From f097174ccb58870723256eb55c885dbdf172583f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 12 Feb 2007 17:54:11 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@299 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- examples/crack/log.crack.12Feb07.liberty.4 | 154 +++++++++ ...ct06.linux.1 => log.crack.12Feb07.linux.1} | 69 ++-- examples/crack/log.crack.1Oct06.liberty.4 | 153 --------- .../flow/log.flow.couette.12Feb07.liberty.4 | 122 +++++++ ...nux.1 => log.flow.couette.12Feb07.linux.1} | 61 ++-- .../flow/log.flow.couette.1Oct06.liberty.4 | 121 ------- ...rty.4 => log.flow.poiss.12Feb07.liberty.4} | 67 ++-- ...linux.1 => log.flow.poiss.12Feb07.linux.1} | 57 ++-- .../friction/log.friction.12Feb07.liberty.4 | 140 ++++++++ .../friction/log.friction.12Feb07.linux.1 | 140 ++++++++ .../friction/log.friction.1Oct06.liberty.4 | 139 -------- examples/friction/log.friction.1Oct06.linux.1 | 139 -------- examples/indent/log.indent.12Feb07.liberty.4 | 169 ++++++++++ examples/indent/log.indent.12Feb07.linux.1 | 169 ++++++++++ examples/indent/log.indent.1Oct06.liberty.4 | 168 ---------- examples/indent/log.indent.1Oct06.linux.1 | 168 ---------- examples/meam/{data.sic => data.meam} | 0 examples/meam/{in.sic => in.meam} | 8 +- .../meam/{in.shear_meam => in.meam.shear} | 4 +- examples/meam/log.meam.12Feb07.liberty.4 | 59 ++++ examples/meam/log.meam.12Feb07.linux.1 | 59 ++++ .../meam/log.meam.shear.12Feb07.liberty.4 | 163 ++++++++++ examples/meam/log.meam.shear.12Feb07.linux.1 | 163 ++++++++++ ...6.liberty.4 => log.melt.12Feb07.liberty.4} | 15 +- ...Oct06.linux.1 => log.melt.12Feb07.linux.1} | 15 +- ...iberty.4 => log.micelle.12Feb07.liberty.4} | 30 +- ...06.linux.1 => log.micelle.12Feb07.linux.1} | 30 +- ...06.liberty.4 => log.min.12Feb07.liberty.4} | 28 +- ...1Oct06.linux.1 => log.min.12Feb07.linux.1} | 28 +- .../obstacle/log.obstacle.12Feb07.liberty.4 | 134 ++++++++ .../obstacle/log.obstacle.12Feb07.linux.1 | 134 ++++++++ .../obstacle/log.obstacle.1Oct06.liberty.4 | 133 -------- examples/obstacle/log.obstacle.1Oct06.linux.1 | 133 -------- .../peptide/log.peptide.12Feb07.liberty.4 | 154 +++++++++ examples/peptide/log.peptide.12Feb07.linux.1 | 154 +++++++++ examples/peptide/log.peptide.1Oct06.liberty.4 | 154 --------- examples/peptide/log.peptide.1Oct06.linux.1 | 154 --------- examples/pour/log.pour.12Feb07.liberty.4 | 136 ++++++++ examples/pour/log.pour.12Feb07.linux.1 | 136 ++++++++ examples/pour/log.pour.1Oct06.liberty.4 | 135 -------- examples/pour/log.pour.1Oct06.linux.1 | 135 -------- ...iberty.4 => log.pour.2d.12Feb07.liberty.4} | 23 +- ...06.linux.1 => log.pour.2d.12Feb07.linux.1} | 23 +- ....liberty.4 => log.rigid.12Feb07.liberty.4} | 14 +- ...ct06.linux.1 => log.rigid.12Feb07.linux.1} | 14 +- ...ty.4 => log.rigid.poems.12Feb07.liberty.4} | 14 +- .../rigid/log.rigid.poems.12Feb07.linux.1 | 305 +++++++++++++++++ examples/rigid/log.rigid.poems.1Oct06.linux.1 | 305 ----------------- ...y.4 => log.rigid.poems2.12Feb07.liberty.4} | 14 +- .../rigid/log.rigid.poems2.12Feb07.linux.1 | 306 ++++++++++++++++++ .../rigid/log.rigid.poems2.1Oct06.linux.1 | 306 ------------------ examples/shear/log.shear.12Feb07.liberty.4 | 159 +++++++++ examples/shear/log.shear.12Feb07.linux.1 | 159 +++++++++ examples/shear/log.shear.1Oct06.liberty.4 | 160 --------- examples/shear/log.shear.1Oct06.linux.1 | 160 --------- .../shear/log.shear.void.12Feb07.liberty.4 | 160 +++++++++ examples/shear/log.shear.void.12Feb07.linux.1 | 160 +++++++++ .../shear/log.shear.void.1Oct06.liberty.4 | 161 --------- examples/shear/log.shear.void.1Oct06.linux.1 | 161 --------- examples/shear/niu3.eam | 304 +++++++++++++++++ 60 files changed, 4000 insertions(+), 3238 deletions(-) create mode 100644 examples/crack/log.crack.12Feb07.liberty.4 rename examples/crack/{log.crack.1Oct06.linux.1 => log.crack.12Feb07.linux.1} (66%) delete mode 100644 examples/crack/log.crack.1Oct06.liberty.4 create mode 100644 examples/flow/log.flow.couette.12Feb07.liberty.4 rename examples/flow/{log.flow.couette.1Oct06.linux.1 => log.flow.couette.12Feb07.linux.1} (50%) delete mode 100644 examples/flow/log.flow.couette.1Oct06.liberty.4 rename examples/flow/{log.flow.poiss.1Oct06.liberty.4 => log.flow.poiss.12Feb07.liberty.4} (51%) rename examples/flow/{log.flow.poiss.1Oct06.linux.1 => log.flow.poiss.12Feb07.linux.1} (54%) create mode 100644 examples/friction/log.friction.12Feb07.liberty.4 create mode 100644 examples/friction/log.friction.12Feb07.linux.1 delete mode 100644 examples/friction/log.friction.1Oct06.liberty.4 delete mode 100644 examples/friction/log.friction.1Oct06.linux.1 create mode 100644 examples/indent/log.indent.12Feb07.liberty.4 create mode 100644 examples/indent/log.indent.12Feb07.linux.1 delete mode 100644 examples/indent/log.indent.1Oct06.liberty.4 delete mode 100644 examples/indent/log.indent.1Oct06.linux.1 rename examples/meam/{data.sic => data.meam} (100%) rename examples/meam/{in.sic => in.meam} (69%) rename examples/meam/{in.shear_meam => in.meam.shear} (94%) create mode 100644 examples/meam/log.meam.12Feb07.liberty.4 create mode 100644 examples/meam/log.meam.12Feb07.linux.1 create mode 100644 examples/meam/log.meam.shear.12Feb07.liberty.4 create mode 100644 examples/meam/log.meam.shear.12Feb07.linux.1 rename examples/melt/{log.melt.1Oct06.liberty.4 => log.melt.12Feb07.liberty.4} (80%) rename examples/melt/{log.melt.1Oct06.linux.1 => log.melt.12Feb07.linux.1} (81%) rename examples/micelle/{log.micelle.1Oct06.liberty.4 => log.micelle.12Feb07.liberty.4} (93%) rename examples/micelle/{log.micelle.1Oct06.linux.1 => log.micelle.12Feb07.linux.1} (93%) rename examples/min/{log.min.1Oct06.liberty.4 => log.min.12Feb07.liberty.4} (84%) rename examples/min/{log.min.1Oct06.linux.1 => log.min.12Feb07.linux.1} (85%) create mode 100644 examples/obstacle/log.obstacle.12Feb07.liberty.4 create mode 100644 examples/obstacle/log.obstacle.12Feb07.linux.1 delete mode 100644 examples/obstacle/log.obstacle.1Oct06.liberty.4 delete mode 100644 examples/obstacle/log.obstacle.1Oct06.linux.1 create mode 100644 examples/peptide/log.peptide.12Feb07.liberty.4 create mode 100644 examples/peptide/log.peptide.12Feb07.linux.1 delete mode 100644 examples/peptide/log.peptide.1Oct06.liberty.4 delete mode 100644 examples/peptide/log.peptide.1Oct06.linux.1 create mode 100644 examples/pour/log.pour.12Feb07.liberty.4 create mode 100644 examples/pour/log.pour.12Feb07.linux.1 delete mode 100644 examples/pour/log.pour.1Oct06.liberty.4 delete mode 100644 examples/pour/log.pour.1Oct06.linux.1 rename examples/pour/{log.pour.2d.1Oct06.liberty.4 => log.pour.2d.12Feb07.liberty.4} (84%) rename examples/pour/{log.pour.2d.1Oct06.linux.1 => log.pour.2d.12Feb07.linux.1} (84%) rename examples/rigid/{log.rigid.1Oct06.liberty.4 => log.rigid.12Feb07.liberty.4} (98%) rename examples/rigid/{log.rigid.1Oct06.linux.1 => log.rigid.12Feb07.linux.1} (98%) rename examples/rigid/{log.rigid.poems.1Oct06.liberty.4 => log.rigid.poems.12Feb07.liberty.4} (98%) create mode 100644 examples/rigid/log.rigid.poems.12Feb07.linux.1 delete mode 100644 examples/rigid/log.rigid.poems.1Oct06.linux.1 rename examples/rigid/{log.rigid.poems2.1Oct06.liberty.4 => log.rigid.poems2.12Feb07.liberty.4} (98%) create mode 100644 examples/rigid/log.rigid.poems2.12Feb07.linux.1 delete mode 100644 examples/rigid/log.rigid.poems2.1Oct06.linux.1 create mode 100644 examples/shear/log.shear.12Feb07.liberty.4 create mode 100644 examples/shear/log.shear.12Feb07.linux.1 delete mode 100644 examples/shear/log.shear.1Oct06.liberty.4 delete mode 100644 examples/shear/log.shear.1Oct06.linux.1 create mode 100644 examples/shear/log.shear.void.12Feb07.liberty.4 create mode 100644 examples/shear/log.shear.void.12Feb07.linux.1 delete mode 100644 examples/shear/log.shear.void.1Oct06.liberty.4 delete mode 100644 examples/shear/log.shear.void.1Oct06.linux.1 create mode 100755 examples/shear/niu3.eam diff --git a/examples/crack/log.crack.12Feb07.liberty.4 b/examples/crack/log.crack.12Feb07.liberty.4 new file mode 100644 index 0000000000..61cb406d6b --- /dev/null +++ b/examples/crack/log.crack.12Feb07.liberty.4 @@ -0,0 +1,154 @@ +LAMMPS (12 Feb 2007) +# 2d LJ crack simulation + +dimension 2 +boundary s s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.93 +Lattice spacing in x,y,z = 1.11428 1.92998 1.11428 +region box block 0 100 0 40 -0.25 0.25 +create_box 5 box +Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569) + 2 by 2 by 1 processor grid +create_atoms 1 +Created 8141 atoms + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 +mass 4 1.0 +mass 5 1.0 + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +302 atoms in group lower +region 2 block INF INF 38.75 INF INF INF +group upper region 2 +302 atoms in group upper +group boundary union lower upper +604 atoms in group boundary +group mobile subtract all boundary +7537 atoms in group mobile + +region leftupper block INF 20 20 INF INF INF +region leftlower block INF 20 INF 20 INF INF +group leftupper region leftupper +820 atoms in group leftupper +group leftlower region leftlower +841 atoms in group leftlower + +set leftupper atom 2 + 820 settings made +set leftlower atom 3 + 841 settings made +set lower atom 4 + 302 settings made +set upper atom 5 + 302 settings made + +# initial velocities + +compute new mobile temp +velocity mobile create 0.01 887723 temp new +velocity upper set 0.0 0.02 0.0 +velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes + +# fixes + +fix 1 all nve +fix 2 boundary setforce NULL 0.0 0.0 + +# run + +timestep 0.003 +thermo 1000 +thermo_modify temp new + +neigh_modify exclude type 2 3 +dump 1 all atom 250 dump.crack +run 50000 +Memory usage per processor = 1.59725 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.010256158 -3.2595015 0 -3.2500081 -0.10145141 4792.6107 + 1000 0.0050480673 -3.2546391 0 -3.2499665 -0.12639136 4792.6107 + 2000 0.0051369915 -3.2543578 0 -3.2496028 -0.15975041 4807.2492 + 3000 0.0052553075 -3.2540343 0 -3.2491699 -0.1774021 4810.8238 + 4000 0.0050641166 -3.2533514 0 -3.2486639 -0.19022921 4811.9955 + 5000 0.0050025515 -3.2525683 0 -3.2479378 -0.24015028 4816.2645 + 6000 0.0049701482 -3.2516756 0 -3.2470751 -0.30916368 4828.9736 + 7000 0.0051250335 -3.2507402 0 -3.2459963 -0.39169622 4833.0704 + 8000 0.0048713476 -3.2493641 0 -3.2448551 -0.47693724 4840.7084 + 9000 0.0049779793 -3.2481153 0 -3.2435076 -0.53299012 4846.9925 + 10000 0.0049128574 -3.2466686 0 -3.2421212 -0.55373718 4857.8418 + 11000 0.0049168986 -3.2450986 0 -3.2405474 -0.55984041 4861.948 + 12000 0.0048612336 -3.2434103 0 -3.2389106 -0.58141697 4864.2222 + 13000 0.0047721181 -3.2414759 0 -3.2370587 -0.62552646 4869.2639 + 14000 0.0048830775 -3.2396196 0 -3.2350997 -0.69800852 4875.2845 + 15000 0.0048743586 -3.2375595 0 -3.2330476 -0.76818454 4889.0238 + 16000 0.0046772021 -3.2352919 0 -3.2309626 -0.82750427 4897.7014 + 17000 0.0047699454 -3.2330635 0 -3.2286483 -0.8579342 4904.3594 + 18000 0.0047753426 -3.2307014 0 -3.2262813 -0.86808974 4910.4271 + 19000 0.0047514879 -3.2281706 0 -3.2237725 -0.85125679 4912.8684 + 20000 0.0048479568 -3.2256981 0 -3.2212107 -0.83903361 4916.6492 + 21000 0.0050005972 -3.223304 0 -3.2186754 -0.86141301 4923.3107 + 22000 0.0051837721 -3.2210129 0 -3.2162147 -0.91497358 4935.0337 + 23000 0.0055014883 -3.2187173 0 -3.213625 -0.98259066 4945.2474 + 24000 0.0059415321 -3.2164221 0 -3.2109225 -1.0173765 4957.1622 + 25000 0.0064260911 -3.2142138 0 -3.2082656 -0.99854249 4959.1051 + 26000 0.0068764456 -3.2118739 0 -3.2055089 -0.96174337 4961.1023 + 27000 0.0067647514 -3.2089962 0 -3.2027346 -0.91577995 4957.1713 + 28000 0.0073747742 -3.2067583 0 -3.199932 -0.9190562 4964.7136 + 29000 0.0081414686 -3.2046855 0 -3.1971496 -0.97705845 4980.1961 + 30000 0.0088053861 -3.2024749 0 -3.1943244 -0.99081318 4997.4212 + 31000 0.0093650101 -3.2005673 0 -3.1918989 -1.0220683 5011.6892 + 32000 0.0098581693 -3.1984747 0 -3.1893498 -1.0266826 5014.6599 + 33000 0.011028173 -3.1969382 0 -3.1867302 -0.94832256 5010.2518 + 34000 0.011643915 -3.1949468 0 -3.184169 -0.90746422 5017.2254 + 35000 0.01332772 -3.1938256 0 -3.1814891 -0.85591111 5047.1343 + 36000 0.014454124 -3.1918323 0 -3.1784532 -0.86634436 5054.2179 + 37000 0.016378188 -3.190944 0 -3.175784 -0.92602308 5077.4837 + 38000 0.017843754 -3.1898052 0 -3.1732887 -0.90546324 5086.0006 + 39000 0.019366756 -3.1887586 0 -3.1708323 -0.80190332 5089.7603 + 40000 0.022135202 -3.1894278 0 -3.168939 -0.71192011 5093.5652 + 41000 0.024807374 -3.1902712 0 -3.1673089 -0.629612 5095.3221 + 42000 0.027696152 -3.1913199 0 -3.1656837 -0.65566924 5086.8449 + 43000 0.028906545 -3.1904171 0 -3.1636605 -0.62599838 5095.1026 + 44000 0.029856229 -3.1894006 0 -3.161765 -0.63227312 5109.8945 + 45000 0.031334749 -3.1888949 0 -3.1598907 -0.62759443 5122.9902 + 46000 0.034602854 -3.1903219 0 -3.1582927 -0.67305941 5123.8907 + 47000 0.034415071 -3.1883711 0 -3.1565157 -0.67895291 5133.6318 + 48000 0.035822122 -3.188003 0 -3.1548452 -0.56873296 5146.4656 + 49000 0.035461417 -3.1863792 0 -3.1535553 -0.49114989 5146.0215 + 50000 0.036039942 -3.1854474 0 -3.152088 -0.47443899 5165.9937 +Loop time of 71.7721 on 4 procs for 50000 steps with 8141 atoms + +Pair time (%) = 45.6852 (63.6532) +Neigh time (%) = 0.910263 (1.26827) +Comm time (%) = 11.0603 (15.4103) +Outpt time (%) = 3.16426 (4.40877) +Other time (%) = 10.9521 (15.2595) + +Nlocal: 2035.25 ave 2093 max 1983 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 201.5 ave 246 max 141 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 17745.5 ave 18295 max 17485 min +Histogram: 2 1 0 0 0 0 0 0 0 1 + +Total # of neighbors = 70982 +Ave neighs/atom = 8.71908 +Neighbor list builds = 491 +Dangerous builds = 0 diff --git a/examples/crack/log.crack.1Oct06.linux.1 b/examples/crack/log.crack.12Feb07.linux.1 similarity index 66% rename from examples/crack/log.crack.1Oct06.linux.1 rename to examples/crack/log.crack.12Feb07.linux.1 index f55529a69f..ab853d017c 100644 --- a/examples/crack/log.crack.1Oct06.linux.1 +++ b/examples/crack/log.crack.