 @@ -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 - diff --git a/examples/reax/log.reaxc.tatb.1Feb14.linux.4 b/examples/reax/log.reaxc.tatb.1Feb14.linux.4 deleted file mode 100644 index d9d39c4447..0000000000 --- a/examples/reax/log.reaxc.tatb.1Feb14.linux.4 +++ /dev/null @@ -1,86 +0,0 @@ -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 - diff --git a/examples/rigid/log.rigid.1Feb14.linux.1 b/examples/rigid/log.rigid.1Feb14.linux.1 deleted file mode 100644 index 261f43bf8b..0000000000 --- a/examples/rigid/log.rigid.1Feb14.linux.1 +++ /dev/null @@ -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 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 diff --git a/examples/rigid/log.rigid.1Feb14.linux.4 b/examples/rigid/log.rigid.1Feb14.linux.4 deleted file mode 100644 index b2ee4357c8..0000000000 --- a/examples/rigid/log.rigid.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/rigid/log.rigid.poems.1Feb14.linux.1 b/examples/rigid/log.rigid.poems.1Feb14.linux.1 deleted file mode 100644 index b7ba426853..0000000000 --- a/examples/rigid/log.rigid.poems.1Feb14.linux.1 +++ /dev/null @@ -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 - diff --git a/examples/rigid/log.rigid.poems.1Feb14.linux.4 b/examples/rigid/log.rigid.poems.1Feb14.linux.4 deleted file mode 100644 index 74bbe818d1..0000000000 --- a/examples/rigid/log.rigid.poems.1Feb14.linux.4 +++ /dev/null @@ -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 - diff --git a/examples/rigid/log.rigid.poems2.1Feb14.linux.1 b/examples/rigid/log.rigid.poems2.1Feb14.linux.1 deleted file mode 100644 index 25b9c10f70..0000000000 --- a/examples/rigid/log.rigid.poems2.1Feb14.linux.1 +++ /dev/null @@ -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 - diff --git a/examples/rigid/log.rigid.poems2.1Feb14.linux.4 b/examples/rigid/log.rigid.poems2.1Feb14.linux.4 deleted file mode 100644 index 3aa54059ce..0000000000 --- a/examples/rigid/log.rigid.poems2.1Feb14.linux.4 +++ /dev/null @@ -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 - diff --git a/examples/rigid/log.rigid.tnr.1Feb14.linux.1 b/examples/rigid/log.rigid.tnr.1Feb14.linux.1 deleted file mode 100644 index 7ecf450197..0000000000 --- a/examples/rigid/log.rigid.tnr.1Feb14.linux.1 +++ /dev/null @@ -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 - diff --git a/examples/rigid/log.rigid.tnr.1Feb14.linux.4 b/examples/rigid/log.rigid.tnr.1Feb14.linux.4 deleted file mode 100644 index 06233cd229..0000000000 --- a/examples/rigid/log.rigid.tnr.1Feb14.linux.4 +++ /dev/null @@ -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 - diff --git a/examples/shear/log.shear.1Feb14.linux.1 b/examples/shear/log.shear.1Feb14.linux.1 deleted file mode 100644 index 09ad732d7a..0000000000 --- a/examples/shear/log.shear.1Feb14.linux.1 +++ /dev/null @@ -1,168 +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) - 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 diff --git a/examples/shear/log.shear.1Feb14.linux.4 b/examples/shear/log.shear.1Feb14.linux.4 deleted file mode 100644 index 503b7c9fb5..0000000000 --- a/examples/shear/log.shear.1Feb14.linux.4 +++ /dev/null @@ -1,168 +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 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 diff --git a/examples/shear/log.shear.void.1Feb14.linux.1 b/examples/shear/log.shear.void.1Feb14.linux.1 deleted file mode 100644 index ebf90fffc7..0000000000 --- a/examples/shear/log.shear.void.1Feb14.linux.1 +++ /dev/null @@ -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) - 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 diff --git a/examples/shear/log.shear.void.1Feb14.linux.4 b/examples/shear/log.shear.void.1Feb14.linux.4 deleted file mode 100644 index 226f642c54..0000000000 --- a/examples/shear/log.shear.void.1Feb14.linux.4 +++ /dev/null @@ -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 diff --git a/examples/snap/log.snap.5Sep14.linux.1 b/examples/snap/log.snap.5Sep14.linux.1 deleted file mode 100644 index 20f85f2903..0000000000 --- a/examples/snap/log.snap.5Sep14.linux.1 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (29 Aug 2014) -# Demonstrate SNAP Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 128 atoms - -mass 1 180.88 - -# choose potential - -include Ta06A_pot.snap -# Definition of SNAP potential Ta_Cand06A -# Assumes 1 LAMMPS atom type - -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 73 - -# Specify hybrid with SNAP, ZBL - -pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 4.8 snap -pair_coeff * * zbl 0.0 # Needed to activate hybrid cross-types -pair_coeff 1 1 zbl ${zblz} -pair_coeff 1 1 zbl 73 -pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta -SNAP Element = Ta, Radius 0.5, Weight 1 -SNAP keyword rcutfac 4.67637 -SNAP keyword twojmax 6 -SNAP keyword gamma 1 -SNAP keyword rfac0 0.99363 -SNAP keyword rmin0 0 -SNAP keyword diagonalstyle 3 - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 -fix 1 all nve -run ${nsteps} -run 100 -Memory usage per processor = 2.92823 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 300 -11.85157 0 -11.813095 2717.1661 - 10 295.96579 -11.851053 0 -11.813095 2696.1559 - 20 284.32535 -11.84956 0 -11.813095 2301.3713 - 30 266.04602 -11.847215 0 -11.813095 1832.1745 - 40 242.2862 -11.844168 0 -11.813095 1492.6765 - 50 214.48968 -11.840603 0 -11.813094 1312.8908 - 60 184.32523 -11.836734 0 -11.813094 1284.582 - 70 153.58055 -11.832791 0 -11.813094 1374.4457 - 80 124.04276 -11.829003 0 -11.813094 1537.703 - 90 97.37622 -11.825582 0 -11.813094 1734.9662 - 100 75.007873 -11.822714 0 -11.813094 1930.8005 -Loop time of 5.3587 on 1 procs for 100 steps with 128 atoms - -Pair time (%) = 5.35751 (99.9777) -Neigh time (%) = 0 (0) -Comm time (%) = 0.000583649 (0.0108916) -Outpt time (%) = 0.000120401 (0.00224684) -Other time (%) = 0.000491381 (0.00916977) - -Nlocal: 128 ave 128 max 128 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 727 ave 727 max 727 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3712 ave 3712 max 3712 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 7424 ave 7424 max 7424 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - diff --git a/examples/snap/log.snap.5Sep14.linux.4 b/examples/snap/log.snap.5Sep14.linux.4 deleted file mode 100644 index ab2bbbf89a..0000000000 --- a/examples/snap/log.snap.5Sep14.linux.4 +++ /dev/null @@ -1,116 +0,0 @@ -LAMMPS (29 Aug 2014) -# Demonstrate SNAP Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 128 atoms - -mass 1 180.88 - -# choose potential - -include Ta06A_pot.snap -# Definition of SNAP potential Ta_Cand06A -# Assumes 1 LAMMPS atom type - -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 73 - -# Specify hybrid with SNAP, ZBL - -pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 ${zblcutouter} snap -pair_style hybrid/overlay zbl 4 4.8 snap -pair_coeff * * zbl 0.0 # Needed to activate hybrid cross-types -pair_coeff 1 1 zbl ${zblz} -pair_coeff 1 1 zbl 73 -pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta -SNAP Element = Ta, Radius 0.5, Weight 1 -SNAP keyword rcutfac 4.67637 -SNAP keyword twojmax 6 -SNAP keyword gamma 1 -SNAP keyword rfac0 0.99363 -SNAP keyword rmin0 0 -SNAP keyword diagonalstyle 3 - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 -fix 1 all nve -run ${nsteps} -run 100 -Memory usage per processor = 2.91109 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 300 -11.85157 0 -11.813095 2717.1661 - 10 295.8664 -11.85104 0 -11.813095 2702.935 - 20 283.95868 -11.849513 0 -11.813095 2301.3242 - 30 265.29535 -11.847119 0 -11.813095 1870.3173 - 40 241.09337 -11.844015 0 -11.813095 1568.1549 - 50 212.86732 -11.840395 0 -11.813094 1409.2092 - 60 182.35256 -11.836481 0 -11.813094 1389.0527 - 70 151.38968 -11.83251 0 -11.813094 1474.9232 - 80 121.80051 -11.828715 0 -11.813094 1627.6911 - 90 95.262635 -11.825311 0 -11.813094 1812.9327 - 100 73.194645 -11.822481 0 -11.813094 1995.2199 -Loop time of 1.41452 on 4 procs for 100 steps with 128 atoms - -Pair time (%) = 1.36282 (96.3451) -Neigh time (%) = 0 (0) -Comm time (%) = 0.0507569 (3.58828) -Outpt time (%) = 0.000217676 (0.0153887) -Other time (%) = 0.000724733 (0.0512353) - -Nlocal: 32 ave 32 max 32 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 431 ave 431 max 431 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 928 ave 928 max 928 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1856 ave 1856 max 1856 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - diff --git a/examples/srd/log.srd.mixture.1Feb14.linux.1 b/examples/srd/log.srd.mixture.1Feb14.linux.1 deleted file mode 100644 index cf84b0696d..0000000000 --- a/examples/srd/log.srd.mixture.1Feb14.linux.1 +++ /dev/null @@ -1,232 +0,0 @@ -LAMMPS (1 Feb 2014) -# 2d SRD test: big + small particles - -units lj -atom_style sphere -atom_modify first big -dimension 2 - -# create big particles with sigma 1.0 - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region box block 0 10 0 10 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) - 1 by 1 by 1 MPI processor grid -create_atoms 1 region box -Created 100 atoms -set type 1 mass 1.0 - 100 settings made for mass -set type 1 diameter 1.0 - 100 settings made for diameter - -group big type 1 -100 atoms in group big -velocity big create 1.44 87287 loop geom - -# equilibrate big particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 big nve -fix 2 all enforce2d - -run 1000 -Memory usage per processor = 2.74778 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -0.54272 0 0.88288 -0.041088 - 1000 1.8791467 -0.97185784 0 0.8884974 0.61487656 -Loop time of 0.0157461 on 1 procs for 1000 steps with 100 atoms - -Pair time (%) = 0.00811386 (51.5293) -Neigh time (%) = 0.00263572 (16.7388) -Comm time (%) = 0.00207138 (13.1549) -Outpt time (%) = 7.86781e-06 (0.0499667) -Other time (%) = 0.00291729 (18.527) - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 88 ave 88 max 88 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 459 ave 459 max 459 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 459 -Ave neighs/atom = 4.59 -Neighbor list builds = 129 -Dangerous builds = 0 - -unfix 1 -unfix 2 - -# add small particles as hi density lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region plane block 0 10 0 10 -0.001 0.001 -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 2 region plane -Created 21316 atoms -set type 2 mass 0.01 - 21316 settings made for mass -set type 2 diameter 0.0 - 21316 settings made for diameter - -group small type 2 -21316 atoms in group small - -velocity small create 1.0 593849 loop geom - -# delete overlaps -# must set 1-2 cutoff to non-zero value - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.5 - -delete_atoms overlap 0.5 small big -Deleted 6700 atoms, new total = 14716 - -# SRD run - -reset_timestep 0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -communicate multi group big vel yes -neigh_modify include big - -# no pairwise interactions with small particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -# use fix SRD to push small particles out from inside big ones - -timestep 0.001 - -fix 1 big nve -fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip -fix 3 all enforce2d - -# diagnostics - -compute tbig big temp -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] - -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439) -thermo 100 - -#dump 1 all atom 250 dump.srd.mixture - -#dump 2 all image 250 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2 - -#dump 3 all movie 250 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2 - -run 5000 -SRD info: - SRD/big particles = 14616 100 - big particle diameter max/min = 0.88 0.88 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 63 63 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 - SRD per actual grid cell = 4.86648 - SRD viscosity = 0.463448 - big/SRD mass density ratio = 2.12808 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) - # of rescaled SRD velocities = 0 - ave/max small velocity = 13.2944 24.262 - ave/max big velocity = 1.69284 5.10989 -Memory usage per processor = 12.7948 Mbytes -Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10] - 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0 - 100 1.1596877 3969 0.00179671 -0.88368702 0.26440384 0.85824544 7578 83 83 0 14 12996 3000 1.0041859 0 - 200 1.2193121 3969 0.001834514 -0.93715195 0.26996708 0.70474789 7511 90 90 0 53 12996 3022 1.0188814 0 - 300 0.99964232 3969 -0.00024687038 -1.0259753 -0.036329445 0.17545201 7647 91 91 0 84 12996 3012 1.0119139 0 - 400 1.0499322 3969 0.00055095426 -0.95835442 0.081078429 0.36186511 7386 108 108 0 111 12996 2998 1.0216118 0 - 500 1.0774128 3969 0.00085873911 -0.94026661 0.12637205 0.44079381 7472 85 85 0 138 12996 2996 1.0224021 0 - 600 1.0713454 3969 0.00045284139 -0.99399184 0.066640139 0.10369128 7656 83 83 0 159 12996 3007 1.030888 0 - 700 0.98148416 3969 0.00027332701 -0.93144651 0.040222802 0.40064794 7616 68 68 0 194 12996 2999 1.0156811 0 - 800 1.038835 3969 0.00026382768 -0.98962177 0.038824881 0.26546656 7518 100 100 0 217 12996 3018 1.0169426 0 - 900 1.0976069 3969 0.0005211042 -1.0099451 0.076685694 0.28307539 7658 91 91 0 243 12996 3028 1.037322 0 - 1000 1.0541417 3969 0.00060061674 -0.95521356 0.088386759 0.61226289 7577 78 78 0 285 12996 2996 1.019357 0 - 1100 1.0332458 3969 0.00050159758 -0.94909829 0.073815099 0.6685224 7581 79 79 0 317 12996 3000 1.0327932 0 - 1200 0.89438281 3969 -0.00096584613 -1.0275729 -0.14213392 0.37403554 7576 96 96 0 346 12996 2999 1.0185657 0 - 1300 1.0211539 3969 2.286332e-05 -1.0075778 0.0033645662 0.56342549 7660 94 94 0 385 12996 2994 1.019908 0 - 1400 0.99883891 3969 0.00024046091 -0.9534643 0.035386228 0.5689857 7634 82 82 0 416 12996 3022 