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2d LJ crack simulation dimension 2 @@ -11,6 +11,7 @@ neigh_modify delay 5 # create geometry lattice hex 0.93 +Lattice spacing in x,y,z = 1.11428 1.92998 1.11428 region box block 0 100 0 40 -0.25 0.25 create_box 5 box Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569) @@ -45,12 +46,12 @@ group mobile subtract all boundary 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 +820 atoms in group leftupper group leftlower region leftlower 841 atoms in group leftlower set leftupper atom 2 - 841 settings made + 820 settings made set leftlower atom 3 841 settings made set lower atom 4 @@ -60,7 +61,7 @@ set upper atom 5 # initial velocities -temperature new mobile full +compute new mobile temp velocity mobile create 0.01 887723 temp new velocity upper set 0.0 0.02 0.0 velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes @@ -112,42 +113,42 @@ Step Temp E_pair E_mol TotEng Press Volume 28000 0.0068038044 -3.2067846 0 -3.2004869 -0.86598793 4967.889 29000 0.0077170662 -3.2049416 0 -3.1977985 -0.91334819 4981.938 30000 0.0081816546 -3.2027043 0 -3.1951312 -0.9653003 4996.292 - 31000 0.0089120183 -3.2008682 0 -3.192619 -0.99183521 5012.9271 - 32000 0.0095675927 -3.1988646 0 -3.1900086 -0.98991289 5018.881 - 33000 0.010803232 -3.1974474 0 -3.1874477 -0.94112062 5012.4944 - 34000 0.011158339 -3.195224 0 -3.1848955 -0.88514756 5006.3799 - 35000 0.011756548 -3.193118 0 -3.1822359 -0.83787516 5002.794 - 36000 0.011908147 -3.1908085 0 -3.179786 -0.82041392 5013.2137 - 37000 0.01424843 -3.1903622 0 -3.1771736 -0.86593745 5045.4358 - 38000 0.015513677 -3.1889279 0 -3.1745681 -0.84618406 5058.7819 - 39000 0.017516672 -3.1885197 0 -3.1723059 -0.73798007 5086.8443 - 40000 0.019448731 -3.1885754 0 -3.1705732 -0.59681319 5093.1044 - 41000 0.021088915 -3.1885922 0 -3.1690718 -0.5085097 5089.6132 - 42000 0.023948616 -3.1898036 0 -3.1676362 -0.45605083 5082.7572 - 43000 0.025588509 -3.1896794 0 -3.1659941 -0.34855967 5111.1438 - 44000 0.027568866 -3.1906457 0 -3.1651273 -0.41081127 5116.295 - 45000 0.028445821 -3.1899978 0 -3.1636677 -0.36970991 5130.3322 - 46000 0.028961863 -3.1898316 0 -3.1630238 -0.30874643 5129.4113 - 47000 0.029932222 -3.1901868 0 -3.1624809 -0.28285013 5154.4915 - 48000 0.030490267 -3.1898412 0 -3.1616187 -0.29218244 5175.3972 - 49000 0.031743277 -3.1900262 0 -3.1606438 -0.26145795 5180.1115 - 50000 0.031723195 -3.1891208 0 -3.1597571 -0.2519514 5202.1573 -Loop time of 512.873 on 1 procs for 50000 steps with 8141 atoms + 31000 0.0089120184 -3.2008682 0 -3.192619 -0.99183522 5012.9271 + 32000 0.0095675926 -3.1988646 0 -3.1900086 -0.98991289 5018.881 + 33000 0.010803233 -3.1974474 0 -3.1874477 -0.94112056 5012.4944 + 34000 0.011158338 -3.195224 0 -3.1848955 -0.8851475 5006.3799 + 35000 0.011756558 -3.193118 0 -3.1822359 -0.83787524 5002.794 + 36000 0.011908028 -3.1908083 0 -3.179786 -0.82041394 5013.2137 + 37000 0.014248791 -3.1903606 0 -3.1771716 -0.86591483 5045.4357 + 38000 0.015514642 -3.1889367 0 -3.1745759 -0.84629532 5058.8659 + 39000 0.017625744 -3.1886096 0 -3.1722948 -0.72912473 5086.8791 + 40000 0.020166221 -3.1891916 0 -3.1705253 -0.57976268 5092.6354 + 41000 0.024585629 -3.191961 0 -3.169204 -0.45986861 5092.2489 + 42000 0.025792679 -3.191911 0 -3.1680367 -0.41104431 5084.743 + 43000 0.027413976 -3.1918738 0 -3.1664988 -0.317039 5103.4238 + 44000 0.029084803 -3.1924106 0 -3.165489 -0.35382128 5093.6381 + 45000 0.028426053 -3.1910339 0 -3.1647221 -0.40685905 5115.0911 + 46000 0.028866755 -3.190439 0 -3.1637193 -0.44541816 5121.2964 + 47000 0.02908918 -3.189657 0 -3.1627313 -0.4265388 5149.429 + 48000 0.028710143 -3.1882276 0 -3.1616528 -0.45494173 5166.6376 + 49000 0.03082438 -3.1885404 0 -3.1600086 -0.4068 5164.3287 + 50000 0.032521821 -3.1887517 0 -3.1586487 -0.31047628 5170.302 +Loop time of 449.517 on 1 procs for 50000 steps with 8141 atoms -Pair time (%) = 421.19 (82.1237) -Neigh time (%) = 6.63742 (1.29416) -Comm time (%) = 0.619009 (0.120694) -Outpt time (%) = 7.54941 (1.47198) -Other time (%) = 76.8767 (14.9894) +Pair time (%) = 363.166 (80.7903) +Neigh time (%) = 6.23528 (1.38711) +Comm time (%) = 0.552309 (0.122867) +Outpt time (%) = 7.92898 (1.76389) +Other time (%) = 71.6341 (15.9358) Nlocal: 8141 ave 8141 max 8141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 70611 ave 70611 max 70611 min +Neighs: 70714 ave 70714 max 70714 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 70611 -Ave neighs/atom = 8.6735 -Neighbor list builds = 495 +Total # of neighbors = 70714 +Ave neighs/atom = 8.68616 +Neighbor list builds = 488 Dangerous builds = 0 diff --git a/examples/crack/log.crack.1Oct06.liberty.4 b/examples/crack/log.crack.1Oct06.liberty.4 deleted file mode 100644 index f28eb66433..0000000000 --- a/examples/crack/log.crack.1Oct06.liberty.4 +++ /dev/null @@ -1,153 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 100 0 40 -0.25 0.25 -create_box 5 box -Created box = (0 0 -0.278569) to (111.428 77.1994 0.278569) - 2 by 2 by 1 processor grid -create_atoms 1 -Created 8141 atoms - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 -mass 4 1.0 -mass 5 1.0 - -# LJ potentials - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -302 atoms in group lower -region 2 block INF INF 38.75 INF INF INF -group upper region 2 -302 atoms in group upper -group boundary union lower upper -604 atoms in group boundary -group mobile subtract all boundary -7537 atoms in group mobile - -region leftupper block INF 20 20 INF INF INF -region leftlower block INF 20 INF 20 INF INF -group leftupper region leftupper -841 atoms in group leftupper -group leftlower region leftlower -841 atoms in group leftlower - -set leftupper atom 2 - 841 settings made -set leftlower atom 3 - 841 settings made -set lower atom 4 - 302 settings made -set upper atom 5 - 302 settings made - -# initial velocities - -temperature new mobile full -velocity mobile create 0.01 887723 temp new -velocity upper set 0.0 0.02 0.0 -velocity mobile ramp vy 0.0 0.02 y 1.25 38.75 sum yes - -# fixes - -fix 1 all nve -fix 2 boundary setforce NULL 0.0 0.0 - -# run - -timestep 0.003 -thermo 1000 -thermo_modify temp new - -neigh_modify exclude type 2 3 -dump 1 all atom 250 dump.crack -run 50000 -Memory usage per processor = 1.59725 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.010256205 -3.2595015 0 -3.2500081 -0.10145136 4792.6107 - 1000 0.0050437246 -3.254635 0 -3.2499665 -0.12740271 4792.6107 - 2000 0.0051505282 -3.2543692 0 -3.2496018 -0.15978403 4805.4017 - 3000 0.0052701189 -3.2540454 0 -3.2491672 -0.17795883 4809.4575 - 4000 0.0050604962 -3.2533431 0 -3.2486589 -0.18962575 4812.2411 - 5000 0.0049888551 -3.2525578 0 -3.24794 -0.23962697 4815.939 - 6000 0.0049676582 -3.251678 0 -3.2470799 -0.30927631 4820.4945 - 7000 0.0051188772 -3.2507304 0 -3.2459922 -0.3909741 4828.8381 - 8000 0.0048922662 -3.2493836 0 -3.2448552 -0.47790517 4841.9077 - 9000 0.0049338477 -3.2480837 0 -3.2435168 -0.53340641 4849.3327 - 10000 0.0049211223 -3.2466777 0 -3.2421226 -0.55379297 4855.6764 - 11000 0.004895836 -3.2450776 0 -3.2405459 -0.56007065 4862.5721 - 12000 0.004847489 -3.2434006 0 -3.2389137 -0.57998486 4863.9277 - 13000 0.0047955582 -3.2415024 0 -3.2370635 -0.62542252 4870.6003 - 14000 0.0048552089 -3.2396028 0 -3.2351087 -0.697236 4879.871 - 15000 0.0048752032 -3.2375516 0 -3.233039 -0.76918523 4884.5734 - 16000 0.0046965458 -3.2352968 0 -3.2309496 -0.82908331 4893.1926 - 17000 0.0047868592 -3.2330762 0 -3.2286454 -0.85754888 4901.71 - 18000 0.0047852616 -3.2307132 0 -3.2262838 -0.86919067 4909.8698 - 19000 0.0047361082 -3.2281639 0 -3.2237801 -0.85109691 4912.5836 - 20000 0.0048659736 -3.2257135 0 -3.2212095 -0.83986478 4916.5374 - 21000 0.0049814043 -3.2232926 0 -3.2186817 -0.86128523 4923.9807 - 22000 0.0049472744 -3.2207762 0 -3.2161969 -0.90337572 4931.7271 - 23000 0.0053349592 -3.218575 0 -3.2136369 -0.97893232 4945.9715 - 24000 0.0057755443 -3.2162642 0 -3.2109182 -1.0095182 4956.3791 - 25000 0.0062190601 -3.2140052 0 -3.2082487 -1.0088874 4960.5377 - 26000 0.0068001305 -3.2117942 0 -3.2054998 -0.96727393 4962.4079 - 27000 0.0068225494 -3.2091441 0 -3.2028289 -0.91504959 4962.4468 - 28000 0.0069100602 -3.2064225 0 -3.2000264 -0.9131624 4963.4009 - 29000 0.0077073146 -3.2044225 0 -3.1972885 -0.97931905 4976.6434 - 30000 0.0085530911 -3.2023628 0 -3.1944458 -1.0335604 4991.859 - 31000 0.0090489847 -3.2000739 0 -3.191698 -1.0499238 5006.1205 - 32000 0.009457073 -3.197803 0 -3.1890493 -1.0415395 5007.1136 - 33000 0.0097449781 -3.1954191 0 -3.1863989 -0.97523426 5008.9351 - 34000 0.010638648 -3.1933196 0 -3.1834722 -0.90641914 5009.8972 - 35000 0.011724943 -3.1915042 0 -3.1806513 -0.86280832 5030.2601 - 36000 0.012543854 -3.1897197 0 -3.1781088 -0.84498685 5058.0726 - 37000 0.01425216 -3.1884117 0 -3.1752195 -0.89131599 5072.3266 - 38000 0.017711377 -3.188949 0 -3.1725549 -0.83909256 5084.0891 - 39000 0.022008898 -3.19099 0 -3.1706181 -0.75142283 5087.7576 - 40000 0.026220897 -3.1935289 0 -3.1692583 -0.62636117 5093.7415 - 41000 0.025508399 -3.1919886 0 -3.1683775 -0.42605643 5088.3384 - 42000 0.026889328 -3.192089 0 -3.1671996 -0.34017637 5066.1245 - 43000 0.028720644 -3.1925244 0 -3.1659399 -0.19561049 5083.1913 - 44000 0.031213331 -3.1937329 0 -3.1648411 -0.35065498 5095.7582 - 45000 0.031451475 -3.1922953 0 -3.1631831 -0.53502981 5109.9177 - 46000 0.030623132 -3.1903208 0 -3.1619753 -0.55300441 5125.4041 - 47000 0.031375 -3.1895766 0 -3.1605352 -0.5385838 5157.0846 - 48000 0.030875482 -3.1879308 0 -3.1593517 -0.48509753 5161.8136 - 49000 0.031761391 -3.1879906 0 -3.1585915 -0.44146775 5160.5089 - 50000 0.032235944 -3.1871767 0 -3.1573383 -0.38658394 5152.5279 -Loop time of 71.1028 on 4 procs for 50000 steps with 8141 atoms - -Pair time (%) = 45.4344 (63.8997) -Neigh time (%) = 0.87692 (1.23331) -Comm time (%) = 10.6446 (14.9707) -Outpt time (%) = 2.95593 (4.15726) -Other time (%) = 11.1909 (15.7391) - -Nlocal: 2035.25 ave 2081 max 1974 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 203.5 ave 245 max 162 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 17703.8 ave 18117 max 17273 min -Histogram: 1 1 0 0 0 0 0 0 1 1 - -Total # of neighbors = 70815 -Ave neighs/atom = 8.69856 -Neighbor list builds = 467 -Dangerous builds = 0 diff --git a/examples/flow/log.flow.couette.12Feb07.liberty.4 b/examples/flow/log.flow.couette.12Feb07.liberty.4 new file mode 100644 index 0000000000..9a884e84bc --- /dev/null +++ b/examples/flow/log.flow.couette.12Feb07.liberty.4 @@ -0,0 +1,122 @@ +LAMMPS (12 Feb 2007) +# 2-d LJ flow simulation + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 +region box block 0 20 0 10 -0.25 0.25 +create_box 3 box +Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) + 2 by 2 by 1 processor grid +create_atoms 1 +Created 420 atoms + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials + +pair_style lj/cut 1.12246 +pair_coeff * * 1.0 1.0 1.12246 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +60 atoms in group lower +region 2 block INF INF 8.75 INF INF INF +group upper region 2 +60 atoms in group upper +group boundary union lower upper +120 atoms in group boundary +group flow subtract all boundary +300 atoms in group flow + +set lower atom 2 + 60 settings made +set upper atom 3 + 60 settings made + +# initial velocities + +compute mobile flow temp +velocity flow create 1.0 482748 temp mobile +fix 1 all nve +fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 +fix_modify 2 temp mobile + +# Couette flow + +velocity lower set 0.0 0.0 0.0 +velocity upper set 3.0 0.0 0.0 +fix 3 boundary setforce 0.0 0.0 0.0 +fix 4 all enforce2d + +# Poisseuille flow + +#velocity boundary set 0.0 0.0 0.0 +#fix 3 lower setforce 0.0 0.0 0.0 +#fix 4 upper setforce 0.0 NULL 0.0 +#fix 5 upper aveforce 0.0 -1.0 0.0 +#fix 6 flow addforce 0.5 0.0 0.0 +#fix 7 all enforce2d + +# Run + +timestep 0.003 +thermo 500 +thermo_modify temp mobile + +dump 1 all atom 50 dump.flow +run 10000 +Memory usage per processor = 1.44615 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 0 0 0.71071429 0.54228995 366.96236 + 500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236 + 1000 1 -0.36129869 0 0.3494156 3.254923 366.96236 + 1500 1.1299217 -0.37859354 0 0.42445794 3.0386512 366.96236 + 2000 1 -0.34287549 0 0.3678388 3.1412475 366.96236 + 2500 1.0894638 -0.38358068 0 0.3907168 2.9575357 366.96236 + 3000 1 -0.38250431 0 0.32820997 2.9128345 366.96236 + 3500 1.1577825 -0.41389292 0 0.40895962 3.0892503 366.96236 + 4000 1 -0.42306155 0 0.28765273 2.5216835 366.96236 + 4500 1.0340697 -0.39435146 0 0.34057665 2.5709158 366.96236 + 5000 1 -0.43445662 0 0.27625767 2.7074512 366.96236 + 5500 1.1091102 -0.45430683 0 0.33395366 2.451199 366.96236 + 6000 1 -0.41166346 0 0.29905082 2.7464633 366.96236 + 6500 1.0003563 -0.40533723 0 0.30563029 2.5834633 366.96236 + 7000 1 -0.3904519 0 0.32026238 2.5201459 366.96236 + 7500 1.1170747 -0.40190088 0 0.39202009 2.6487896 366.96236 + 8000 1 -0.46477384 0 0.24594045 2.6442771 366.96236 + 8500 1.1344912 -0.38276439 0 0.4235347 2.7888644 366.96236 + 9000 1 -0.39709912 0 0.31361516 2.4730908 366.96236 + 9500 0.99852413 -0.45682444 0 0.25284093 2.3290285 366.96236 + 10000 1 -0.45069251 0 0.26002177 2.5361799 366.96236 +Loop time of 2.01982 on 4 procs for 10000 steps with 420 atoms + +Pair time (%) = 0.0898595 (4.4489) +Neigh time (%) = 0.0443295 (2.19473) +Comm time (%) = 1.36553 (67.6066) +Outpt time (%) = 0.164397 (8.13922) +Other time (%) = 0.355701 (17.6106) + +Nlocal: 105 ave 115 max 96 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 40.25 ave 44 max 37 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 237.5 ave 296 max 179 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 950 +Ave neighs/atom = 2.2619 +Neighbor list builds = 984 +Dangerous builds = 0 diff --git a/examples/flow/log.flow.couette.1Oct06.linux.1 b/examples/flow/log.flow.couette.12Feb07.linux.1 similarity index 50% rename from examples/flow/log.flow.couette.1Oct06.linux.1 rename to examples/flow/log.flow.couette.12Feb07.linux.1 index 9323ba7680..e5083890cd 100644 --- a/examples/flow/log.flow.couette.1Oct06.linux.1 +++ b/examples/flow/log.flow.couette.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2-d LJ flow simulation dimension 2 @@ -11,6 +11,7 @@ neigh_modify delay 5 # create geometry lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 region box block 0 20 0 10 -0.25 0.25 create_box 3 box Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) @@ -47,7 +48,7 @@ set upper atom 3 # initial velocities -temperature mobile flow full +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 @@ -82,40 +83,40 @@ Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71071429 0.54228995 366.96236 500 1.0604224 -0.31549525 0 0.4381621 3.1208962 366.96236 1000 1 -0.34356865 0 0.36714563 3.0305145 366.96236 - 1500 1.1738082 -0.38202601 0 0.45221625 2.9197883 366.96236 - 2000 1 -0.42682396 0 0.28389033 2.8469301 366.96236 - 2500 1.024752 -0.41856176 0 0.30974413 2.9396683 366.96236 - 3000 1 -0.43670738 0 0.27400691 2.7241981 366.96236 - 3500 1.0895615 -0.42577755 0 0.34858934 2.6026891 366.96236 - 4000 1 -0.44573495 0 0.26497934 2.4799192 366.96236 - 4500 1.0711285 -0.4375466 0 0.32371976 2.8408151 366.96236 - 5000 1 -0.46692482 0 0.24378947 2.7249453 366.96236 - 5500 1.0960047 -0.497188 0 0.28175821 2.5610363 366.96236 - 6000 1 -0.4129622 0 0.29775209 2.3978555 366.96236 - 6500 1.0887159 -0.39206737 0 0.3816986 2.5437398 366.96236 - 7000 1 -0.36776877 0 0.34294551 2.7427873 366.96236 - 7500 1.1794747 -0.45276333 0 0.38550621 2.4854834 366.96236 - 8000 1 -0.42255618 0 0.2881581 2.5061969 366.96236 - 8500 1.098024 -0.45909879 0 0.32128255 2.4143874 366.96236 - 9000 1 -0.42247096 0 0.28824333 2.2773041 366.96236 - 9500 1.1248064 -0.40810854 0 0.39130741 2.1964254 366.96236 - 10000 1 -0.36640887 0 0.34430541 2.4787391 366.96236 -Loop time of 2.20605 on 1 procs for 10000 steps with 420 atoms + 1500 1.1738082 -0.382026 0 0.45221626 2.9197883 366.96236 + 2000 1 -0.42682511 0 0.28388918 2.8469183 366.96236 + 2500 1.0256109 -0.41905835 0 0.30985794 2.9371918 366.96236 + 3000 1 -0.47521752 0 0.23549677 2.5062527 366.96236 + 3500 1.1314909 -0.4206347 0 0.38353207 2.7478302 366.96236 + 4000 1 -0.43576251 0 0.27495178 2.6141195 366.96236 + 4500 1.0005992 -0.42588084 0 0.28525931 2.7421664 366.96236 + 5000 1 -0.42282912 0 0.28788516 2.7688981 366.96236 + 5500 1.0686835 -0.4761288 0 0.28339982 2.5689028 366.96236 + 6000 1 -0.42978507 0 0.28092922 2.6551983 366.96236 + 6500 1.0786904 -0.43713715 0 0.3295035 2.5141669 366.96236 + 7000 1 -0.4121221 0 0.29859218 2.594973 366.96236 + 7500 1.0939854 -0.40293252 0 0.37457856 2.6974983 366.96236 + 8000 1 -0.45181425 0 0.25890004 2.6049049 366.96236 + 8500 1.0257333 -0.400669 0 0.32833428 2.5577387 366.96236 + 9000 1 -0.42858125 0 0.28213304 2.5725646 366.96236 + 9500 1.0823613 -0.38920599 0 0.38004366 2.6543624 366.96236 + 10000 1 -0.42341732 0 0.28729697 2.4806728 366.96236 +Loop time of 2.23208 on 1 procs for 10000 steps with 420 atoms -Pair time (%) = 0.754591 (34.2056) -Neigh time (%) = 0.308539 (13.9861) -Comm time (%) = 0.107975 (4.8945) -Outpt time (%) = 0.41017 (18.593) -Other time (%) = 0.624773 (28.3209) +Pair time (%) = 0.69644 (31.2014) +Neigh time (%) = 0.270545 (12.1208) +Comm time (%) = 0.109265 (4.89521) +Outpt time (%) = 0.417752 (18.7158) +Other time (%) = 0.738079 (33.0669) Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 50 ave 50 max 50 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 957 ave 957 max 957 min +Neighs: 955 ave 955 max 955 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 957 -Ave neighs/atom = 2.27857 -Neighbor list builds = 1000 +Total # of neighbors = 955 +Ave neighs/atom = 2.27381 +Neighbor list builds = 1003 Dangerous builds = 0 diff --git a/examples/flow/log.flow.couette.1Oct06.liberty.4 b/examples/flow/log.flow.couette.1Oct06.liberty.4 deleted file mode 100644 index 42318dc8ed..0000000000 --- a/examples/flow/log.flow.couette.1Oct06.liberty.4 +++ /dev/null @@ -1,121 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 20 0 10 -0.25 0.25 -create_box 3 box -Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) - 2 by 2 by 1 processor grid -create_atoms 1 -Created 420 atoms - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 - -# LJ potentials - -pair_style lj/cut 1.12246 -pair_coeff * * 1.0 1.0 1.12246 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -60 atoms in group lower -region 2 block INF INF 8.75 INF INF INF -group upper region 2 -60 atoms in group upper -group boundary union lower upper -120 atoms in group boundary -group flow subtract all boundary -300 atoms in group flow - -set lower atom 2 - 60 settings made -set upper atom 3 - 60 settings made - -# initial velocities - -temperature mobile flow full -velocity flow create 1.0 482748 temp mobile -fix 1 all nve -fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 -fix_modify 2 temp mobile - -# Couette flow - -velocity lower set 0.0 0.0 0.0 -velocity upper set 3.0 0.0 0.0 -fix 3 boundary setforce 0.0 0.0 0.0 -fix 4 all enforce2d - -# Poisseuille flow - -#velocity boundary set 0.0 0.0 0.0 -#fix 3 lower setforce 0.0 0.0 0.0 -#fix 4 upper setforce 0.0 NULL 0.0 -#fix 5 upper aveforce 0.0 -1.0 0.0 -#fix 6 flow addforce 0.5 0.0 0.0 -#fix 7 all enforce2d - -# Run - -timestep 0.003 -thermo 500 -thermo_modify temp mobile - -dump 1 all atom 50 dump.flow -run 10000 -Memory usage per processor = 1.44615 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1 0 0 0.71071429 0.54228995 366.96236 - 500 1.0967867 -0.3465085 0 0.43299345 3.3754137 366.96236 - 1000 1 -0.36129869 0 0.3494156 3.254923 366.96236 - 1500 1.1299217 -0.37859354 0 0.42445795 3.0386513 366.96236 - 2000 1 -0.34287377 0 0.36784052 3.1412593 366.96236 - 2500 1.0899881 -0.38633626 0 0.38833382 2.9555542 366.96236 - 3000 1 -0.39357685 0 0.31713744 2.9220544 366.96236 - 3500 1.0725076 -0.43228066 0 0.32996578 3.0634077 366.96236 - 4000 0.98425607 -0.50499218 0 0.19453267 2.6894642 366.96236 - 4500 1.12295 -0.43026613 0 0.36783048 2.8383488 366.96236 - 5000 1 -0.38936492 0 0.32134937 2.7396424 366.96236 - 5500 1.0704014 -0.42922975 0 0.33151984 2.9491395 366.96236 - 6000 1 -0.44518162 0 0.26553266 2.558761 366.96236 - 6500 1.027497 -0.39375667 0 0.33650011 2.6024776 366.96236 - 7000 1 -0.36769731 0 0.34301697 2.5197126 366.96236 - 7500 1.0817191 -0.41108702 0 0.35770623 2.5206643 366.96236 - 8000 1 -0.38737307 0 0.32334122 2.9522698 366.96236 - 8500 1.1947509 -0.43799992 0 0.4111266 2.5630133 366.96236 - 9000 1 -0.37870561 0 0.33200868 3.0568213 366.96236 - 9500 1.1262643 -0.38699772 0 0.41345443 2.631997 366.96236 - 10000 1 -0.39282605 0 0.31788823 2.7840067 366.96236 -Loop time of 1.95426 on 4 procs for 10000 steps with 420 atoms - -Pair time (%) = 0.093526 (4.78575) -Neigh time (%) = 0.0450768 (2.30659) -Comm time (%) = 1.28476 (65.7414) -Outpt time (%) = 0.177726 (9.0943) -Other time (%) = 0.353174 (18.072) - -Nlocal: 105 ave 113 max 98 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 41.5 ave 44 max 39 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 239.25 ave 292 max 197 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 957 -Ave neighs/atom = 2.27857 -Neighbor list builds = 997 -Dangerous builds = 0 diff --git a/examples/flow/log.flow.poiss.1Oct06.liberty.4 b/examples/flow/log.flow.poiss.12Feb07.liberty.4 similarity index 51% rename from examples/flow/log.flow.poiss.1Oct06.liberty.4 rename to examples/flow/log.flow.poiss.12Feb07.liberty.4 index a4103b9335..a9ec87575a 100644 --- a/examples/flow/log.flow.poiss.1Oct06.liberty.4 +++ b/examples/flow/log.flow.poiss.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2-d LJ flow simulation dimension 2 @@ -11,6 +11,7 @@ neigh_modify delay 5 # create geometry lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 region box block 0 20 0 10 -0.25 0.25 create_box 3 box Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) @@ -47,7 +48,7 @@ set upper atom 3 # initial velocities -temperature mobile flow full +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 @@ -84,38 +85,38 @@ Step Temp E_pair E_mol TotEng Press Volume 1000 1 -0.38740705 0 0.32330724 2.2684877 375.93354 1500 1.2052679 -0.37768559 0 0.47891551 1.6193029 376.17118 2000 1 -0.38060118 0 0.33011311 1.4972142 371.27032 - 2500 1.2211446 -0.39689946 0 0.47098547 1.5612989 364.09539 - 3000 1 -0.4663268 0 0.24438748 1.5629904 356.17692 - 3500 1.2338563 -0.57458788 0 0.3023314 1.8175737 344.96843 - 4000 1 -0.69828914 0 0.012425149 2.3062239 333.07337 - 4500 1.2223948 -0.68025643 0 0.18851702 3.0030445 323.53576 - 5000 1 -0.77041655 0 -0.059702267 3.1645089 320.77015 - 5500 1.206787 -0.74655306 0 0.11112772 2.6751057 324.35217 - 6000 1 -0.68123467 0 0.029479617 2.3163646 329.78023 - 6500 1.1974539 -0.67787899 0 0.17316861 2.1501471 332.21584 - 7000 1 -0.63878551 0 0.071928781 1.9059071 332.869 - 7500 1.2099494 -0.6450312 0 0.21489713 2.0613881 331.14731 - 8000 1 -0.662565 0 0.048149283 2.1186993 326.88679 - 8500 1.2200684 -0.75842085 0 0.10869919 2.566873 324.24936 - 9000 1 -0.72471449 0 -0.0140002 2.5966104 323.69555 - 9500 1.1858651 -0.72008706 0 0.12272424 2.6583911 324.95806 - 10000 1 -0.6877267 0 0.022987584 2.263132 327.94921 -Loop time of 2.32195 on 4 procs for 10000 steps with 420 atoms + 2500 1.2211446 -0.39689946 0 0.47098548 1.5612989 364.09539 + 3000 1 -0.46394625 0 0.24676803 1.5629864 356.17691 + 3500 1.2338136 -0.5721878 0 0.30470115 1.8177807 344.96808 + 4000 1 -0.69530976 0 0.015404522 2.3144776 333.06418 + 4500 1.2279548 -0.72662695 0 0.14609808 2.9985939 323.55709 + 5000 1 -0.81185506 0 -0.10114077 3.1833009 321.19482 + 5500 1.2171627 -0.73966198 0 0.12539291 2.711954 325.39659 + 6000 1 -0.66983997 0 0.040874311 2.1579634 329.73937 + 6500 1.2267682 -0.66743744 0 0.20444422 2.1114545 331.88829 + 7000 1 -0.64509348 0 0.065620807 1.9028431 332.49532 + 7500 1.2202538 -0.6816503 0 0.18560148 2.1227978 329.88213 + 8000 1 -0.72110847 0 -0.010394181 2.3587956 327.78501 + 8500 1.2103845 -0.76502979 0 0.095207788 2.5823624 325.21722 + 9000 1 -0.75191645 0 -0.041202164 2.4020904 324.81713 + 9500 1.2094179 -0.74196652 0 0.11758403 2.5289414 326.12345 + 10000 1 -0.7568777 0 -0.046163412 2.5601376 326.60462 +Loop time of 2.55875 on 4 procs for 10000 steps with 420 atoms -Pair time (%) = 0.0970009 (4.17756) -Neigh time (%) = 0.026122 (1.125) -Comm time (%) = 1.20093 (51.7207) -Outpt time (%) = 0.296236 (12.758) -Other time (%) = 0.701664 (30.2187) +Pair time (%) = 0.0984794 (3.84874) +Neigh time (%) = 0.0253601 (0.991114) +Comm time (%) = 1.34455 (52.547) +Outpt time (%) = 0.313694 (12.2597) +Other time (%) = 0.776668 (30.3534) -Nlocal: 105 ave 107 max 103 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 41.75 ave 42 max 41 min -Histogram: 1 0 0 0 0 0 0 0 0 3 -Neighs: 279 ave 283 max 274 min -Histogram: 1 0 0 0 1 0 0 1 0 1 +Nlocal: 105 ave 106 max 103 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 43.75 ave 45 max 41 min +Histogram: 1 0 0 0 0 0 0 1 0 2 +Neighs: 276.5 ave 291 max 256 min +Histogram: 1 0 0 1 0 0 0 0 0 2 -Total # of neighbors = 1116 -Ave neighs/atom = 2.65714 -Neighbor list builds = 560 +Total # of neighbors = 1106 +Ave neighs/atom = 2.63333 +Neighbor list builds = 553 Dangerous builds = 0 diff --git a/examples/flow/log.flow.poiss.1Oct06.linux.1 b/examples/flow/log.flow.poiss.12Feb07.linux.1 similarity index 54% rename from examples/flow/log.flow.poiss.1Oct06.linux.1 rename to examples/flow/log.flow.poiss.12Feb07.linux.1 index 0f0c2a204b..1c912a3fed 100644 --- a/examples/flow/log.flow.poiss.1Oct06.linux.1 +++ b/examples/flow/log.flow.poiss.