1.0247654 0 - 1500 0.93938218 3969 -0.00014395945 -0.95117343 -0.021185072 0.53463026 7632 87 87 0 441 12996 3012 1.0411548 0 - 1600 1.2197277 3969 0.0011523527 -1.0379502 0.16958023 0.3478121 7659 82 82 0 466 12996 3011 1.0361286 0 - 1700 0.96932134 3969 -0.00064508306 -1.0545586 -0.094930423 0.29578009 7332 92 92 0 506 12996 2993 1.0361228 0 - 1800 1.0534784 3969 -4.2619236e-05 -1.0492155 -0.0062718467 0.42534773 7647 94 94 0 533 12996 3030 1.0252953 0 - 1900 1.1715618 3969 0.00031188504 -1.1139492 0.045897003 0.23182966 7624 78 78 0 557 12996 2987 1.0274073 0 - 2000 0.9840555 3969 -0.00078568321 -1.0898361 -0.11562114 0.24175316 7571 77 77 0 582 12996 3016 1.0207729 0 - 2100 0.91303589 3969 -0.001459571 -1.118696 -0.21479047 0.27799152 7668 84 84 0 599 12996 3022 1.024854 0 - 2200 0.97316562 3969 -0.00087469617 -1.0921543 -0.12872029 0.40701899 7422 96 96 0 634 12996 3003 1.030247 0 - 2300 1.1071289 3969 0.00055485995 -1.0144044 0.08165319 0.70028696 7242 86 86 0 659 12996 3013 1.0181269 0 - 2400 0.95313231 3969 -0.00066790967 -1.0418906 -0.098289587 0.56977108 7370 88 88 0 693 12996 3037 1.0174525 0 - 2500 1.0789299 3969 -0.00067288654 -1.1671626 -0.099021984 0.1320041 7485 84 84 0 723 12996 3011 1.0310304 0 - 2600 1.0013882 3969 -0.00086378434 -1.1184888 -0.1271145 0.31303314 7412 82 82 0 753 12996 2983 1.0183276 0 - 2700 0.99821888 3969 -0.00016681979 -1.0127859 -0.024549201 0.71198483 7543 93 93 0 788 12996 3025 1.0179264 0 - 2800 1.032743 3969 -0.00066018247 -1.119568 -0.097152452 0.34329585 7442 106 106 0 826 12996 2981 1.0218667 0 - 2900 1.158581 3969 0.00061952386 -1.055826 0.091169131 0.55199976 7462 85 85 0 853 12996 3022 1.0105531 0 - 3000 1.0890666 3969 -5.0289217e-05 -1.0855765 -0.0074005612 0.35916031 7412 77 77 0 886 12996 2994 1.0387853 0 - 3100 0.98273391 3969 -0.00062906795 -1.0654802 -0.09257364 0.32240559 7489 71 71 0 922 12996 3007 1.038908 0 - 3200 1.0182699 3969 -0.00092197839 -1.1437655 -0.13567834 0.060449966 7464 94 94 0 954 12996 3008 1.0137212 0 - 3300 0.92962276 3969 -0.0012252227 -1.1006303 -0.18030378 0.2692969 7449 98 98 0 985 12996 3011 1.0121446 0 - 3400 1.0270974 3969 -0.00078991522 -1.1330703 -0.11624392 0.28393475 7555 74 74 0 1013 12996 2981 1.0218996 0 - 3500 0.91276883 3969 -0.0012028955 -1.0806592 -0.1770181 0.48380351 7422 100 100 0 1045 12996 3019 1.0270228 0 - 3600 1.1604674 3969 0.00041287296 -1.0881043 0.060758384 0.4937285 7451 78 78 0 1084 12996 3001 1.021449 0 - 3700 0.92829756 3969 -0.0012843951 -1.1080262 -0.18901158 0.28403593 7502 80 80 0 1106 12996 3011 1.0140255 0 - 3800 0.99862294 3969 -0.00028587151 -1.0307056 -0.042068851 0.57880501 7353 84 84 0 1136 12996 3011 1.0238774 0 - 3900 1.0748889 3969 -0.00039644261 -1.1224805 -0.058340495 0.3117021 7199 95 95 0 1169 12996 2997 1.0141241 0 - 4000 1.1443251 3969 0.00073233367 -1.0251116 0.10777022 0.72975938 7478 90 90 0 1203 12996 3000 1.016123 0 - 4100 1.0573661 3969 -8.8349019e-05 -1.0597939 -0.013001442 0.62403315 7528 77 77 0 1235 12996 2993 1.0207081 0 - 4200 0.93387975 3969 -0.0012090318 -1.1024621 -0.17792112 0.50858912 7397 80 80 0 1285 12996 3007 1.0232781 0 - 4300 0.99747825 3969 -0.00050121316 -1.061262 -0.073758528 0.63526459 7355 90 90 0 1313 12996 3015 1.0210677 0 - 4400 0.91351004 3969 -0.0013423585 -1.1019164 -0.19754147 0.44962963 7448 94 94 0 1344 12996 3009 1.0203146 0 - 4500 1.112129 3969 -9.3639925e-05 -1.1147878 -0.013780051 0.5084257 7570 77 77 0 1375 12996 2993 1.0224154 0 - 4600 1.0070341 3969 -0.00044065884 -1.0618111 -0.064847355 0.50331376 7503 74 74 0 1406 12996 3001 1.0099788 0 - 4700 1.1678442 3969 0.00045268406 -1.0895488 0.066616986 0.46676039 7514 81 81 0 1436 12996 2983 1.0099861 0 - 4800 1.1647145 3969 0.00063121154 -1.0601783 0.092889091 0.52493522 7437 89 89 0 1467 12996 3016 1.0214313 0 - 4900 1.1545752 3969 -0.00015064108 -1.1651978 -0.022168341 0.098732178 7561 85 85 0 1490 12996 2999 1.0108506 0 - 5000 1.2758575 3969 0.0016719011 -1.017062 0.24603697 0.63374434 7283 77 77 0 1521 12996 2989 1.0136454 0 -Loop time of 2.94861 on 1 procs for 5000 steps with 14716 atoms - -Pair time (%) = 0.0425909 (1.44444) -Neigh time (%) = 0.207188 (7.02665) -Comm time (%) = 0.0410075 (1.39074) -Outpt time (%) = 0.00202203 (0.0685757) -Other time (%) = 2.6558 (90.0696) - -Nlocal: 14716 ave 14716 max 14716 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 80 ave 80 max 80 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 490 ave 490 max 490 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 490 -Ave neighs/atom = 0.0332971 -Neighbor list builds = 250 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/srd/log.srd.mixture.1Feb14.linux.4 b/examples/srd/log.srd.mixture.1Feb14.linux.4 deleted file mode 100644 index 1ee08dc1e0..0000000000 --- a/examples/srd/log.srd.mixture.1Feb14.linux.4 +++ /dev/null @@ -1,232 +0,0 @@ -LAMMPS (1 Feb 2014) -# 2d SRD test: big + small particles - -units lj -atom_style sphere -atom_modify first big -dimension 2 - -# create big particles with sigma 1.0 - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region box block 0 10 0 10 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) - 2 by 2 by 1 MPI processor grid -create_atoms 1 region box -Created 100 atoms -set type 1 mass 1.0 - 100 settings made for mass -set type 1 diameter 1.0 - 100 settings made for diameter - -group big type 1 -100 atoms in group big -velocity big create 1.44 87287 loop geom - -# equilibrate big particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 big nve -fix 2 all enforce2d - -run 1000 -Memory usage per processor = 2.74724 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -0.54272 0 0.88288 -0.041088 - 1000 1.8791467 -0.97185784 0 0.8884974 0.61487657 -Loop time of 0.0147891 on 4 procs for 1000 steps with 100 atoms - -Pair time (%) = 0.00214434 (14.4994) -Neigh time (%) = 0.000745177 (5.03869) -Comm time (%) = 0.00851029 (57.5443) -Outpt time (%) = 2.07424e-05 (0.140255) -Other time (%) = 0.00336856 (22.7773) - -Nlocal: 25 ave 26 max 23 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 47 ave 48 max 46 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 114.75 ave 124 max 100 min -Histogram: 1 0 0 0 0 1 0 0 0 2 - -Total # of neighbors = 459 -Ave neighs/atom = 4.59 -Neighbor list builds = 129 -Dangerous builds = 0 - -unfix 1 -unfix 2 - -# add small particles as hi density lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region plane block 0 10 0 10 -0.001 0.001 -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 2 region plane -Created 21316 atoms -set type 2 mass 0.01 - 21316 settings made for mass -set type 2 diameter 0.0 - 21316 settings made for diameter - -group small type 2 -21316 atoms in group small - -velocity small create 1.0 593849 loop geom - -# delete overlaps -# must set 1-2 cutoff to non-zero value - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.5 - -delete_atoms overlap 0.5 small big -Deleted 6700 atoms, new total = 14716 - -# SRD run - -reset_timestep 0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -communicate multi group big vel yes -neigh_modify include big - -# no pairwise interactions with small particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -# use fix SRD to push small particles out from inside big ones - -timestep 0.001 - -fix 1 big nve -fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip -fix 3 all enforce2d - -# diagnostics - -compute tbig big temp -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] - -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439) -thermo 100 - -#dump 1 all atom 250 dump.srd.mixture - -#dump 2 all image 250 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2 - -#dump 3 all movie 250 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2 - -run 5000 -SRD info: - SRD/big particles = 14616 100 - big particle diameter max/min = 0.88 0.88 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 63 63 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 - SRD per actual grid cell = 4.86648 - SRD viscosity = 0.463448 - big/SRD mass density ratio = 2.12808 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2875) - # of rescaled SRD velocities = 0 - ave/max small velocity = 13.2944 24.262 - ave/max big velocity = 1.69284 5.10989 -Memory usage per processor = 6.52001 Mbytes -Step Temp 2[7] TotEng pebig ebig Press 2[1] 2[2] 2[3] 2[4] 2[5] 2[6] 2[8] 2[9] 2[10] - 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0 - 100 1.4044369 3969 0.0030633087 -0.93959598 0.45079651 0.78900114 7464 99 99 0 17 22500 3005 1.028131 0 - 200 1.1569395 3969 0.0010544039 -0.99020406 0.15516608 0.50132859 7393 82 82 0 43 22500 2996 1.014347 0 - 300 1.0082066 3969 1.5754289e-06 -0.99789266 0.00023184012 0.36859357 7443 90 90 0 82 22500 3003 1.0238037 0 - 400 1.1459472 3969 0.0010570023 -0.97893929 0.15554845 0.47616067 7327 81 81 0 104 22500 2993 1.0108719 0 - 500 1.0836955 3969 0.00072569678 -0.966065 0.10679354 0.49205907 7447 89 89 0 133 22500 2982 1.0221211 0 - 600 0.95868561 3969 -0.00031108604 -0.99487817 -0.045779421 0.3676888 7488 90 90 0 162 22500 2994 0.99760594 0 - 700 0.98121671 3969 -0.00022225428 -1.0041115 -0.03270694 0.3605398 7393 80 80 0 209 22500 2992 1.0032861 0 - 800 1.0870893 3969 0.00028589178 -1.0341466 0.042071834 0.3576364 7506 96 96 0 241 22500 3004 1.0173044 0 - 900 1.087553 3969 8.795578e-05 -1.0637339 0.012943573 0.28026879 7405 82 82 0 276 22500 2999 1.0082354 0 - 1000 1.0160539 3969 7.5618714e-05 -0.99476531 0.01112805 0.60009776 7334 88 88 0 312 22500 2998 1.020285 0 - 1100 0.94619807 3969 -0.00084794884 -1.0615202 -0.12478415 0.36153566 7565 89 89 0 338 22500 3009 1.0274592 0 - 1200 1.2187057 3969 0.00079088888 -1.0901314 0.11638721 0.34195358 7558 94 94 0 375 22500 2987 1.0120179 0 - 1300 1.0297116 3969 -6.2029069e-05 -1.0285427 -0.0091281978 0.44490154 7365 76 76 0 398 22500 2983 1.0132722 0 - 1400 1.0723726 3969 3.8902675e-05 -1.055924 0.0057249176 0.40617642 7524 90 90 0 439 22500 3009 1.0114417 0 - 1500 1.0661279 3969 -0.00010841884 -1.0714216 -0.015954917 0.49701435 7285 69 69 0 470 22500 2997 1.0209628 0 - 1600 1.2175256 3969 0.00087968156 -1.0758964 0.12945394 0.64512981 7286 89 89 0 510 22500 3007 1.0143888 0 - 1700 1.1985014 3969 0.0014648642 -0.970947 0.21556942 1.0479949 7228 85 85 0 537 22500 2983 1.0107134 0 - 1800 1.2075839 3969 0.00072247447 -1.0891887 0.10631934 0.57872746 7449 87 87 0 561 22500 2992 1.011785 0 - 1900 1.2255534 3969 0.00088656095 -1.0828315 0.13046631 0.65685308 7385 76 76 0 581 22500 3003 0.99158619 0 - 2000 1.291624 3969 0.0012489132 -1.0949177 0.18379006 0.54486534 7460 88 88 0 609 22500 2985 1.0084802 0 - 2100 1.1111637 3969 8.680692e-05 -1.0872776 0.012774506 0.54623825 7399 79 79 0 652 22500 2974 0.99115959 0 - 2200 1.1101509 3969 -0.00019790624 -1.1281733 -0.029123882 0.36938914 7394 80 80 0 687 22500 3009 1.0098928 0 - 2300 0.99008142 3969 -0.0010221939 -1.1306067 -0.15042605 0.49715741 7403 77 77 0 707 22500 2997 0.99398166 0 - 2400 1.1298599 3969 -0.00028442155 -1.1604168 -0.041855476 0.62622034 7213 99 99 0 739 22500 2981 1.0151717 0 - 2500 0.96755195 3969 -0.0013882655 -1.1621736 -0.20429715 0.53854953 7302 91 91 0 762 22500 2981 1.0095159 0 - 2600 0.92289325 3969 -0.0018295583 -1.1829021 -0.2692378 0.48117908 7387 114 114 0 796 22500 2984 0.99596772 0 - 2700 1.0556828 3969 -0.0010119543 -1.1940452 -0.14891919 0.38438637 7379 77 77 0 821 22500 2990 0.9995489 0 - 2800 0.96725457 3969 -0.0014988251 -1.1781491 -0.2205671 0.45335869 7311 77 77 0 850 22500 3000 1.0021877 0 - 2900 1.0133684 3969 -0.0012783239 -1.1913529 -0.18811815 0.47922787 7445 91 91 0 871 22500 3012 1.0157316 0 - 3000 0.97710883 3969 -0.0011590153 -1.1378984 -0.17056069 0.64470243 7454 90 90 0 907 22500 2982 0.99909177 0 - 3100 0.85234697 3969 -0.002077265 -1.1495138 -0.30569031 0.55071072 7386 95 95 0 935 22500 2963 1.0015568 0 - 3200 1.052911 3969 -0.00084248304 -1.1663617 -0.1239798 0.49920749 7410 84 84 0 962 22500 3023 1.0268965 0 - 3300 1.1427076 3969 0.00052348324 -1.0542447 0.077035793 0.97657677 7268 70 70 0 999 22500 2991 1.0309378 0 - 3400 1.1749571 3969 -0.00049301879 -1.2357602 -0.072552645 0.2551001 7443 77 77 0 1024 22500 2992 1.0153988 0 - 3500 0.99448585 3969 -0.0015705474 -1.2156628 -0.23112176 0.31069295 7502 97 97 0 1051 22500 2999 1.0325626 0 - 3600 1.0615674 3969 -0.00088670873 -1.1814398 -0.13048806 0.42774035 7386 70 70 0 1075 22500 3015 1.0004252 0 - 3700 0.92549328 3969 -0.0018599812 -1.1899532 -0.27371483 0.36471531 7459 81 81 0 1106 22500 3009 1.0256903 0 - 3800 0.85987993 3969 -0.0018189231 -1.1189538 -0.26767272 0.42802928 7232 75 75 0 1134 22500 2973 1.0167911 0 - 3900 0.92111833 3969 -0.0011824977 -1.0859235 -0.17401636 0.73992354 7351 80 80 0 1165 22500 3024 1.0274158 0 - 4000 0.91817371 3969 -0.0014469814 -1.1219298 -0.21293778 0.64725317 7478 86 86 0 1195 22500 3003 1.0213446 0 - 4100 1.0607641 3969 -0.00061451533 -1.1405885 -0.090432076 0.54575249 7474 87 87 0 1222 22500 3005 1.0432431 0 - 4200 1.1112883 3969 0.00012926229 -1.0811532 0.019022238 0.71771029 7527 67 67 0 1261 22500 2995 1.0263853 0 - 4300 1.3096702 3969 0.00060322354 -1.2078031 0.088770376 0.31006723 7617 88 88 0 1298 22500 2997 1.0462257 0 - 4400 1.2076765 3969 0.001009301 -1.047071 0.14852873 0.83105522 7355 97 97 0 1333 22500 2972 1.0438217 0 - 4500 0.94049473 3969 -0.0011505342 -1.1004024 -0.16931262 0.46258624 7403 78 78 0 1360 22500 3004 1.0378682 0 - 4600 0.8241741 3969 -0.0025714658 -1.1943493 -0.37841691 0.010193689 7604 99 99 0 1393 22500 3031 1.0288913 0 - 4700 0.98678642 3969 -0.0011664864 -1.1485787 -0.17166013 0.16963181 7691 94 94 0 1421 22500 3008 1.0074925 0 - 4800 0.97602307 3969 -0.0010910984 -1.1268289 -0.16056604 0.24433738 7547 85 85 0 1453 22500 2991 1.0124834 0 - 4900 1.0427787 3969 -0.00050976935 -1.1073686 -0.075017657 0.30774039 7563 85 85 0 1494 22500 2994 1.0235529 0 - 5000 1.3048873 3969 0.0015736036 -1.0602669 0.23157151 0.49881308 7529 104 104 0 1524 22500 2984 1.0094313 0 -Loop time of 0.868197 on 4 procs for 5000 steps with 14716 atoms - -Pair time (%) = 0.0116689 (1.34403) -Neigh time (%) = 0.0541446 (6.23644) -Comm time (%) = 0.0662674 (7.63276) -Outpt time (%) = 0.00228554 (0.263251) -Other time (%) = 0.733831 (84.5235) - -Nlocal: 3679 ave 4052 max 3370 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Nghost: 49 ave 53 max 42 min -Histogram: 1 0 0 0 0 0 0 1 1 1 -Neighs: 120.5 ave 162 max 85 min -Histogram: 1 0 0 1 0 1 0 0 0 1 - -Total # of neighbors = 482 -Ave neighs/atom = 0.0327535 -Neighbor list builds = 250 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/srd/log.srd.pure.1Feb14.linux.1 b/examples/srd/log.srd.pure.1Feb14.linux.1 deleted file mode 100644 index b5b17f0c0a..0000000000 --- a/examples/srd/log.srd.pure.1Feb14.linux.1 +++ /dev/null @@ -1,148 +0,0 @@ -LAMMPS (1 Feb 2014) -# 2d SRD only test - -units lj -atom_style atomic -atom_modify first empty -dimension 2 - -# create box with big lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region box block 0 10 0 10 -0.5 0.5 -create_box 1 box -Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) - 1 by 1 by 1 MPI processor grid - -# add SRD particles as hi density lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region plane block 0 10 0 10 -0.001 0.001 -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 1 region plane -Created 21316 atoms - -group empty type 2 -0 atoms in group empty - -mass 1 0.01 -velocity all create 1.0 593849 loop geom - -# settings - need dummy empty group to enable no communication - -neighbor 0.3 bin -neigh_modify delay 1 every 1 check no - -communicate single group empty - -# timestep is big and SRD frequency is 1 - -timestep 0.02 - -fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip -fix 2 all enforce2d - -# diagnostics - -thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] -thermo 100 - -#dump 1 all atom 250 dump.srd.pure - -#dump 2 all image 250 image.*.jpg type type zoom 1.6 adiam 0.2 -#dump_modify 2 pad 4 - -#dump 3 all movie 250 movie.mpg type type zoom 1.6 adiam 0.2 -#dump_modify 3 pad 4 - -run 5000 -SRD info: - SRD/big particles = 21316 0 - big particle diameter max/min = 0 1e+20 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 63 63 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 - SRD per actual grid cell = 5.37062 - SRD viscosity = 0.439647 - big/SRD mass density ratio = 0 - # of rescaled SRD velocities = 0 - ave/max all velocity = 13.2735 24.2873 -Memory usage per processor = 4.83622 Mbytes -Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6] - 0 1 0 0.99995309 85.26 0 0 0 - 100 0.97820615 3969 0.97816026 83.401857 0 0 0 - 200 0.9609326 3969 0.96088752 81.929113 0 0 0 - 300 0.94460302 3969 0.9445587 80.536853 0 0 0 - 400 0.93098293 3969 0.93093925 79.375605 0 0 0 - 500 0.91803208 3969 0.91798901 78.271415 0 0 0 - 600 0.90779378 3969 0.90775119 77.398497 0 0 0 - 700 0.89695247 3969 0.89691039 76.474168 0 0 0 - 800 0.88637078 3969 0.88632919 75.571972 0 0 0 - 900 0.87833669 3969 0.87829548 74.886986 0 0 0 - 1000 0.87030089 3969 0.87026006 74.201854 0 0 0 - 1100 0.86318709 3969 0.86314659 73.595331 0 0 0 - 1200 0.85736665 3969 0.85732643 73.099081 0 0 0 - 1300 0.85147901 3969 0.85143906 72.5971 0 0 0 - 1400 0.84496088 3969 0.84492124 72.041365 0 0 0 - 1500 0.83857476 3969 0.83853542 71.496884 0 0 0 - 1600 0.8336916 3969 0.83365249 71.080546 0 0 0 - 1700 0.82954371 3969 0.8295048 70.726897 0 0 0 - 1800 0.82570979 3969 0.82567105 70.400016 0 0 0 - 1900 0.82189413 3969 0.82185557 70.074693 0 0 0 - 2000 0.81818525 3969 0.81814687 69.758475 0 0 0 - 2100 0.81436257 3969 0.81432436 69.432552 0 0 0 - 2200 0.80997949 3969 0.80994149 69.058851 0 0 0 - 2300 0.80685831 3969 0.80682045 68.792739 0 0 0 - 2400 0.80374622 3969 0.80370851 68.527402 0 0 0 - 2500 0.80103773 3969 0.80100015 68.296477 0 0 0 - 2600 0.79858358 3969 0.79854611 68.087236 0 0 0 - 2700 0.79617295 3969 0.7961356 67.881706 0 0 0 - 2800 0.79312496 3969 0.79308775 67.621834 0 0 0 - 2900 0.79126456 3969 0.79122744 67.463216 0 0 0 - 3000 0.78897033 3969 0.78893331 67.26761 0 0 0 - 3100 0.78632296 3969 0.78628607 67.041895 0 0 0 - 3200 0.78442284 3969 0.78438604 66.879892 0 0 0 - 3300 0.78168316 3969 0.78164649 66.646306 0 0 0 - 3400 0.7788658 3969 0.77882926 66.406098 0 0 0 - 3500 0.77703408 3969 0.77699762 66.249925 0 0 0 - 3600 0.77441139 3969 0.77437506 66.026315 0 0 0 - 3700 0.7723528 3969 0.77231656 65.850799 0 0 0 - 3800 0.77019626 3969 0.77016013 65.666933 0 0 0 - 3900 0.76835687 3969 0.76832082 65.510107 0 0 0 - 4000 0.76701071 3969 0.76697473 65.395333 0 0 0 - 4100 0.76552115 3969 0.76548523 65.268333 0 0 0 - 4200 0.76360426 3969 0.76356843 65.104899 0 0 0 - 4300 0.76173186 3969 0.76169613 64.945259 0 0 0 - 4400 0.75933463 3969 0.759299 64.74087 0 0 0 - 4500 0.75806391 3969 0.75802835 64.632529 0 0 0 - 4600 0.75692832 3969 0.75689281 64.535709 0 0 0 - 4700 0.75569109 3969 0.75565564 64.430222 0 0 0 - 4800 0.75446697 3969 0.75443157 64.325854 0 0 0 - 4900 0.75276753 3969 0.75273221 64.180959 0 0 0 - 5000 0.75113693 3969 0.75110169 64.041935 0 0 0 -Loop time of 7.7539 on 1 procs for 5000 steps with 21316 atoms - -Pair time (%) = 0 (0) -Neigh time (%) = 5.22542 (67.3908) -Comm time (%) = 0.631161 (8.13992) -Outpt time (%) = 0.00308609 (0.0398005) -Other time (%) = 1.89424 (24.4295) - -Nlocal: 21316 ave 21316 max 21316 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 -Neighbor list builds = 5000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/srd/log.srd.pure.1Feb14.linux.4 b/examples/srd/log.srd.pure.1Feb14.linux.4 deleted file mode 100644 index 4f5ca71ab3..0000000000 --- a/examples/srd/log.srd.pure.1Feb14.linux.4 +++ /dev/null @@ -1,148 +0,0 @@ -LAMMPS (1 Feb 2014) -# 2d SRD only test - -units lj -atom_style atomic -atom_modify first empty -dimension 2 - -# create box with big lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region box block 0 10 0 10 -0.5 0.5 -create_box 1 box -Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) - 2 by 2 by 1 MPI processor grid - -# add SRD particles as hi density lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region plane block 0 10 0 10 -0.001 0.001 -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 1 region plane -Created 21316 atoms - -group empty type 2 -0 atoms in group empty - -mass 1 0.01 -velocity all create 1.0 593849 loop geom - -# settings - need dummy empty group to enable no communication - -neighbor 0.3 bin -neigh_modify delay 1 every 1 check no - -communicate single group empty - -# timestep is big and SRD frequency is 1 - -timestep 0.02 - -fix 1 all srd 1 NULL 1.0 0.25 49894 collision slip -fix 2 all enforce2d - -# diagnostics - -thermo_style custom step temp f_1[7] etotal press f_1[3] f_1[4] f_1[6] -thermo 100 - -#dump 1 all atom 250 dump.srd.pure - -#dump 2 all image 250 image.