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2-d LJ flow simulation dimension 2 @@ -11,6 +11,7 @@ neigh_modify delay 5 # create geometry lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 region box block 0 20 0 10 -0.25 0.25 create_box 3 box Created box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) @@ -47,7 +48,7 @@ set upper atom 3 # initial velocities -temperature mobile flow full +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 @@ -84,38 +85,38 @@ Step Temp E_pair E_mol TotEng Press Volume 1000 1 -0.40278179 0 0.30793249 2.0566706 375.56836 1500 1.2346487 -0.41204291 0 0.46543956 1.6254791 376.55032 2000 1 -0.40773469 0 0.3029796 1.5174808 374.73899 - 2500 1.2225527 -0.43831256 0 0.43057311 1.538442 366.48806 - 3000 1 -0.49535329 0 0.215361 1.5818851 355.29346 - 3500 1.2493652 -0.59970719 0 0.28823452 1.7494829 344.5223 - 4000 1 -0.67604277 0 0.034671516 2.0751068 332.82226 - 4500 1.1963622 -0.74392294 0 0.10634877 2.9790662 322.98092 - 5000 1 -0.77322139 0 -0.062507105 3.3772359 320.78002 - 5500 1.2048992 -0.77634312 0 0.079995929 2.9951611 324.35044 - 6000 1 -0.68526989 0 0.025444398 2.3511721 331.72304 - 6500 1.2079513 -0.59742461 0 0.26108363 1.8598207 336.52669 - 7000 1 -0.60208737 0 0.10862692 1.9011673 336.55357 - 7500 1.2390152 -0.68215629 0 0.19842954 1.9783028 333.8701 - 8000 1 -0.69342292 0 0.01729137 2.3176685 328.52309 - 8500 1.23233 -0.69508948 0 0.18074504 2.4605225 324.4685 - 9000 1 -0.78017888 0 -0.069464593 2.5102443 323.83769 - 9500 1.2049045 -0.78839912 0 0.067943719 2.6572163 323.67252 - 10000 1 -0.72912664 0 -0.018412351 2.4438564 325.74175 -Loop time of 2.71301 on 1 procs for 10000 steps with 420 atoms + 2500 1.2225527 -0.43831258 0 0.43057311 1.538442 366.48806 + 3000 1 -0.49535282 0 0.21536146 1.5818917 355.29347 + 3500 1.2493993 -0.59973642 0 0.28822953 1.7491905 344.52279 + 4000 1 -0.67338979 0 0.037324493 2.0787539 332.81149 + 4500 1.1956948 -0.72693321 0 0.12286419 3.0234335 322.85596 + 5000 1 -0.74958096 0 -0.038866674 3.2864093 320.05477 + 5500 1.1735028 -0.73256028 0 0.10146491 2.7725647 321.70778 + 6000 1 -0.68197653 0 0.028737759 2.4161345 328.01856 + 6500 1.1989708 -0.63163198 0 0.2204937 2.0979387 331.80767 + 7000 1 -0.65810386 0 0.052610422 2.1889649 331.12128 + 7500 1.2335065 -0.65237655 0 0.22429412 2.1016554 330.36358 + 8000 1 -0.68661166 0 0.024102628 2.1253504 327.99967 + 8500 1.2297323 -0.72995326 0 0.14403503 2.4289517 324.51364 + 9000 1 -0.72767623 0 -0.016961948 2.4354045 323.49316 + 9500 1.2252226 -0.75893761 0 0.1118456 2.5476916 324.00783 + 10000 1 -0.73637225 0 -0.025657963 2.3491973 324.64848 +Loop time of 2.7534 on 1 procs for 10000 steps with 420 atoms -Pair time (%) = 0.850197 (31.3377) -Neigh time (%) = 0.171296 (6.31386) -Comm time (%) = 0.096819 (3.56869) -Outpt time (%) = 0.824351 (30.3851) -Other time (%) = 0.770352 (28.3947) +Pair time (%) = 0.762382 (27.6888) +Neigh time (%) = 0.157095 (5.70549) +Comm time (%) = 0.098925 (3.59283) +Outpt time (%) = 0.84692 (30.7591) +Other time (%) = 0.888077 (32.2538) Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 47 ave 47 max 47 min +Nghost: 53 ave 53 max 53 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1117 ave 1117 max 1117 min +Neighs: 1128 ave 1128 max 1128 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 1117 -Ave neighs/atom = 2.65952 +Total # of neighbors = 1128 +Ave neighs/atom = 2.68571 Neighbor list builds = 558 Dangerous builds = 0 diff --git a/examples/friction/log.friction.12Feb07.liberty.4 b/examples/friction/log.friction.12Feb07.liberty.4 new file mode 100644 index 0000000000..cee41e9bbb --- /dev/null +++ b/examples/friction/log.friction.12Feb07.liberty.4 @@ -0,0 +1,140 @@ +LAMMPS (12 Feb 2007) +# 2d friction simulation + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.9 +Lattice spacing in x,y,z = 1.1327 1.96189 1.1327 +region box block 0 50 0 22 -0.25 0.25 +create_box 4 box +Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174) + 2 by 2 by 1 processor grid + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 +mass 4 1.0 + +# atom regions + +region lo-fixed block INF INF INF 1.1 INF INF +region lo-slab block INF INF INF 7 INF INF +region above-lo block INF INF INF 7 INF INF side out +region hi-fixed block INF INF 20.9 INF INF INF +region hi-slab block INF INF 15 INF INF INF +region below-hi block INF INF 15 INF INF INF side out +region lo-asperity sphere 32 7 0 8 +region hi-asperity sphere 18 15 0 8 +region lo-half-sphere intersect 2 lo-asperity above-lo +region hi-half-sphere intersect 2 hi-asperity below-hi + +# create 2 surfaces with asperities + +create_atoms 1 region lo-slab +Created 750 atoms +create_atoms 1 region hi-slab +Created 750 atoms +create_atoms 2 region lo-half-sphere +Created 110 atoms +create_atoms 3 region hi-half-sphere +Created 112 atoms + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# define groups + +group lo region lo-slab +750 atoms in group lo +group lo type 2 +860 atoms in group lo +group hi region hi-slab +750 atoms in group hi +group hi type 3 +862 atoms in group hi +group lo-fixed region lo-fixed +150 atoms in group lo-fixed +group hi-fixed region hi-fixed +150 atoms in group hi-fixed +group boundary union lo-fixed hi-fixed +300 atoms in group boundary +group mobile subtract all boundary +1422 atoms in group mobile + +set lo-fixed atom 4 + 150 settings made +set hi-fixed atom 4 + 150 settings made + +# initial velocities + +compute new mobile temp/partial 0 1 0 +velocity mobile create 0.1 482748 temp new +velocity hi set 1.0 0.0 0.0 sum yes + +# fixes + +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 +fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0 +fix_modify 3 temp new + +# Run + +timestep 0.0025 +thermo 1000 +thermo_modify temp new + +dump 1 all atom 100 dump.friction +run 20000 +Memory usage per processor = 1.46023 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128 + 1000 0.088860957 -3.0636883 0 -3.0270758 0.0047805196 1384.4128 + 2000 0.087112073 -3.066344 0 -3.030452 -0.63632956 1384.4128 + 3000 0.10058239 -3.0642114 0 -3.0227694 -0.25555813 1384.4128 + 4000 0.093260137 -3.0555323 0 -3.0171072 -0.40761447 1384.4128 + 5000 0.11067201 -3.0399212 0 -2.994322 0.066689705 1384.4128 + 6000 0.10526463 -3.0390544 0 -2.9956832 -0.51522958 1384.4128 + 7000 0.11541593 -3.0403447 0 -2.992791 -0.41397003 1384.4128 + 8000 0.10197576 -3.0347747 0 -2.9927585 -0.5486861 1384.4128 + 9000 0.11134064 -3.0333357 0 -2.9874611 -0.35496419 1384.4128 + 10000 0.11080628 -3.0436254 0 -2.9979709 -0.46700659 1384.4128 + 11000 0.11943821 -3.0413975 0 -2.9921865 -0.30699848 1384.4128 + 12000 0.10413208 -3.0510277 0 -3.0081231 -0.36572201 1384.4128 + 13000 0.099296169 -3.039397 0 -2.9984849 -0.4947437 1384.4128 + 14000 0.10330462 -3.0420671 0 -2.9995034 -0.39995589 1384.4128 + 15000 0.10870951 -3.038746 0 -2.9939554 -0.50477181 1384.4128 + 16000 0.11417657 -3.0464982 0 -2.9994551 -0.32657064 1384.4128 + 17000 0.10800189 -3.047902 0 -3.0034029 -0.41936081 1384.4128 + 18000 0.10829723 -3.0458306 0 -3.0012098 -0.41668893 1384.4128 + 19000 0.10404908 -3.0526816 0 -3.0098112 -0.41121519 1384.4128 + 20000 0.10691019 -3.0411759 0 -2.9971266 -0.23642395 1384.4128 +Loop time of 9.48287 on 4 procs for 20000 steps with 1722 atoms + +Pair time (%) = 3.73598 (39.3971) +Neigh time (%) = 0.214309 (2.25996) +Comm time (%) = 3.45572 (36.4417) +Outpt time (%) = 0.605395 (6.38409) +Other time (%) = 1.47147 (15.5171) + +Nlocal: 430.5 ave 482 max 375 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 92 ave 117 max 76 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Neighs: 3601.25 ave 4057 max 3129 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 14405 +Ave neighs/atom = 8.36527 +Neighbor list builds = 750 +Dangerous builds = 0 diff --git a/examples/friction/log.friction.12Feb07.linux.1 b/examples/friction/log.friction.12Feb07.linux.1 new file mode 100644 index 0000000000..6d8285e287 --- /dev/null +++ b/examples/friction/log.friction.12Feb07.linux.1 @@ -0,0 +1,140 @@ +LAMMPS (12 Feb 2007) +# 2d friction simulation + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.9 +Lattice spacing in x,y,z = 1.1327 1.96189 1.1327 +region box block 0 50 0 22 -0.25 0.25 +create_box 4 box +Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174) + 1 by 1 by 1 processor grid + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 +mass 4 1.0 + +# atom regions + +region lo-fixed block INF INF INF 1.1 INF INF +region lo-slab block INF INF INF 7 INF INF +region above-lo block INF INF INF 7 INF INF side out +region hi-fixed block INF INF 20.9 INF INF INF +region hi-slab block INF INF 15 INF INF INF +region below-hi block INF INF 15 INF INF INF side out +region lo-asperity sphere 32 7 0 8 +region hi-asperity sphere 18 15 0 8 +region lo-half-sphere intersect 2 lo-asperity above-lo +region hi-half-sphere intersect 2 hi-asperity below-hi + +# create 2 surfaces with asperities + +create_atoms 1 region lo-slab +Created 750 atoms +create_atoms 1 region hi-slab +Created 750 atoms +create_atoms 2 region lo-half-sphere +Created 110 atoms +create_atoms 3 region hi-half-sphere +Created 112 atoms + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# define groups + +group lo region lo-slab +750 atoms in group lo +group lo type 2 +860 atoms in group lo +group hi region hi-slab +750 atoms in group hi +group hi type 3 +862 atoms in group hi +group lo-fixed region lo-fixed +150 atoms in group lo-fixed +group hi-fixed region hi-fixed +150 atoms in group hi-fixed +group boundary union lo-fixed hi-fixed +300 atoms in group boundary +group mobile subtract all boundary +1422 atoms in group mobile + +set lo-fixed atom 4 + 150 settings made +set hi-fixed atom 4 + 150 settings made + +# initial velocities + +compute new mobile temp/partial 0 1 0 +velocity mobile create 0.1 482748 temp new +velocity hi set 1.0 0.0 0.0 sum yes + +# fixes + +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 +fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0 +fix_modify 3 temp new + +# Run + +timestep 0.0025 +thermo 1000 +thermo_modify temp new + +dump 1 all atom 100 dump.friction +run 20000 +Memory usage per processor = 1.53816 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.1 -3.1332695 0 -3.0920674 -1.3452097 1384.4128 + 1000 0.088253389 -3.0560474 0 -3.0196852 0.050420633 1384.4128 + 2000 0.087864125 -3.0547262 0 -3.0185243 -0.67004561 1384.4128 + 3000 0.10557467 -3.0607837 0 -3.0172848 -0.221612 1384.4128 + 4000 0.085491315 -3.0478702 0 -3.012646 -0.42154648 1384.4128 + 5000 0.10534884 -3.051862 0 -3.0084561 -0.087935136 1384.4128 + 6000 0.10556767 -3.0559544 0 -3.0124583 -0.54210169 1384.4128 + 7000 0.098711954 -3.0590419 0 -3.0183705 -0.42838742 1384.4128 + 8000 0.11529691 -3.0366296 0 -2.9891248 -0.4457814 1384.4128 + 9000 0.1 -3.0333227 0 -2.9921206 -0.49174903 1384.4128 + 10000 0.11644796 -3.04181 0 -2.993831 -0.41991946 1384.4128 + 11000 0.1051652 -3.0340308 0 -2.9907005 -0.61535665 1384.4128 + 12000 0.10761127 -3.0351207 0 -2.9907826 -0.30937044 1384.4128 + 13000 0.11361189 -3.0354003 0 -2.9885898 -0.44289723 1384.4128 + 14000 0.11530172 -3.037545 0 -2.9900383 -0.31673329 1384.4128 + 15000 0.098629121 -3.0397602 0 -2.9991229 -0.44569024 1384.4128 + 16000 0.10525229 -3.0429476 0 -2.9995815 -0.29935796 1384.4128 + 17000 0.10467455 -3.0381932 0 -2.9950651 -0.48920299 1384.4128 + 18000 0.10817926 -3.0402364 0 -2.9956643 -0.37596363 1384.4128 + 19000 0.10816167 -3.0452456 0 -3.0006808 -0.35822139 1384.4128 + 20000 0.11364667 -3.0448494 0 -2.9980246 -0.40159119 1384.4128 +Loop time of 39.1823 on 1 procs for 20000 steps with 1722 atoms + +Pair time (%) = 28.9006 (73.7594) +Neigh time (%) = 1.39861 (3.5695) +Comm time (%) = 0.380868 (0.972041) +Outpt time (%) = 3.67569 (9.381) +Other time (%) = 4.82651 (12.3181) + +Nlocal: 1722 ave 1722 max 1722 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 146 ave 146 max 146 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 14398 ave 14398 max 14398 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14398 +Ave neighs/atom = 8.36121 +Neighbor list builds = 728 +Dangerous builds = 0 diff --git a/examples/friction/log.friction.1Oct06.liberty.4 b/examples/friction/log.friction.1Oct06.liberty.4 deleted file mode 100644 index 4787550987..0000000000 --- a/examples/friction/log.friction.1Oct06.liberty.4 +++ /dev/null @@ -1,139 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 50 0 22 -0.25 0.25 -create_box 4 box -Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174) - 2 by 2 by 1 processor grid - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 -mass 4 1.0 - -# atom regions - -region lo-fixed block INF INF INF 1.1 INF INF -region lo-slab block INF INF INF 7 INF INF -region above-lo block INF INF INF 7 INF INF side out -region hi-fixed block INF INF 20.9 INF INF INF -region hi-slab block INF INF 15 INF INF INF -region below-hi block INF INF 15 INF INF INF side out -region lo-asperity sphere 32 7 0 8 -region hi-asperity sphere 18 15 0 8 -region lo-half-sphere intersect 2 lo-asperity above-lo -region hi-half-sphere intersect 2 hi-asperity below-hi - -# create 2 surfaces with asperities - -create_atoms 1 lo-slab -Created 750 atoms -create_atoms 1 hi-slab -Created 750 atoms -create_atoms 2 lo-half-sphere -Created 112 atoms -create_atoms 3 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 lo-fixed atom 4 - 150 settings made -set hi-fixed atom 4 - 150 settings made - -# initial velocities - -temperature new mobile partial 0 1 0 -velocity mobile create 0.1 482748 temp new -velocity hi set 1.0 0.0 0.0 sum yes - -# fixes - -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 -fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0 -fix_modify 3 temp new - -# Run - -timestep 0.0025 -thermo 1000 -thermo_modify temp new - -dump 1 all atom 100 dump.friction -run 20000 -Memory usage per processor = 1.4603 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.1 -3.1333672 0 -3.0921549 -1.3466755 1384.4128 - 1000 0.08936608 -3.060858 0 -3.0240282 0.018536372 1384.4128 - 2000 0.087353242 -3.0615115 0 -3.0255112 -0.58816858 1384.4128 - 3000 0.097185838 -3.0626106 0 -3.0225581 -0.099745896 1384.4128 - 4000 0.10514697 -3.0540883 0 -3.0107549 -0.40469143 1384.4128 - 5000 0.10965701 -3.0502726 0 -3.0050804 0.15587748 1384.4128 - 6000 0.1142368 -3.0461587 0 -2.9990791 -0.27554064 1384.4128 - 7000 0.1 -3.038824 0 -2.9976117 -0.38655949 1384.4128 - 8000 0.11116929 -3.0485103 0 -3.0026949 -0.50529564 1384.4128 - 9000 0.11426746 -3.044549 0 -2.9974568 -0.4678125 1384.4128 - 10000 0.10652378 -3.0503221 0 -3.0064212 -0.52457375 1384.4128 - 11000 0.1102547 -3.0498241 0 -3.0043856 -0.45053087 1384.4128 - 12000 0.11548097 -3.0510641 0 -3.0034718 -0.27052982 1384.4128 - 13000 0.10919538 -3.0438158 0 -2.9988139 -0.53868739 1384.4128 - 14000 0.10742456 -3.045668 0 -3.0013959 -0.25306386 1384.4128 - 15000 0.10795006 -3.0436862 0 -2.9991975 -0.44644395 1384.4128 - 16000 0.11271512 -3.0478462 0 -3.0013937 -0.28516203 1384.4128 - 17000 0.11209577 -3.0497319 0 -3.0035347 -0.39432942 1384.4128 - 18000 0.1 -3.050733 0 -3.0095207 -0.34607727 1384.4128 - 19000 0.092061676 -3.048521 0 -3.0105803 -0.37268438 1384.4128 - 20000 0.10666663 -3.0598394 0 -3.0158797 -0.33025583 1384.4128 -Loop time of 8.99743 on 4 procs for 20000 steps with 1724 atoms - -Pair time (%) = 3.6897 (41.0084) -Neigh time (%) = 0.202473 (2.25034) -Comm time (%) = 3.18145 (35.3595) -Outpt time (%) = 0.579402 (6.43964) -Other time (%) = 1.3444 (14.9421) - -Nlocal: 431 ave 484 max 381 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Nghost: 100.5 ave 119 max 87 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 3597.5 ave 4163 max 3176 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 14390 -Ave neighs/atom = 8.34687 -Neighbor list builds = 720 -Dangerous builds = 0 diff --git a/examples/friction/log.friction.1Oct06.linux.1 b/examples/friction/log.friction.1Oct06.linux.1 deleted file mode 100644 index 9efdb4c783..0000000000 --- a/examples/friction/log.friction.1Oct06.linux.1 +++ /dev/null @@ -1,139 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 50 0 22 -0.25 0.25 -create_box 4 box -Created box = (0 0 -0.283174) to (56.6348 43.1615 0.283174) - 1 by 1 by 1 processor grid - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 -mass 4 1.0 - -# atom regions - -region lo-fixed block INF INF INF 1.1 INF INF -region lo-slab block INF INF INF 7 INF INF -region above-lo block INF INF INF 7 INF INF side out -region hi-fixed block INF INF 20.9 INF INF INF -region hi-slab block INF INF 15 INF INF INF -region below-hi block INF INF 15 INF INF INF side out -region lo-asperity sphere 32 7 0 8 -region hi-asperity sphere 18 15 0 8 -region lo-half-sphere intersect 2 lo-asperity above-lo -region hi-half-sphere intersect 2 hi-asperity below-hi - -# create 2 surfaces with asperities - -create_atoms 1 lo-slab -Created 750 atoms -create_atoms 1 hi-slab -Created 750 atoms -create_atoms 2 lo-half-sphere -Created 112 atoms -create_atoms 3 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 lo-fixed atom 4 - 150 settings made -set hi-fixed atom 4 - 150 settings made - -# initial velocities - -temperature new mobile partial 0 1 0 -velocity mobile create 0.1 482748 temp new -velocity hi set 1.0 0.0 0.0 sum yes - -# fixes - -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 -fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0 -fix_modify 3 temp new - -# Run - -timestep 0.0025 -thermo 1000 -thermo_modify temp new - -dump 1 all atom 100 dump.friction -run 20000 -Memory usage per processor = 1.53824 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.1 -3.1333672 0 -3.0921549 -1.3466755 1384.4128 - 1000 0.085622556 -3.0583969 0 -3.0231098 0.040017208 1384.4128 - 2000 0.085921887 -3.0572271 0 -3.0218167 -0.60479351 1384.4128 - 3000 0.10739474 -3.0650606 0 -3.0208008 -0.04184404 1384.4128 - 4000 0.089682132 -3.04809 0 -3.01113 -0.22441446 1384.4128 - 5000 0.10934102 -3.0485926 0 -3.0035307 0.12177364 1384.4128 - 6000 0.10817011 -3.0584907 0 -3.0139113 -0.36521995 1384.4128 - 7000 0.10519415 -3.0511557 0 -3.0078027 -0.279893 1384.4128 - 8000 0.11660453 -3.0348037 0 -2.9867483 -0.47310792 1384.4128 - 9000 0.1 -3.0308672 0 -2.9896549 -0.35351908 1384.4128 - 10000 0.10012993 -3.0431145 0 -3.0018486 -0.4837576 1384.4128 - 11000 0.11987001 -3.0484839 0 -2.9990827 -0.45971209 1384.4128 - 12000 0.11063404 -3.0457139 0 -3.000119 -0.32411476 1384.4128 - 13000 0.11214672 -3.0407157 0 -2.9944974 -0.4453681 1384.4128 - 14000 0.11127122 -3.0431707 0 -2.9973132 -0.35672869 1384.4128 - 15000 0.11311298 -3.0456742 0 -2.9990577 -0.42235702 1384.4128 - 16000 0.11003354 -3.0519914 0 -3.0066441 -0.24377861 1384.4128 - 17000 0.095617549 -3.0478455 0 -3.0084393 -0.54070059 1384.4128 - 18000 0.10655281 -3.0497371 0 -3.0058242 -0.2968023 1384.4128 - 19000 0.096661108 -3.0630512 0 -3.0232149 -0.35284808 1384.4128 - 20000 0.099961152 -3.0606412 0 -3.0194449 -0.39275101 1384.4128 -Loop time of 42.478 on 1 procs for 20000 steps with 1724 atoms - -Pair time (%) = 34.1596 (80.4171) -Neigh time (%) = 1.4565 (3.42883) -Comm time (%) = 0.402718 (0.948062) -Outpt time (%) = 1.64536 (3.87344) -Other time (%) = 4.81384 (11.3326) - -Nlocal: 1724 ave 1724 max 1724 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 141 ave 141 max 141 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 14389 ave 14389 max 14389 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 14389 -Ave neighs/atom = 8.34629 -Neighbor list builds = 730 -Dangerous builds = 0 diff --git a/examples/indent/log.indent.12Feb07.liberty.4 b/examples/indent/log.indent.12Feb07.liberty.4 new file mode 100644 index 0000000000..c9808596f7 --- /dev/null +++ b/examples/indent/log.indent.12Feb07.liberty.4 @@ -0,0 +1,169 @@ +LAMMPS (12 Feb 2007) +# 2d indenter simulation + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.9 +Lattice spacing in x,y,z = 1.1327 1.96189 1.1327 +region box block 0 20 0 10 -0.25 0.25 +create_box 2 box +Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) + 2 by 2 by 1 processor grid +create_atoms 1 +Created 420 atoms + +mass 1 1.0 +mass 2 1.0 + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +60 atoms in group lower +group mobile subtract all lower +360 atoms in group mobile +set lower atom 2 + 60 settings made + +# initial velocities + +compute new mobile temp +velocity mobile create 0.2 482748 temp new +fix 1 all nve +fix 2 lower setforce 0.0 0.0 0.0 +fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0 + +# indenter + +fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0 +fix 5 all enforce2d + +# Run with indenter + +timestep 0.003 +thermo 1000 +thermo_modify temp new + +dump 1 all atom 250 dump.indent +run 30000 +Memory usage per processor = 1.44615 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 + 1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681 + 2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856 + 3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439 + 4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265 + 5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573 + 6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734648 249.1402 + 7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327 + 8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825 + 9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265 + 10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407 + 11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776 + 12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714 + 13000 0.11341039 -3.0596733 0 -2.9628694 1.1566167 249.36303 + 14000 0.1176102 -3.058063 0 -2.9576743 1.2083863 249.05567 + 15000 0.12582683 -3.054119 0 -2.9467168 1.052489 254.01804 + 16000 0.11716129 -3.0359809 0 -2.9359753 1.1111189 259.94912 + 17000 0.11836208 -3.0276209 0 -2.9265904 1.0821166 257.9832 + 18000 0.12271609 -3.0171547 0 -2.9124077 1.511924 264.99507 + 19000 0.11746326 -3.0102961 0 -2.9100328 1.6305608 267.60875 + 20000 0.12091083 -2.996777 0 -2.893571 1.7996398 268.87085 + 21000 0.1263182 -2.9950013 0 -2.8871797 1.8539429 271.55393 + 22000 0.12425331 -2.9761891 0 -2.87013 1.5415686 276.54337 + 23000 0.11563313 -2.9874945 0 -2.8887934 1.2018805 279.40748 + 24000 0.11553831 -2.9945403 0 -2.8959201 1.5305748 278.38798 + 25000 0.11085112 -2.9896742 0 -2.8950548 1.8815906 275.87487 + 26000 0.12077848 -2.986181 0 -2.883088 1.9122673 275.91918 + 27000 0.12399848 -2.9814354 0 -2.8755938 1.9167983 278.64025 + 28000 0.12143106 -3.0225278 0 -2.9188777 0.56589243 290.55803 + 29000 0.11959029 -3.0121799 0 -2.9101011 0.49660855 295.49221 + 30000 0.11931566 -3.0215043 0 -2.9196598 0.83146141 294.35452 +Loop time of 7.1529 on 4 procs for 30000 steps with 420 atoms + +Pair time (%) = 1.4201 (19.8535) +Neigh time (%) = 0.0487321 (0.681291) +Comm time (%) = 4.28154 (59.8574) +Outpt time (%) = 0.109681 (1.53338) +Other time (%) = 1.29285 (18.0744) + +Nlocal: 105 ave 125 max 79 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 92.75 ave 104 max 77 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 901 ave 1133 max 620 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3604 +Ave neighs/atom = 8.58095 +Neighbor list builds = 622 +Dangerous builds = 0 + +# Run without indenter + +unfix 4 +run 30000 +Memory usage per processor = 1.4468 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 30000 0.11931566 -3.0215043 0 -2.9196598 0.83281489 293.87614 + 31000 0.1167364 -3.0429651 0 -2.9433222 -0.36091255 293.88145 + 32000 0.12641731 -3.0639714 0 -2.9560652 -0.46898184 290.09909 + 33000 0.10706313 -3.0741804 0 -2.9827944 0.00022078579 285.15883 + 34000 0.11367315 -3.0688054 0 -2.9717772 -0.76240201 289.87707 + 35000 0.10655807 -3.0627342 0 -2.9717793 -0.26051048 288.22641 + 36000 0.11703008 -3.0716705 0 -2.971777 -0.1853764 285.83663 + 37000 0.11221734 -3.0675632 0 -2.9717776 -0.73386022 290.12632 + 38000 0.11874224 -3.0731334 0 -2.9717784 -0.12687563 285.36376 + 39000 0.1189778 -3.0733361 0 -2.9717801 -0.25499323 287.084 + 40000 0.11898338 -3.0620885 0 -2.9605277 -0.62541843 288.73621 + 41000 0.1167364 -3.0735602 0 -2.9739173 -0.11692923 283.98124 + 42000 0.11266172 -3.0700831 0 -2.9739183 -0.39632943 286.59658 + 43000 0.11902827 -3.0755188 0 -2.9739196 -0.57312115 287.53858 + 44000 0.12554232 -3.0810812 0 -2.9739219 -0.070954433 286.20995 + 45000 0.11075688 -3.0684563 0 -2.9739174 -0.55071995 288.55119 + 46000 0.12586051 -3.0707391 0 -2.9633081 -0.48923571 289.30041 + 47000 0.11671697 -3.0736442 0 -2.9740179 -0.12378289 285.31819 + 48000 0.10853944 -3.0666634 0 -2.9740172 -0.57661015 289.17231 + 49000 0.1167364 -3.0679033 0 -2.9682604 -0.28913991 286.84813 + 50000 0.10777198 -3.0602483 0 -2.9682572 -0.2607135 286.76228 + 51000 0.10971818 -3.0619099 0 -2.9682576 -0.50602899 289.54807 + 52000 0.12283301 -3.0731069 0 -2.9682602 -0.17101974 286.39074 + 53000 0.11323492 -3.0762744 0 -2.9796203 -0.39853784 289.81061 + 54000 0.12076965 -3.0709553 0 -2.9678698 -0.3939254 288.24037 + 55000 0.12319168 -3.0730238 0 -2.9678709 -0.17986864 284.15611 + 56000 0.12040501 -3.0706451 0 -2.9678708 -0.34825544 286.68764 + 57000 0.12192823 -3.0719452 0 -2.9678707 -0.42539274 287.8374 + 58000 0.11878678 -3.0692629 0 -2.9678699 -0.24575165 286.73167 + 59000 0.11418711 -3.0653342 0 -2.9678674 -0.51388179 287.99512 + 60000 0.11462897 -3.0657114 0 -2.9678673 -0.4538483 288.11403 +Loop time of 7.11751 on 4 procs for 30000 steps with 420 atoms + +Pair time (%) = 1.39714 (19.6297) +Neigh time (%) = 0.0485521 (0.68215) +Comm time (%) = 4.35769 (61.2249) +Outpt time (%) = 0.111284 (1.56352) +Other time (%) = 1.20284 (16.8997) + +Nlocal: 105 ave 122 max 82 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Nghost: 92 ave 101 max 82 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 888.5 ave 1097 max 643 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3554 +Ave neighs/atom = 8.4619 +Neighbor list builds = 630 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.12Feb07.linux.1 b/examples/indent/log.indent.12Feb07.linux.1 new file mode 100644 index 0000000000..6708d7a767 --- /dev/null +++ b/examples/indent/log.indent.12Feb07.linux.1 @@ -0,0 +1,169 @@ +LAMMPS (12 Feb 2007) +# 2d indenter simulation + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.9 +Lattice spacing in x,y,z = 1.1327 1.96189 1.1327 +region box block 0 20 0 10 -0.25 0.25 +create_box 2 box +Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) + 1 by 1 by 1 processor grid +create_atoms 1 +Created 420 atoms + +mass 1 1.0 +mass 2 1.0 + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +60 atoms in group lower +group mobile subtract all lower +360 atoms in group mobile +set lower atom 2 + 60 settings made + +# initial velocities + +compute new mobile temp +velocity mobile create 0.2 482748 temp new +fix 1 all nve +fix 2 lower setforce 0.0 0.0 0.0 +fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0 + +# indenter + +fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0 +fix 5 all enforce2d + +# Run with indenter + +timestep 0.003 +thermo 1000 +thermo_modify temp new + +dump 1 all atom 