*.jpg type type zoom 1.6 adiam 0.2 -#dump_modify 2 pad 4 - -#dump 3 all movie 250 movie.mpg type type zoom 1.6 adiam 0.2 -#dump_modify 3 pad 4 - -run 5000 -SRD info: - SRD/big particles = 21316 0 - big particle diameter max/min = 0 1e+20 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 63 63 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 - SRD per actual grid cell = 5.37062 - SRD viscosity = 0.439647 - big/SRD mass density ratio = 0 - # of rescaled SRD velocities = 0 - ave/max all velocity = 13.2735 24.2873 -Memory usage per processor = 1.5432 Mbytes -Step Temp 1[7] TotEng Press 1[3] 1[4] 1[6] - 0 1 0 0.99995309 85.26 0 0 0 - 100 0.97718565 3969 0.97713981 83.314849 0 0 0 - 200 0.95953504 3969 0.95949002 81.809957 0 0 0 - 300 0.94384163 3969 0.94379735 80.471937 0 0 0 - 400 0.93018267 3969 0.93013903 79.307374 0 0 0 - 500 0.9189656 3969 0.91892248 78.351007 0 0 0 - 600 0.90794939 3969 0.9079068 77.411765 0 0 0 - 700 0.899123 3969 0.89908081 76.659227 0 0 0 - 800 0.89045828 3969 0.89041651 75.920473 0 0 0 - 900 0.88189664 3969 0.88185527 75.190507 0 0 0 - 1000 0.87511065 3969 0.87506959 74.611934 0 0 0 - 1100 0.86844868 3969 0.86840794 74.043934 0 0 0 - 1200 0.86236759 3969 0.86232713 73.52546 0 0 0 - 1300 0.85644064 3969 0.85640047 73.020129 0 0 0 - 1400 0.85088468 3969 0.85084476 72.546428 0 0 0 - 1500 0.84573938 3969 0.8456997 72.107739 0 0 0 - 1600 0.84169541 3969 0.84165592 71.76295 0 0 0 - 1700 0.83686816 3969 0.8368289 71.351379 0 0 0 - 1800 0.83199161 3969 0.83195258 70.935605 0 0 0 - 1900 0.82774228 3969 0.82770345 70.573307 0 0 0 - 2000 0.82446049 3969 0.82442181 70.293501 0 0 0 - 2100 0.82065145 3969 0.82061295 69.968743 0 0 0 - 2200 0.81761922 3969 0.81758087 69.710215 0 0 0 - 2300 0.81355286 3969 0.8135147 69.363517 0 0 0 - 2400 0.81040375 3969 0.81036573 69.095024 0 0 0 - 2500 0.80651947 3969 0.80648164 68.76385 0 0 0 - 2600 0.80304949 3969 0.80301181 68.467999 0 0 0 - 2700 0.80027966 3969 0.80024211 68.231843 0 0 0 - 2800 0.79726989 3969 0.79723248 67.97523 0 0 0 - 2900 0.79526953 3969 0.79523222 67.80468 0 0 0 - 3000 0.79213985 3969 0.79210268 67.537843 0 0 0 - 3100 0.79008514 3969 0.79004808 67.362659 0 0 0 - 3200 0.78760949 3969 0.78757254 67.151585 0 0 0 - 3300 0.78482758 3969 0.78479077 66.9144 0 0 0 - 3400 0.78225219 3969 0.7822155 66.694822 0 0 0 - 3500 0.78019518 3969 0.78015858 66.519441 0 0 0 - 3600 0.7782201 3969 0.77818359 66.351045 0 0 0 - 3700 0.77626555 3969 0.77622913 66.184401 0 0 0 - 3800 0.77429464 3969 0.77425832 66.016361 0 0 0 - 3900 0.7728635 3969 0.77282724 65.894342 0 0 0 - 4000 0.7712408 3969 0.77120462 65.75599 0 0 0 - 4100 0.76928811 3969 0.76925202 65.589504 0 0 0 - 4200 0.76768117 3969 0.76764516 65.452497 0 0 0 - 4300 0.76576395 3969 0.76572802 65.289034 0 0 0 - 4400 0.76375476 3969 0.76371893 65.117731 0 0 0 - 4500 0.76222055 3969 0.76218479 64.986924 0 0 0 - 4600 0.76007803 3969 0.76004237 64.804252 0 0 0 - 4700 0.75921155 3969 0.75917594 64.730377 0 0 0 - 4800 0.75699084 3969 0.75695533 64.541039 0 0 0 - 4900 0.75590428 3969 0.75586882 64.448399 0 0 0 - 5000 0.75435525 3969 0.75431986 64.316328 0 0 0 -Loop time of 1.83036 on 4 procs for 5000 steps with 21316 atoms - -Pair time (%) = 0 (0) -Neigh time (%) = 0.983628 (53.7394) -Comm time (%) = 0.316691 (17.3021) -Outpt time (%) = 0.00219667 (0.120013) -Other time (%) = 0.527849 (28.8385) - -Nlocal: 5329 ave 5410 max 5266 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Nghost: 0 ave 0 max 0 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 - -Total # of neighbors = 0 -Ave neighs/atom = 0 -Neighbor list builds = 5000 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - diff --git a/examples/streitz/log.streitz.ewald.19Feb15.linux.1 b/examples/streitz/log.streitz.ewald.19Feb15.linux.1 deleted file mode 100644 index 9c4dd98bf1..0000000000 --- a/examples/streitz/log.streitz.ewald.19Feb15.linux.1 +++ /dev/null @@ -1,111 +0,0 @@ -LAMMPS (16 Feb 2015) -# Streitz-Mintmire potential with alpha-alumina -# option to use with Ewald or Wolf sum -# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions -# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications -# Contributing authors: Ray Shan, Chris Weinberger (Sandia) - -units metal -atom_style charge -dimension 3 -boundary p p p - -read_data data.streitz - orthogonal box = (0 0 0) to (24.7337 28.56 25.9798) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2160 atoms - -group type1 type 1 -864 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -1296 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 - -variable qcat equal 2.8 -variable qani equal -${qcat}*count(type1)/count(type2) -variable qani equal -2.8*count(type1)/count(type2) -set group type1 charge ${qcat} -set group type1 charge 2.8 - 864 settings made for charge -set group type2 charge ${qani} -set group type2 charge -1.86666666666667 - 1296 settings made for charge -variable qsum equal count(type1)*c_q1+count(type2)*c_q2 - -# Ewald sum for coul/streitz -pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -kspace_style pppm 1e-6 - -# Wolf sum for coul/streitz -#pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy - -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -Reading potential file AlO.eam.alloy with DATE: 2015-02-19 - -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes -timestep 0.0004 - -thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu -thermo_modify norm yes -thermo 10 - -velocity all create 300.0 42128 -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz -fix 2 all nve - -run 100 -PPPM initialization ... -WARNING: For better accuracy use 'pair_modify table 0' (../kspace.cpp:325) - G vector (1/distance) = 0.312067 - grid = 54 60 54 - stencil order = 5 - estimated absolute RMS force accuracy = 2.14637e-05 - estimated relative force accuracy = 1.49057e-06 - using double precision FFTs - 3d grid and FFT values/proc = 249307 174960 -Neighbor list info ... - 3 neighbor list requests - update every 10 steps, delay 0 steps, check yes - master list distance cutoff = 13 -Memory usage per processor = 68.0137 Mbytes -Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU - 0 300 -6.3402648 -6.3790249 -2.7952901 10.304302 -13.888037 2.8665317 -1.9110211 2.7284841e-12 -26072.38 0 - 10 272.45438 -6.3403051 -6.3755063 -2.790294 10.277076 -13.862288 2.8636996 -1.9091331 -2.2737368e-12 -21774.248 1.0258776 - 20 219.94332 -6.340243 -6.3686598 -2.7790336 10.278005 -13.867631 2.8638745 -1.9092497 2.2737368e-12 -16694.093 1.0991882 - 30 179.36166 -6.3401897 -6.3633633 -2.7689124 10.276578 -13.871029 2.8639192 -1.9092795 4.5474735e-13 -12974.446 1.0985568 - 40 162.6854 -6.3401782 -6.3611972 -2.7652026 10.259213 -13.855207 2.8621763 -1.9081176 2.2737368e-12 -12735.742 1.099401 - 50 152.76284 -6.340189 -6.359926 -2.7673923 10.217907 -13.810441 2.8575296 -1.9050197 2.7284841e-12 -14532.815 1.1011081 - 60 138.38078 -6.3402052 -6.3580841 -2.7714511 10.170646 -13.757279 2.8519579 -1.9013052 -7.730705e-12 -15656.516 1.1002124 - 70 134.95726 -6.3401899 -6.3576264 -2.7740776 10.148683 -13.732232 2.8492767 -1.8995178 3.1832315e-12 -14160.756 1.1022792 - 80 161.55091 -6.3401297 -6.3610022 -2.7741364 10.171874 -13.75874 2.8520584 -1.9013723 -5.9117156e-12 -9666.7511 1.0962745 - 90 207.33026 -6.3400313 -6.3668184 -2.7713862 10.230461 -13.825893 2.8591985 -1.9061323 3.1832315e-12 -2531.0201 1.09851 - 100 233.80643 -6.339937 -6.3701448 -2.7659476 10.293322 -13.897519 2.8668083 -1.9112055 -3.6379788e-12 6120.7834 1.0938448 -Loop time of 91.6543 on 1 procs for 100 steps with 2160 atoms - -Pair time (%) = 40.669 (44.3721) -Kspce time (%) = 3.11322 (3.3967) -Neigh time (%) = 0 (0) -Comm time (%) = 0.0146234 (0.015955) -Outpt time (%) = 0.000924826 (0.00100904) -Other time (%) = 47.8566 (52.2142) - -Nlocal: 2160 ave 2160 max 2160 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 14994 ave 14994 max 14994 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.17893e+06 ave 1.17893e+06 max 1.17893e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 2.35786e+06 ave 2.35786e+06 max 2.35786e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2357856 -Ave neighs/atom = 1091.6 -Neighbor list builds = 0 -Dangerous builds = 0 - diff --git a/examples/streitz/log.streitz.ewald.19Feb15.linux.4 b/examples/streitz/log.streitz.ewald.19Feb15.linux.4 deleted file mode 100644 index 3496c057cb..0000000000 --- a/examples/streitz/log.streitz.ewald.19Feb15.linux.4 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (16 Feb 2015) -# Streitz-Mintmire potential with alpha-alumina -# option to use with Ewald or Wolf sum -# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions -# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications -# Contributing authors: Ray Shan, Chris Weinberger (Sandia) - -units metal -atom_style charge -dimension 3 -boundary p p p - -read_data data.streitz - orthogonal box = (0 0 0) to (24.7337 28.56 25.9798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2160 atoms - -group type1 type 1 -864 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -1296 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 - -variable qcat equal 2.8 -variable qani equal -${qcat}*count(type1)/count(type2) -variable qani equal -2.8*count(type1)/count(type2) -set group type1 charge ${qcat} -set group type1 charge 2.8 - 864 settings made for charge -set group type2 charge ${qani} -set group type2 charge -1.86666666666667 - 1296 settings made for charge -variable qsum equal count(type1)*c_q1+count(type2)*c_q2 - -# Ewald sum for coul/streitz -pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -kspace_style ewald 1e-6 - -# Wolf sum for coul/streitz -#pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy - -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -Reading potential file AlO.eam.alloy with DATE: 2015-02-19 - -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes -timestep 0.0004 - -thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu -thermo_modify norm yes -thermo 10 - -velocity all create 300.0 42128 -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz -fix 2 all nve - -run 100 -Ewald initialization ... - G vector (1/distance) = 0.310132 - estimated absolute RMS force accuracy = 1.9688e-05 - estimated relative force accuracy = 1.36725e-06 - KSpace vectors: actual max1d max3d = 2541 11 6083 - kxmax kymax kzmax = 10 11 10 -Neighbor list info ... - 3 neighbor list requests - update every 10 steps, delay 0 steps, check yes - master list distance cutoff = 13 -Memory usage per processor = 14.8576 Mbytes -Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU - 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801925 2.8665317 -1.9110211 4.5474735e-13 -26072.6 0 - 10 272.45429 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 4.5474735e-13 -21774.214 3.6370816 - 20 219.94295 -6.3402438 -6.3686605 -2.7790335 10.192018 -13.781645 2.8638746 -1.9092497 -4.5474735e-13 -16694.015 3.7869952 - 30 179.36109 -6.3401905 -6.363364 -2.7689124 10.190566 -13.785018 2.8639192 -1.9092795 9.094947e-13 -12974.238 3.8192926 - 40 162.68485 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 -4.5474735e-13 -12735.472 3.920062 - 50 152.76249 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724801 2.8575297 -1.9050198 4.5474735e-13 -14532.583 3.7525128 - 60 138.38062 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671968 2.851958 -1.9013053 4.5474735e-13 -15656.298 3.3005261 - 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063527 -13.647077 2.8492769 -1.8995179 -1.3642421e-12 -14160.655 3.355735 - 80 161.55082 -6.3401305 -6.3610029 -2.7741365 10.086553 -13.673419 2.8520585 -1.9013723 0 -9666.5793 3.3567142 - 90 207.3301 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591985 -1.9061323 0 -2530.8682 3.3502979 - 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668082 -1.9112055 -4.5474735e-13 6120.8881 3.3195196 -Loop time of 28.2106 on 4 procs for 100 steps with 2160 atoms - -Pair time (%) = 11.1197 (39.4167) -Kspce time (%) = 1.29535 (4.59173) -Neigh time (%) = 0 (0) -Comm time (%) = 0.0762554 (0.270308) -Outpt time (%) = 0.00115907 (0.00410864) -Other time (%) = 15.7181 (55.7171) - -Nlocal: 540 ave 540 max 540 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 8994 ave 8994 max 8994 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 294732 ave 294732 max 294732 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 589464 ave 589464 max 589464 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2357856 -Ave neighs/atom = 1091.6 -Neighbor list builds = 0 -Dangerous builds = 0 diff --git a/examples/streitz/log.streitz.wolf.19Feb15.linux.1 b/examples/streitz/log.streitz.wolf.19Feb15.linux.1 deleted file mode 100644 index 9f68939407..0000000000 --- a/examples/streitz/log.streitz.wolf.19Feb15.linux.1 +++ /dev/null @@ -1,100 +0,0 @@ -LAMMPS (16 Feb 2015) -# Streitz-Mintmire potential with alpha-alumina -# option to use with Ewald or Wolf sum -# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions -# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications -# Contributing authors: Ray Shan, Chris Weinberger (Sandia) - -units metal -atom_style charge -dimension 3 -boundary p p p - -read_data data.streitz - orthogonal box = (0 0 0) to (24.7337 28.56 25.9798) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2160 atoms - -group type1 type 1 -864 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -1296 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 - -variable qcat equal 2.8 -variable qani equal -${qcat}*count(type1)/count(type2) -variable qani equal -2.8*count(type1)/count(type2) -set