250 dump.indent +run 30000 +Memory usage per processor = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 + 1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001 + 2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098 + 3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041 + 4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717 + 5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708 + 6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216 + 7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979 + 8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714 + 9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256 + 10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836 + 11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926 + 12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761 + 13000 0.12031568 -3.0583679 0 -2.9556699 1.2700141 247.59077 + 14000 0.1167364 -3.0548463 0 -2.9552034 1.0859392 250.18904 + 15000 0.1167364 -3.0549235 0 -2.9552806 1.2995977 251.78491 + 16000 0.12471796 -3.0524621 0 -2.9460064 1.6452633 249.66328 + 17000 0.12078141 -3.0356474 0 -2.9325519 1.9172375 248.00713 + 18000 0.11737951 -3.0294793 0 -2.9292875 1.984307 254.03132 + 19000 0.12273273 -3.016492 0 -2.9117309 1.9954892 251.8583 + 20000 0.12551089 -3.0011944 0 -2.8940619 1.7797455 260.26155 + 21000 0.12037224 -2.9934253 0 -2.890679 1.3694744 269.07586 + 22000 0.12174807 -3.0193123 0 -2.9153916 0.94134986 270.00347 + 23000 0.12706029 -3.0244275 0 -2.9159725 1.1867392 266.05204 + 24000 0.11467621 -3.0095158 0 -2.9116314 0.73011254 267.48776 + 25000 0.11535618 -3.0158848 0 -2.91742 1.2611256 266.59514 + 26000 0.10710521 -3.0133947 0 -2.9219727 0.67441358 268.32045 + 27000 0.12422208 -3.0164988 0 -2.9104663 1.1543726 268.18532 + 28000 0.11139527 -3.0072089 0 -2.9121251 1.4607146 265.23157 + 29000 0.1167364 -3.0085086 0 -2.9088658 1.6594744 265.37526 + 30000 0.11102647 -3.0064551 0 -2.9116861 1.3943384 268.60718 +Loop time of 15.887 on 1 procs for 30000 steps with 420 atoms + +Pair time (%) = 10.9921 (69.1889) +Neigh time (%) = 0.333033 (2.09625) +Comm time (%) = 0.347973 (2.19029) +Outpt time (%) = 1.87511 (11.8028) +Other time (%) = 2.33885 (14.7218) + +Nlocal: 420 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 109 ave 109 max 109 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3655 ave 3655 max 3655 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3655 +Ave neighs/atom = 8.70238 +Neighbor list builds = 616 +Dangerous builds = 0 + +# Run without indenter + +unfix 4 +run 30000 +Memory usage per processor = 1.45035 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 30000 0.11102647 -3.0064551 0 -2.9116861 1.3929673 268.87157 + 31000 0.12620212 -3.0510755 0 -2.943353 -0.18214813 273.9697 + 32000 0.11450566 -3.0412855 0 -2.9435467 -0.36947207 273.74363 + 33000 0.11300395 -3.0666261 0 -2.9701691 -0.36891232 262.29844 + 34000 0.11360641 -3.0910465 0 -2.9940753 -0.2930611 263.47461 + 35000 0.11792208 -3.0826962 0 -2.9820413 -0.53020156 264.92677 + 36000 0.1167364 -3.0791913 0 -2.9795484 -0.28901516 264.42654 + 37000 0.11195363 -3.075108 0 -2.9795476 -0.35271906 264.6512 + 38000 0.11608571 -3.0786363 0 -2.9795489 -0.5028598 264.60065 + 39000 0.1177969 -3.0800557 0 -2.9795076 -0.32434056 263.66269 + 40000 0.11466668 -3.0774252 0 -2.979549 -0.40950185 263.65927 + 41000 0.11118976 -3.0744545 0 -2.9795461 -0.58454381 264.39108 + 42000 0.11460312 -3.0773684 0 -2.9795464 -0.20755902 262.35795 + 43000 0.11677527 -3.0792261 0 -2.97955 -0.49949012 264.53893 + 44000 0.11158159 -3.0747894 0 -2.9795466 -0.37452501 263.88851 + 45000 0.12176422 -3.0834855 0 -2.979551 -0.16070447 262.66164 + 46000 0.11682005 -3.0792615 0 -2.9795472 -0.63716759 266.07809 + 47000 0.11262188 -3.0756805 0 -2.9795497 -0.15500292 263.19673 + 48000 0.12119234 -3.0829975 0 -2.9795512 -0.39672723 263.37224 + 49000 0.11784014 -3.0801322 0 -2.9795473 -0.42268487 265.07121 + 50000 0.11675902 -3.0792108 0 -2.9795486 -0.1111771 261.69863 + 51000 0.11170649 -3.0748959 0 -2.9795465 -0.46340258 263.55401 + 52000 0.12175858 -3.0834809 0 -2.9795513 -0.48539416 263.47789 + 53000 0.12074224 -3.0964747 0 -2.9934126 -0.4846085 262.58631 + 54000 0.11099551 -3.0767379 0 -2.9819953 -0.39099317 263.38816 + 55000 0.11519489 -3.0803219 0 -2.9819948 -0.38576064 263.5242 + 56000 0.11716036 -3.0820002 0 -2.9819954 -0.26199121 262.69272 + 57000 0.10872156 -3.0792099 0 -2.9864083 -0.49564243 267.348 + 58000 0.12397214 -3.0923068 0 -2.9864877 -0.37680531 262.14403 + 59000 0.11456625 -3.0842744 0 -2.9864839 -0.30718293 263.3254 + 60000 0.11413467 -3.0839074 0 -2.9864853 -0.54302442 263.54231 +Loop time of 13.8006 on 1 procs for 30000 steps with 420 atoms + +Pair time (%) = 10.8642 (78.7224) +Neigh time (%) = 0.336436 (2.43783) +Comm time (%) = 0.357799 (2.59263) +Outpt time (%) = 0.267058 (1.93512) +Other time (%) = 1.97515 (14.312) + +Nlocal: 420 ave 420 max 420 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 101 ave 101 max 101 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3570 ave 3570 max 3570 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3570 +Ave neighs/atom = 8.5 +Neighbor list builds = 630 +Dangerous builds = 0 diff --git a/examples/indent/log.indent.1Oct06.liberty.4 b/examples/indent/log.indent.1Oct06.liberty.4 deleted file mode 100644 index 82bcbdc523..0000000000 --- a/examples/indent/log.indent.1Oct06.liberty.4 +++ /dev/null @@ -1,168 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 20 0 10 -0.25 0.25 -create_box 2 box -Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) - 2 by 2 by 1 processor grid -create_atoms 1 -Created 420 atoms - -mass 1 1.0 -mass 2 1.0 - -# LJ potentials - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -60 atoms in group lower -group mobile subtract all lower -360 atoms in group mobile -set lower atom 2 - 60 settings made - -# initial velocities - -temperature new mobile full -velocity mobile create 0.2 482748 temp new -fix 1 all nve -fix 2 lower setforce 0.0 0.0 0.0 -fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0 - -# indenter - -fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0 -fix 5 all enforce2d - -# Run with indenter - -timestep 0.003 -thermo 1000 -thermo_modify temp new - -dump 1 all atom 250 dump.indent -run 30000 -Memory usage per processor = 1.44615 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 - 1000 0.11576832 -3.0966334 0 -2.9978168 -0.24095347 250.17681 - 2000 0.11528823 -3.0962223 0 -2.9978155 -0.45030047 250.45856 - 3000 0.11379051 -3.0840496 0 -2.9869213 -0.5022142 251.7439 - 4000 0.11595816 -3.085882 0 -2.9869034 -0.047829504 249.09265 - 5000 0.11272851 -3.0844605 0 -2.9882386 -0.57244294 252.48573 - 6000 0.12387775 -3.0900283 0 -2.9842898 0.0072734647 249.1402 - 7000 0.1113616 -3.0914902 0 -2.9964351 -0.12742916 250.29327 - 8000 0.1167364 -3.0879355 0 -2.9882926 0.20678001 250.17825 - 9000 0.11504768 -3.0918767 0 -2.9936753 0.35261539 249.40265 - 10000 0.11864876 -3.0776022 0 -2.976327 0.45724638 249.80407 - 11000 0.12749806 -3.0769801 0 -2.9681514 0.7106404 248.1776 - 12000 0.11068569 -3.0664256 0 -2.9719474 0.77940328 248.88714 - 13000 0.11341038 -3.0596733 0 -2.9628694 1.1566167 249.36303 - 14000 0.1176102 -3.058063 0 -2.9576743 1.2083864 249.05567 - 15000 0.12582681 -3.054119 0 -2.9467168 1.052489 254.01805 - 16000 0.11716135 -3.0359809 0 -2.9359753 1.1111189 259.94911 - 17000 0.11836201 -3.0276208 0 -2.9265904 1.0821175 257.98321 - 18000 0.12271549 -3.0171543 0 -2.9124079 1.5119093 264.99586 - 19000 0.11746211 -3.0102935 0 -2.9100312 1.6305879 267.60889 - 20000 0.12090524 -2.9967767 0 -2.8935754 1.7995263 268.87142 - 21000 0.12612028 -2.994907 0 -2.8872544 1.8540136 271.56724 - 22000 0.1167364 -2.9800486 0 -2.8804058 1.5103597 276.50496 - 23000 0.11371517 -3.0043157 0 -2.9072517 1.1335811 275.4202 - 24000 0.12132941 -3.0096869 0 -2.9061236 1.4605526 274.49424 - 25000 0.12720095 -3.0069871 0 -2.898412 1.6853695 271.79073 - 26000 0.11378571 -2.9920984 0 -2.8949742 1.5810259 275.70735 - 27000 0.12075739 -2.9937473 0 -2.8906722 1.1417712 284.83703 - 28000 0.11405151 -2.9959463 0 -2.8985951 1.1975088 282.69832 - 29000 0.11973002 -2.9904314 0 -2.8882333 0.95237047 287.29831 - 30000 0.11503912 -2.9700786 0 -2.8718845 1.3547537 288.9147 -Loop time of 6.5358 on 4 procs for 30000 steps with 420 atoms - -Pair time (%) = 1.41006 (21.5744) -Neigh time (%) = 0.0485178 (0.742339) -Comm time (%) = 3.8256 (58.533) -Outpt time (%) = 0.108883 (1.66595) -Other time (%) = 1.14274 (17.4844) - -Nlocal: 105 ave 125 max 84 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 94.5 ave 103 max 86 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 921.75 ave 1178 max 667 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 3687 -Ave neighs/atom = 8.77857 -Neighbor list builds = 617 -Dangerous builds = 0 - -# Run without indenter - -unfix 4 -run 30000 -Memory usage per processor = 1.44672 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 30000 0.11503912 -2.9700786 0 -2.8718845 1.3561767 288.61154 - 31000 0.11044364 -3.0076121 0 -2.9133406 -0.52779902 292.44389 - 32000 0.12019156 -2.9928375 0 -2.8902454 -0.4563394 294.0201 - 33000 0.11776824 -3.0170498 0 -2.9165262 0.23283576 288.29221 - 34000 0.11371582 -3.0135113 0 -2.9164467 0.0061511438 287.56456 - 35000 0.11235735 -3.0121578 0 -2.9162528 -0.46926625 292.5539 - 36000 0.1167364 -3.0268323 0 -2.9271895 0.060047839 287.80848 - 37000 0.11117485 -3.022005 0 -2.9271093 -0.118142 289.78382 - 38000 0.10552007 -3.0174083 0 -2.9273394 -0.6700554 288.73054 - 39000 0.12214122 -3.0318714 0 -2.9276151 -0.020293363 284.90615 - 40000 0.1167364 -3.0374431 0 -2.9378003 -0.2576625 282.39621 - 41000 0.12078959 -3.0407878 0 -2.9376852 -0.32963004 283.00597 - 42000 0.12532766 -3.0592415 0 -2.9522654 -0.13855832 275.59038 - 43000 0.12195787 -3.0696533 0 -2.9655536 -0.59184637 276.4371 - 44000 0.11819255 -3.0663983 0 -2.9655125 -0.40728614 275.67698 - 45000 0.11276783 -3.0618054 0 -2.96555 -0.10571263 272.71725 - 46000 0.11003631 -3.0594741 0 -2.9655503 -0.3808265 275.07036 - 47000 0.11854167 -3.0792116 0 -2.9780278 -0.40824195 274.01648 - 48000 0.10827298 -3.0704447 0 -2.978026 -0.22213637 271.58418 - 49000 0.10975304 -3.0717077 0 -2.9780256 -0.4821176 274.12844 - 50000 0.11981935 -3.0677955 0 -2.9655211 -0.26816116 274.19059 - 51000 0.12079404 -3.0686263 0 -2.9655199 -0.33188148 274.5802 - 52000 0.11731632 -3.076662 0 -2.9765241 -0.48748579 274.88209 - 53000 0.11451375 -3.0742688 0 -2.9765231 -0.25944149 274.6574 - 54000 0.11308706 -3.0730497 0 -2.9765218 -0.44356549 274.44162 - 55000 0.11323885 -3.07318 0 -2.9765225 -0.34236444 275.44349 - 56000 0.11199118 -3.072113 0 -2.9765205 -0.33585978 274.06495 - 57000 0.11740244 -3.0767352 0 -2.9765239 -0.59185176 275.0556 - 58000 0.1159403 -3.0755277 0 -2.9765644 -0.28617471 274.30591 - 59000 0.12463828 -3.0829133 0 -2.9765256 -0.40473725 273.86499 - 60000 0.12095326 -3.069233 0 -2.9659907 -0.39935619 276.71426 -Loop time of 6.56165 on 4 procs for 30000 steps with 420 atoms - -Pair time (%) = 1.39105 (21.1996) -Neigh time (%) = 0.0485317 (0.739626) -Comm time (%) = 3.91511 (59.6666) -Outpt time (%) = 0.117233 (1.78663) -Other time (%) = 1.08973 (16.6075) - -Nlocal: 105 ave 120 max 86 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 87 ave 92 max 84 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 892.5 ave 1086 max 676 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 3570 -Ave neighs/atom = 8.5 -Neighbor list builds = 625 -Dangerous builds = 0 diff --git a/examples/indent/log.indent.1Oct06.linux.1 b/examples/indent/log.indent.1Oct06.linux.1 deleted file mode 100644 index 1af43eb93c..0000000000 --- a/examples/indent/log.indent.1Oct06.linux.1 +++ /dev/null @@ -1,168 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 20 0 10 -0.25 0.25 -create_box 2 box -Created box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) - 1 by 1 by 1 processor grid -create_atoms 1 -Created 420 atoms - -mass 1 1.0 -mass 2 1.0 - -# LJ potentials - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 2.5 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -60 atoms in group lower -group mobile subtract all lower -360 atoms in group mobile -set lower atom 2 - 60 settings made - -# initial velocities - -temperature new mobile full -velocity mobile create 0.2 482748 temp new -fix 1 all nve -fix 2 lower setforce 0.0 0.0 0.0 -fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0 - -# indenter - -fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0 -fix 5 all enforce2d - -# Run with indenter - -timestep 0.003 -thermo 1000 -thermo_modify temp new - -dump 1 all atom 250 dump.indent -run 30000 -Memory usage per processor = 1.45035 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 0.2 -3.1727576 0 -3.0020433 -1.6911656 251.71282 - 1000 0.11979027 -3.0878285 0 -2.9855789 -0.043690155 249.58001 - 2000 0.12095292 -3.0888211 0 -2.9855791 -0.46999358 251.6098 - 3000 0.1167364 -3.0841547 0 -2.9845118 -0.41054969 250.8041 - 4000 0.12249143 -3.1004175 0 -2.9958623 -0.060853986 248.47717 - 5000 0.10957873 -3.0886367 0 -2.9951034 -0.57642649 251.31708 - 6000 0.12346008 -3.0985964 0 -2.9932144 -0.072968634 250.46216 - 7000 0.10994736 -3.0850721 0 -2.9912241 -0.20324168 251.37979 - 8000 0.11557891 -3.086042 0 -2.9873871 0.22717975 249.49714 - 9000 0.12016755 -3.084536 0 -2.9819645 0.33218396 248.89256 - 10000 0.12659552 -3.0852403 0 -2.977182 0.40666454 249.67836 - 11000 0.12524777 -3.0736607 0 -2.9667528 0.77561215 248.69926 - 12000 0.11844672 -3.0571177 0 -2.9560149 0.77334207 249.761 - 13000 0.12031569 -3.0583679 0 -2.9556699 1.2700141 247.59077 - 14000 0.1167364 -3.0548463 0 -2.9552034 1.0859393 250.18904 - 15000 0.1167364 -3.0549235 0 -2.9552806 1.2995978 251.78491 - 16000 0.12471788 -3.052462 0 -2.9460064 1.6452635 249.66328 - 17000 0.12078161 -3.0356476 0 -2.9325519 1.9172373 248.00711 - 18000 0.11737985 -3.0294795 0 -2.9292874 1.9843046 254.0314 - 19000 0.12273219 -3.0164914 0 -2.9117307 1.9954937 251.85839 - 20000 0.12550051 -3.0011844 0 -2.8940608 1.779848 260.26132 - 21000 0.12036751 -2.9934276 0 -2.8906853 1.3693509 269.07657 - 22000 0.12307091 -3.0182302 0 -2.9131804 0.94154126 269.78997 - 23000 0.11949164 -3.0176126 0 -2.9156179 1.19816 265.98797 - 24000 0.1167364 -3.020151 0 -2.9205082 0.95639973 266.25197 - 25000 0.12252115 -3.0162117 0 -2.9116312 1.5771822 264.20779 - 26000 0.11367117 -3.0238072 0 -2.9267808 0.71311555 265.96581 - 27000 0.12007686 -3.0147427 0 -2.9122485 1.185271 266.21643 - 28000 0.11526199 -3.0019986 0 -2.9036143 1.2838023 267.44914 - 29000 0.12754217 -3.0122896 0 -2.9034233 1.3382791 269.93381 - 30000 0.12108464 -2.9981686 0 -2.8948142 1.0638866 269.70142 -Loop time of 16.0381 on 1 procs for 30000 steps with 420 atoms - -Pair time (%) = 12.7017 (79.1969) -Neigh time (%) = 0.325385 (2.02882) -Comm time (%) = 0.319287 (1.9908) -Outpt time (%) = 0.343728 (2.14319) -Other time (%) = 2.34803 (14.6403) - -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: 3647 ave 3647 max 3647 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3647 -Ave neighs/atom = 8.68333 -Neighbor list builds = 621 -Dangerous builds = 0 - -# Run without indenter - -unfix 4 -run 30000 -Memory usage per processor = 1.45035 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 30000 0.12108464 -2.9981686 0 -2.8948142 1.0650921 269.39617 - 31000 0.10657868 -3.0036168 0 -2.9126443 -0.0032557036 272.44965 - 32000 0.1167364 -3.0371073 0 -2.9374644 -0.35201197 275.67834 - 33000 0.11914647 -3.0500345 0 -2.9483345 0.061830594 274.41844 - 34000 0.11331538 -3.062714 0 -2.9659912 -0.45332011 275.96007 - 35000 0.11038437 -3.0765417 0 -2.9823208 -0.36244079 275.11931 - 36000 0.11892267 -3.0721585 0 -2.9706495 -0.29991556 275.37903 - 37000 0.11275568 -3.0668928 0 -2.9706478 -0.48726288 275.34035 - 38000 0.1208952 -3.0738053 0 -2.9706126 -0.29578963 278.34451 - 39000 0.10944817 -3.0773595 0 -2.9839377 -0.37875952 274.00319 - 40000 0.11332842 -3.080676 0 -2.9839421 -0.45568111 275.74499 - 41000 0.12031253 -3.0762241 0 -2.9735288 -0.21242519 276.03968 - 42000 0.12031396 -3.0762248 0 -2.9735282 -0.34222153 274.86604 - 43000 0.11012454 -3.0675234 0 -2.9735242 -0.38191996 274.79485 - 44000 0.11896309 -3.0750688 0 -2.9735254 -0.39778513 275.34531 - 45000 0.11416813 -3.070974 0 -2.9735234 -0.43325648 275.80725 - 46000 0.11899053 -3.0750933 0 -2.9735264 -0.35449325 275.10793 - 47000 0.11629126 -3.0727892 0 -2.9735263 -0.30843482 274.0454 - 48000 0.1167364 -3.0847916 0 -2.9851487 -0.50651671 275.70527 - 49000 0.11521427 -3.0729187 0 -2.9745751 -0.22466242 275.84873 - 50000 0.11128506 -3.0695232 0 -2.9745335 -0.24912645 275.25969 - 51000 0.11019914 -3.0694308 0 -2.975368 -0.31599349 275.27739 - 52000 0.11953699 -3.0773655 0 -2.9753322 -0.26602137 275.2982 - 53000 0.11403111 -3.0727022 0 -2.9753685 -0.51238084 276.07268 - 54000 0.11607222 -3.0744423 0 -2.9753664 -0.44949735 276.40633 - 55000 0.1169534 -3.0751976 0 -2.9753695 -0.25155291 275.66943 - 56000 0.11200164 -3.0709683 0 -2.9753669 -0.49059346 275.98698 - 57000 0.11837073 -3.0764076 0 -2.9753698 -0.36710375 274.96496 - 58000 0.11241958 -3.0713261 0 -2.9753679 -0.35883352 273.98621 - 59000 0.11701473 -3.0752489 0 -2.9753684 -0.37410362 275.64889 - 60000 0.11038413 -3.0695887 0 -2.975368 -0.17138902 275.08559 -Loop time of 15.4958 on 1 procs for 30000 steps with 420 atoms - -Pair time (%) = 12.5699 (81.1182) -Neigh time (%) = 0.328618 (2.12069) -Comm time (%) = 0.33072 (2.13426) -Outpt time (%) = 0.25356 (1.63632) -Other time (%) = 2.01299 (12.9906) - -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: 3560 ave 3560 max 3560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3560 -Ave neighs/atom = 8.47619 -Neighbor list builds = 635 -Dangerous builds = 0 diff --git a/examples/meam/data.sic b/examples/meam/data.meam similarity index 100% rename from examples/meam/data.sic rename to examples/meam/data.meam diff --git a/examples/meam/in.sic b/examples/meam/in.meam similarity index 69% rename from examples/meam/in.sic rename to examples/meam/in.meam index cf3cee03ad..43e83ea1ec 100644 --- a/examples/meam/in.sic +++ b/examples/meam/in.meam @@ -1,11 +1,11 @@ -# Test of MEAM potential for Si-C system +# Test of MEAM potential for SiC system units metal boundary p p p atom_style atomic -read_data data.sic +read_data data.meam pair_style meam pair_coeff * * library.meam Si C sic.meam Si C @@ -17,6 +17,6 @@ fix 1 all nve thermo 10 timestep 0.001 +dump 1 all atom 10 dump.meam + run 100 - - diff --git a/examples/meam/in.shear_meam b/examples/meam/in.meam.shear similarity index 94% rename from examples/meam/in.shear_meam rename to examples/meam/in.meam.shear index 65ba73915b..0771edfb34 100644 --- a/examples/meam/in.shear_meam +++ b/examples/meam/in.meam.shear @@ -1,4 +1,4 @@ -# 3d metal shear simulation with MEAM potential +# 3d metal shear simulation units metal boundary s s p @@ -62,7 +62,7 @@ unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new2d -dump 1 all atom 10 dump.shear +dump 1 all atom 10 dump.meam.shear thermo 100 thermo_modify temp new2d diff --git a/examples/meam/log.meam.12Feb07.liberty.4 b/examples/meam/log.meam.12Feb07.liberty.4 new file mode 100644 index 0000000000..784480f71b --- /dev/null +++ b/examples/meam/log.meam.12Feb07.liberty.4 @@ -0,0 +1,59 @@ +LAMMPS (12 Feb 2007) +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.meam + 2 by 1 by 2 processor grid + 128 atoms + +pair_style meam +pair_coeff * * library.meam Si C sic.meam Si C + +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +dump 1 all atom 10 dump.meam + +run 100 +Memory usage per processor = 4.40047 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -636.93784 0 -636.93784 -76401.859 + 10 1777.5718 -666.27518 0 -637.0945 -150596.32 + 20 1908.6646 -668.42203 0 -637.08932 -120846.06 + 30 1937.3373 -668.90047 0 -637.09706 -101367.81 + 40 2110.906 -671.75978 0 -637.10706 -110475.14 + 50 2057.8682 -670.89589 0 -637.11385 -107817.44 + 60 1887.9614 -668.08977 0 -637.09693 -108906.46 + 70 2036.4427 -670.53667 0 -637.10635 -113836.91 + 80 2111.2748 -671.75001 0 -637.09124 -100964.78 + 90 2087.3167 -671.34241 0 -637.07694 -95316.087 + 100 1990.2171 -669.74712 0 -637.07564 -97755.737 +Loop time of 0.182669 on 4 procs for 100 steps with 128 atoms + +Pair time (%) = 0.149615 (81.905) +Neigh time (%) = 0.00144577 (0.791468) +Comm time (%) = 0.0237137 (12.9818) +Outpt time (%) = 0.00633347 (3.46718) +Other time (%) = 0.00156116 (0.854639) + +Nlocal: 32 ave 33 max 31 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 291.25 ave 297 max 284 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Neighs: 384.25 ave 419 max 351 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +FullNghs: 768.5 ave 805 max 731 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 3074 +Ave neighs/atom = 24.0156 +Neighbor list builds = 10 +Dangerous builds = 10 diff --git a/examples/meam/log.meam.12Feb07.linux.1 b/examples/meam/log.meam.12Feb07.linux.1 new file mode 100644 index 0000000000..cb54807e0c --- /dev/null +++ b/examples/meam/log.meam.12Feb07.linux.1 @@ -0,0 +1,59 @@ +LAMMPS (12 Feb 2007) +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.meam + 1 by 1 by 1 processor grid + 128 atoms + +pair_style meam +pair_coeff * * library.meam Si C sic.meam Si C + +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +dump 1 all atom 10 dump.meam + +run 100 +Memory usage per processor = 4.5032 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -636.93784 0 -636.93784 -76401.859 + 10 1777.5718 -666.27518 0 -637.0945 -150596.32 + 20 1908.6646 -668.42203 0 -637.08932 -120846.06 + 30 1937.3373 -668.90047 0 -637.09706 -101367.81 + 40 2110.906 -671.75978 0 -637.10706 -110475.14 + 50 2057.8682 -670.89589 0 -637.11385 -107817.44 + 60 1887.9614 -668.08977 0 -637.09693 -108906.46 + 70 2036.4427 -670.53667 0 -637.10635 -113836.91 + 80 2111.2748 -671.75001 0 -637.09124 -100964.78 + 90 2087.3167 -671.34241 0 -637.07694 -95316.087 + 100 1990.2171 -669.74712 0 -637.07564 -97755.737 +Loop time of 0.452112 on 1 procs for 100 steps with 128 atoms + +Pair time (%) = 0.425796 (94.1793) +Neigh time (%) = 0.008883 (1.96478) +Comm time (%) = 0.004133 (0.914154) +Outpt time (%) = 0.009616 (2.12691) +Other time (%) = 0.003684 (0.814842) + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 541 ave 541 max 541 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1537 ave 1537 max 1537 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3074 ave 3074 max 3074 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3074 +Ave neighs/atom = 24.0156 +Neighbor list builds = 10 +Dangerous builds = 10 diff --git a/examples/meam/log.meam.shear.12Feb07.liberty.4 b/examples/meam/log.meam.shear.12Feb07.liberty.4 new file mode 100644 index 0000000000..4d4af6e4e1 --- /dev/null +++ b/examples/meam/log.meam.shear.12Feb07.liberty.4 @@ -0,0 +1,163 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 2 by 2 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style meam +pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 5.05583 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346 + 25 223.02513 -8188.2962 0 -8148.4267 8998.4716 19539.346 + 50 300 -8152.0635 0 -8098.4335 10060.658 19678.279 + 75 308.13652 -8164.4552 0 -8109.3706 6520.8872 19773.8 + 100 300 -8178.2806 0 -8124.6506 4001.6051 19951.128 +Loop time of 1.77507 on 4 procs for 100 steps with 1912 atoms + +Pair time (%) = 1.7326 (97.6074) +Neigh time (%) = 0.00833803 (0.469729) +Comm time (%) = 0.0229964 (1.29552) +Outpt time (%) = 0.000789106 (0.0444549) +Other time (%) = 0.0103461 (0.582853) + +Nlocal: 478 ave 486 max 469 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 809 ave 818 max 801 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 5932.75 ave 6076 max 5807 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 11865.5 ave 12111 max 11653 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 47462 +Ave neighs/atom = 24.8232 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.meam.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 5.10101 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244 + 100 304.48468 -8173.0606 0 -8136.7859 425.54216 19949.638 + 200 292.7057 -8176.0355 0 -8141.1641 -420.37567 19967.921 + 300 300 -8174.2457 0 -8138.5052 -2225.0957 20035.454 + 400 301.8783 -8169.8228 0 -8133.8586 -954.54062 20072.806 + 500 297.3529 -8163.9704 0 -8128.5453 -636.90863 20224.627 + 600 300.21575 -8158.4937 0 -8122.7275 426.04354 20300.212 + 700 294.62668 -8149.3419 0 -8114.2416 2914.3315 20397.69 + 800 297.68293 -8140.221 0 -8104.7566 4382.9813 20500.434 + 900 307.34872 -8129.6288 0 -8093.0129 6273.2975 20626.218 + 1000 299.54856 -8114.9745 0 -8079.2878 9036.1509 20758.108 + 1100 298.61047 -8098.7531 0 -8063.1782 10485.79 20872.901 + 1200 293.03092 -8082.1069 0 -8047.1967 11405.523 21004.792 + 1300 307.76805 -8065.4274 0 -8028.7615 11979.925 21120.806 + 1400 300 -8051.592 0 -8015.8516 12466.399 21238.042 + 1500 308.53314 -8037.7116 0 -8000.9546 15186.116 21363.826 + 1600 300 -8031.857 0 -7996.1166 16229.579 21487.167 + 1700 300 -8022.9424 0 -7987.202 18187.876 21605.624 + 1800 300 -8009.2389 0 -7973.4984 18721.834 21735.072 + 1900 300.26712 -7997.956 0 -7962.1837 18855.604 21848.644 + 2000 300 -7987.6035 0 -7951.8631 18711.312 21976.871 + 2100 300 -7996.1806 0 -7960.4401 16424.414 22100.212 + 2200 305.54436 -8006.7713 0 -7970.3703 13205.691 22211.342 + 2300 300 -8010.5965 0 -7974.8561 11455.319 22342.011 + 2400 300 -8012.9434 0 -7977.2029 12543.014 22469.016 + 2500 300 -8014.3999 0 -7978.6595 12003.377 22583.809 + 2600 296.98849 -8009.1337 0 -7973.7521 11080.253 22707.151 + 2700 300 -8002.4065 0 -7966.666 8890.8608 22836.599 + 2800 300 -8005.4907 0 -7969.7503 7724.8308 22956.277 + 2900 308.79197 -8003.0392 0 -7966.2514 8308.48 23072.291 + 3000 300 -8014.1797 0 -7978.4393 5468.9701 23199.297 +Loop time of 57.0237 on 4 procs for 3000 steps with 1912 atoms + +Pair time (%) = 54.0924 (94.8594) +Neigh time (%) = 0.376733 (0.660661) +Comm time (%) = 0.885298 (1.55251) +Outpt time (%) = 1.00536 (1.76305) +Other time (%) = 0.663957 (1.16435) + +Nlocal: 478 ave 521 max 447 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 790.5 ave 838 max 745 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 5842.25 ave 6343 max 5608 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +FullNghs: 11684.5 ave 12654 max 11231 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 46738 +Ave neighs/atom = 24.4446 +Neighbor list builds = 225 +Dangerous builds = 0 diff --git a/examples/meam/log.meam.shear.12Feb07.linux.1 b/examples/meam/log.meam.shear.12Feb07.linux.1 new file mode 100644 index 0000000000..53422490d8 --- /dev/null +++ b/examples/meam/log.meam.shear.12Feb07.linux.1 @@ -0,0 +1,163 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 1 by 1 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style meam +pair_coeff * * library.meam Ni4 ni.meam Ni4 Ni4 Ni4 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 5.90372 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1387.2089 19539.346 + 25 222.78953 -8188.1215 0 -8148.2941 9099.4735 19539.346 + 50 300 -8149.7654 0 -8096.1353 10637.302 19676.681 + 75 304.80657 -8163.4557 0 -8108.9665 7048.2094 19752.029 + 100 300 -8173.6884 0 -8120.0584 5954.839 19878.848 +Loop time of 8.44709 on 1 procs for 100 steps with 1912 atoms + +Pair time (%) = 8.32882 (98.5999) +Neigh time (%) = 0.064361 (0.761931) +Comm time (%) = 0.015878 (0.18797) +Outpt time (%) = 0.001083 (0.012821) +Other time (%) = 0.036945 (0.43737) + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1672 ave 1672 max 1672 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23806 ave 23806 max 23806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 47612 ave 47612 max 47612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 47612 +Ave neighs/atom = 24.9017 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.meam.