group type1 charge ${qcat} -set group type1 charge 2.8 - 864 settings made for charge -set group type2 charge ${qani} -set group type2 charge -1.86666666666667 - 1296 settings made for charge -variable qsum equal count(type1)*c_q1+count(type2)*c_q2 - -# Ewald sum for coul/streitz -#pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -#kspace_style ewald 1e-6 - -# Wolf sum for coul/streitz -pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy - -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -Reading potential file AlO.eam.alloy with DATE: 2015-02-19 - -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes -timestep 0.0004 - -thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu -thermo_modify norm yes -thermo 10 - -velocity all create 300.0 42128 -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz -fix 2 all nve - -run 100 -Neighbor list info ... - 3 neighbor list requests - update every 10 steps, delay 0 steps, check yes - master list distance cutoff = 13 -Memory usage per processor = 42.889 Mbytes -Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU - 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 2.7284841e-12 -25874.942 0 - 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -5.9117156e-12 -21564.556 0.80309312 - 20 220.54622 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -2.7284841e-12 -16449.483 0.85307492 - 30 180.22122 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 -4.0927262e-12 -12688.515 0.85132792 - 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 5.9117156e-12 -12334.208 0.85162604 - 50 153.73808 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 -1.3642421e-12 -13908.747 0.85314959 - 60 139.1264 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.9016079 -2.7284841e-12 -14717.564 0.84952939 - 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 4.5474735e-13 -12982.145 0.84585695 - 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 9.094947e-13 -8388.9494 0.8653011 - 90 205.15419 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -9.094947e-13 -1208.0269 0.86572501 - 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675277 -1.9116851 -1.8189894e-12 7331.3742 0.86504622 -Loop time of 117.645 on 1 procs for 100 steps with 2160 atoms - -Pair time (%) = 69.2129 (58.8318) -Neigh time (%) = 0 (0) -Comm time (%) = 0.0104485 (0.00888132) -Outpt time (%) = 0.000833988 (0.0007089) -Other time (%) = 48.4212 (41.1586) - -Nlocal: 2160 ave 2160 max 2160 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 14994 ave 14994 max 14994 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.17893e+06 ave 1.17893e+06 max 1.17893e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 2.35786e+06 ave 2.35786e+06 max 2.35786e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2357856 -Ave neighs/atom = 1091.6 -Neighbor list builds = 0 -Dangerous builds = 0 diff --git a/examples/streitz/log.streitz.wolf.19Feb15.linux.4 b/examples/streitz/log.streitz.wolf.19Feb15.linux.4 deleted file mode 100644 index fbec6781b5..0000000000 --- a/examples/streitz/log.streitz.wolf.19Feb15.linux.4 +++ /dev/null @@ -1,100 +0,0 @@ -LAMMPS (16 Feb 2015) -# Streitz-Mintmire potential with alpha-alumina -# option to use with Ewald or Wolf sum -# EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions -# Streitz Mintmire (coul/streitz) does not include 2004 Zhou modifications -# Contributing authors: Ray Shan, Chris Weinberger (Sandia) - -units metal -atom_style charge -dimension 3 -boundary p p p - -read_data data.streitz - orthogonal box = (0 0 0) to (24.7337 28.56 25.9798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2160 atoms - -group type1 type 1 -864 atoms in group type1 -compute charge1 type1 property/atom q -compute q1 type1 reduce ave c_charge1 -group type2 type 2 -1296 atoms in group type2 -compute charge2 type2 property/atom q -compute q2 type2 reduce ave c_charge2 - -variable qcat equal 2.8 -variable qani equal -${qcat}*count(type1)/count(type2) -variable qani equal -2.8*count(type1)/count(type2) -set group type1 charge ${qcat} -set group type1 charge 2.8 - 864 settings made for charge -set group type2 charge ${qani} -set group type2 charge -1.86666666666667 - 1296 settings made for charge -variable qsum equal count(type1)*c_q1+count(type2)*c_q2 - -# Ewald sum for coul/streitz -#pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -#kspace_style ewald 1e-6 - -# Wolf sum for coul/streitz -pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy - -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -Reading potential file AlO.eam.alloy with DATE: 2015-02-19 - -neighbor 1.0 bin -neigh_modify every 10 delay 0 check yes -timestep 0.0004 - -thermo_style custom step temp etotal pe evdwl ecoul elong c_q1 c_q2 v_qsum press spcpu -thermo_modify norm yes -thermo 10 - -velocity all create 300.0 42128 -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz -fix 2 all nve - -run 100 -Neighbor list info ... - 3 neighbor list requests - update every 10 steps, delay 0 steps, check yes - master list distance cutoff = 13 -Memory usage per processor = 13.4993 Mbytes -Step Temp TotEng PotEng E_vdwl E_coul E_long q1 q2 qsum Press S/CPU - 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 4.5474735e-13 -25874.956 0 - 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -1.3642421e-12 -21564.555 2.5368258 - 20 220.54623 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -1.3642421e-12 -16449.483 2.7928265 - 30 180.22123 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 1.3642421e-12 -12688.521 2.77078 - 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 -9.094947e-13 -12334.216 2.7848078 - 50 153.73807 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 4.5474735e-13 -13908.735 2.7815539 - 60 139.12639 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.901608 0 -14717.582 3.2282139 - 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 -4.5474735e-13 -12982.152 3.2626153 - 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 -4.5474735e-13 -8388.9691 3.2231707 - 90 205.15418 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -1.3642421e-12 -1208.0315 3.2301545 - 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675276 -1.9116851 0 7331.4547 3.2611713 -Loop time of 33.7451 on 4 procs for 100 steps with 2160 atoms - -Pair time (%) = 18.3646 (54.4215) -Neigh time (%) = 0 (0) -Comm time (%) = 0.0638899 (0.189331) -Outpt time (%) = 0.00117451 (0.00348053) -Other time (%) = 15.3154 (45.3856) - -Nlocal: 540 ave 540 max 540 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 8994 ave 8994 max 8994 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 294732 ave 294732 max 294732 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 589464 ave 589464 max 589464 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2357856 -Ave neighs/atom = 1091.6 -Neighbor list builds = 0 -Dangerous builds = 0