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 6.13252 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554 + 100 292.43462 -8178.5214 0 -8143.6823 2595.8245 19846.142 + 200 302.79029 -8177.5966 0 -8141.5238 928.09995 20038.569 + 300 291.68573 -8173.4974 0 -8138.7474 -1202.8487 20113.221 + 400 300 -8170.0629 0 -8134.3225 -1617.1537 20115.738 + 500 308.49792 -8164.7324 0 -8127.9796 -346.62656 20250.005 + 600 308.95879 -8159.1257 0 -8122.3179 1160.1349 20280.432 + 700 303.02599 -8150.2418 0 -8114.1409 2807.9227 20434.583 + 800 305.36804 -8140.8077 0 -8104.4278 3218.2338 20500.434 + 900 305.593 -8128.943 0 -8092.5363 3121.7248 20628.661 + 1000 308.39114 -8113.6413 0 -8076.9012 5180.0491 20758.108 + 1100 304.62199 -8096.7999 0 -8060.5088 8173.3442 20874.123 + 1200 293.41155 -8082.676 0 -8047.7205 9884.2077 20987.695 + 1300 303.32764 -8066.7733 0 -8030.6365 10196.38 21108.594 + 1400 304.17521 -8049.5115 0 -8013.2736 11518.937 21249.033 + 1500 300 -8038.1747 0 -8002.4342 12554.583 21361.383 + 1600 304.95273 -8030.5805 0 -7994.2501 12166.296 21483.504 + 1700 302.82122 -8019.1918 0 -7983.1152 11726.855 21604.403 + 1800 300 -8010.2021 0 -7974.4617 11039.327 21737.514 + 1900 309.75034 -7999.8523 0 -7962.9503 10360.771 21859.635 + 2000 303.95534 -7995.5876 0 -7959.3759 11106.855 21974.428 + 2100 300 -7998.4845 0 -7962.7441 9592.4431 22092.885 + 2200 300 -8010.3787 0 -7974.6383 7011.3257 22223.554 + 2300 300 -8013.8118 0 -7978.0714 7206.5123 22334.684 + 2400 300 -8016.5277 0 -7980.7872 8333.0814 22469.016 + 2500 309.73732 -8019.4133 0 -7982.5128 8734.2461 22586.252 + 2600 300 -8018.1897 0 -7982.4492 9088.9471 22702.266 + 2700 300.98484 -8016.4337 0 -7980.576 11358.168 22821.944 + 2800 309.26899 -8013.3976 0 -7976.5529 11582.101 22956.277 + 2900 305.82563 -8013.711 0 -7977.2765 8649.9858 23077.176 + 3000 309.93922 -8013.2879 0 -7976.3634 6488.7794 23187.085 +Loop time of 283.508 on 1 procs for 3000 steps with 1912 atoms + +Pair time (%) = 272.659 (96.1731) +Neigh time (%) = 2.77687 (0.979467) +Comm time (%) = 0.520133 (0.183463) +Outpt time (%) = 6.37939 (2.25016) +Other time (%) = 1.17315 (0.413799) + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1659 ave 1659 max 1659 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23351 ave 23351 max 23351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 46702 ave 46702 max 46702 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 46702 +Ave neighs/atom = 24.4257 +Neighbor list builds = 216 +Dangerous builds = 0 diff --git a/examples/melt/log.melt.1Oct06.liberty.4 b/examples/melt/log.melt.12Feb07.liberty.4 similarity index 80% rename from examples/melt/log.melt.1Oct06.liberty.4 rename to examples/melt/log.melt.12Feb07.liberty.4 index 72c26da253..4ffb3e4e31 100644 --- a/examples/melt/log.melt.1Oct06.liberty.4 +++ b/examples/melt/log.melt.12Feb07.liberty.4 @@ -1,10 +1,11 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 3d Lennard-Jones melt units lj atom_style atomic lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 20 0 20 0 20 create_box 1 box Created box = (0 0 0) to (33.5919 33.5919 33.5919) @@ -35,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press 150 1.6468325 -4.7503201 0 -2.2801485 5.857928 200 1.64095 -4.741475 0 -2.280127 5.8888655 250 1.6425393 -4.7441579 0 -2.2804259 5.8751067 -Loop time of 8.12523 on 4 procs for 250 steps with 32000 atoms +Loop time of 8.2969 on 4 procs for 250 steps with 32000 atoms -Pair time (%) = 4.33835 (53.3935) -Neigh time (%) = 0.377536 (4.64646) -Comm time (%) = 1.54992 (19.0754) -Outpt time (%) = 1.44447 (17.7775) -Other time (%) = 0.414967 (5.10714) +Pair time (%) = 4.39721 (52.9983) +Neigh time (%) = 0.378456 (4.56141) +Comm time (%) = 1.61733 (19.4932) +Outpt time (%) = 1.49492 (18.0178) +Other time (%) = 0.408981 (4.92932) Nlocal: 8000 ave 8011 max 7981 min Histogram: 1 0 0 0 0 0 0 2 0 1 diff --git a/examples/melt/log.melt.1Oct06.linux.1 b/examples/melt/log.melt.12Feb07.linux.1 similarity index 81% rename from examples/melt/log.melt.1Oct06.linux.1 rename to examples/melt/log.melt.12Feb07.linux.1 index fdf1abe79c..e892258c66 100644 --- a/examples/melt/log.melt.1Oct06.linux.1 +++ b/examples/melt/log.melt.12Feb07.linux.1 @@ -1,10 +1,11 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 3d Lennard-Jones melt units lj atom_style atomic lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 20 0 20 0 20 create_box 1 box Created box = (0 0 0) to (33.5919 33.5919 33.5919) @@ -35,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press 150 1.6434235 -4.7448489 0 -2.2797906 5.868853 200 1.6427413 -4.7436699 0 -2.279635 5.8804726 250 1.6373146 -4.7362602 0 -2.2803651 5.8998494 -Loop time of 43.5069 on 1 procs for 250 steps with 32000 atoms +Loop time of 39.819 on 1 procs for 250 steps with 32000 atoms -Pair time (%) = 34.5536 (79.421) -Neigh time (%) = 2.68746 (6.1771) -Comm time (%) = 0.753433 (1.73175) -Outpt time (%) = 3.74752 (8.61363) -Other time (%) = 1.76488 (4.05655) +Pair time (%) = 30.7479 (77.2193) +Neigh time (%) = 2.71683 (6.82296) +Comm time (%) = 0.67844 (1.70381) +Outpt time (%) = 3.83524 (9.63168) +Other time (%) = 1.84053 (4.62225) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/micelle/log.micelle.1Oct06.liberty.4 b/examples/micelle/log.micelle.12Feb07.liberty.4 similarity index 93% rename from examples/micelle/log.micelle.1Oct06.liberty.4 rename to examples/micelle/log.micelle.12Feb07.liberty.4 index 1a09f500e4..1bcf2e818d 100644 --- a/examples/micelle/log.micelle.1Oct06.liberty.4 +++ b/examples/micelle/log.micelle.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2d micelle simulation dimension 2 @@ -60,14 +60,14 @@ Step Temp E_pair E_mol TotEng Press 900 0.45 0.48352312 0.097223467 1.0301841 19.049897 950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988 1000 0.45 0.46260893 0.10106179 1.0131082 19.538971 -Loop time of 0.280434 on 4 procs for 1000 steps with 1200 atoms +Loop time of 0.303232 on 4 procs for 1000 steps with 1200 atoms -Pair time (%) = 0.0796104 (28.3883) -Bond time (%) = 0.00600582 (2.14162) -Neigh time (%) = 0.0159584 (5.69061) -Comm time (%) = 0.135316 (48.2525) -Outpt time (%) = 0.00330371 (1.17807) -Other time (%) = 0.0402393 (14.3489) +Pair time (%) = 0.0798574 (26.3354) +Bond time (%) = 0.0064292 (2.12022) +Neigh time (%) = 0.0161344 (5.3208) +Comm time (%) = 0.154442 (50.932) +Outpt time (%) = 0.00368738 (1.21603) +Other time (%) = 0.0426817 (14.0756) Nlocal: 300 ave 302 max 294 min Histogram: 1 0 0 0 0 0 0 0 0 3 @@ -176,14 +176,14 @@ Step Temp E_pair E_mol TotEng Press 58000 0.45181349 -2.1311357 0.05656415 -1.6233228 2.1515038 59000 0.45 -2.1345398 0.060573082 -1.6245292 1.715299 60000 0.45068289 -2.1230762 0.055943523 -1.6170131 2.1657885 -Loop time of 22.0261 on 4 procs for 60000 steps with 1200 atoms +Loop time of 23.1686 on 4 procs for 60000 steps with 1200 atoms -Pair time (%) = 7.22825 (32.8167) -Bond time (%) = 0.357983 (1.62527) -Neigh time (%) = 1.44528 (6.56168) -Comm time (%) = 9.7253 (44.1535) -Outpt time (%) = 0.557863 (2.53273) -Other time (%) = 2.71144 (12.3101) +Pair time (%) = 7.28988 (31.4644) +Bond time (%) = 0.388005 (1.6747) +Neigh time (%) = 1.50522 (6.49679) +Comm time (%) = 10.6076 (45.7844) +Outpt time (%) = 0.564966 (2.4385) +Other time (%) = 2.81294 (12.1412) Nlocal: 300 ave 308 max 291 min Histogram: 1 0 1 0 0 0 0 0 1 1 diff --git a/examples/micelle/log.micelle.1Oct06.linux.1 b/examples/micelle/log.micelle.12Feb07.linux.1 similarity index 93% rename from examples/micelle/log.micelle.1Oct06.linux.1 rename to examples/micelle/log.micelle.12Feb07.linux.1 index 4918c08b1b..e08d2d98be 100644 --- a/examples/micelle/log.micelle.1Oct06.linux.1 +++ b/examples/micelle/log.micelle.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2d micelle simulation dimension 2 @@ -60,14 +60,14 @@ Step Temp E_pair E_mol TotEng Press 900 0.45 0.48352312 0.097223467 1.0301841 19.049897 950 0.49451225 0.46619517 0.094098428 1.0541877 19.588988 1000 0.45 0.46260893 0.10106179 1.0131082 19.538971 -Loop time of 0.856573 on 1 procs for 1000 steps with 1200 atoms +Loop time of 0.878466 on 1 procs for 1000 steps with 1200 atoms -Pair time (%) = 0.502955 (58.7171) -Bond time (%) = 0.042687 (4.98346) -Neigh time (%) = 0.117298 (13.6939) -Comm time (%) = 0.027584 (3.22027) -Outpt time (%) = 0.002443 (0.285206) -Other time (%) = 0.163606 (19.1001) +Pair time (%) = 0.50753 (57.7746) +Bond time (%) = 0.04176 (4.75374) +Neigh time (%) = 0.106436 (12.1161) +Comm time (%) = 0.026899 (3.06204) +Outpt time (%) = 0.01353 (1.54018) +Other time (%) = 0.182311 (20.7533) Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -176,14 +176,14 @@ Step Temp E_pair E_mol TotEng Press 58000 0.46418464 -2.1277093 0.060472378 -1.6036325 1.7271421 59000 0.45 -2.1304819 0.057808836 -1.6232356 1.6864115 60000 0.45599586 -2.1338576 0.053131762 -1.6253 2.201508 -Loop time of 92.2957 on 1 procs for 60000 steps with 1200 atoms +Loop time of 82.7474 on 1 procs for 60000 steps with 1200 atoms -Pair time (%) = 65.5829 (71.0574) -Bond time (%) = 2.58619 (2.80207) -Neigh time (%) = 10.2969 (11.1565) -Comm time (%) = 2.26542 (2.45452) -Outpt time (%) = 1.35733 (1.47063) -Other time (%) = 10.2069 (11.0589) +Pair time (%) = 55.7131 (67.3292) +Bond time (%) = 2.54046 (3.07013) +Neigh time (%) = 9.8923 (11.9548) +Comm time (%) = 2.21129 (2.67234) +Outpt time (%) = 1.4498 (1.75208) +Other time (%) = 10.9404 (13.2215) Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/min/log.min.1Oct06.liberty.4 b/examples/min/log.min.12Feb07.liberty.4 similarity index 84% rename from examples/min/log.min.1Oct06.liberty.4 rename to examples/min/log.min.12Feb07.liberty.4 index beeeb20a59..0ee353dc9c 100644 --- a/examples/min/log.min.1Oct06.liberty.4 +++ b/examples/min/log.min.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2d Lennard-Jones melt and subsequent energy minimization units lj @@ -6,6 +6,7 @@ dimension 2 atom_style atomic lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 region box block 0 20 0 20 -0.1 0.1 create_box 1 box Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) @@ -26,7 +27,6 @@ fix 1 all nve fix 2 all enforce2d dump 1 all atom 100 dump.min -dump_modify 1 scale no thermo 100 @@ -44,13 +44,13 @@ Step Temp E_pair E_mol TotEng Press 800 3.2765339 -0.87171428 0 2.3986761 34.272397 900 3.4084164 -1.0031926 0 2.398833 32.606983 1000 3.3077995 -0.90272314 0 2.3988743 33.989676 -Loop time of 0.366177 on 4 procs for 1000 steps with 800 atoms +Loop time of 0.377246 on 4 procs for 1000 steps with 800 atoms -Pair time (%) = 0.0971868 (26.5409) -Neigh time (%) = 0.0321494 (8.77974) -Comm time (%) = 0.162145 (44.2804) -Outpt time (%) = 0.0241919 (6.60661) -Other time (%) = 0.0505046 (13.7924) +Pair time (%) = 0.098482 (26.1055) +Neigh time (%) = 0.0318925 (8.45403) +Comm time (%) = 0.175421 (46.5006) +Outpt time (%) = 0.0234827 (6.22477) +Other time (%) = 0.0479671 (12.7151) Nlocal: 200 ave 202 max 198 min Histogram: 1 0 0 0 0 2 0 0 0 1 @@ -80,7 +80,7 @@ Step Temp E_pair E_mol TotEng Press 1030 3.3077995 -2.9235394 0 0.37805797 3.8445956 1035 3.3077995 -2.9410562 0 0.36054119 3.6772327 1038 3.3077995 -2.9486794 0 0.35291801 3.5714315 -Loop time of 0.0907032 on 4 procs for 38 steps with 800 atoms +Loop time of 0.0975236 on 4 procs for 38 steps with 800 atoms Minimization stats: E initial, next-to-last, final = -0.902723 -2.94694 -2.94868 @@ -89,11 +89,11 @@ Minimization stats: Iterations = 38 Force evaluations = 185 -Pair time (%) = 0.0224806 (24.7848) -Neigh time (%) = 0.00274897 (3.03073) -Comm time (%) = 0.0270339 (29.8047) -Outpt time (%) = 0.016743 (18.4591) -Other time (%) = 0.0216968 (23.9206) +Pair time (%) = 0.0225257 (23.0977) +Neigh time (%) = 0.00271821 (2.78723) +Comm time (%) = 0.0309407 (31.7263) +Outpt time (%) = 0.0167403 (17.1654) +Other time (%) = 0.0245988 (25.2234) Nlocal: 200 ave 201 max 198 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/examples/min/log.min.1Oct06.linux.1 b/examples/min/log.min.12Feb07.linux.1 similarity index 85% rename from examples/min/log.min.1Oct06.linux.1 rename to examples/min/log.min.12Feb07.linux.1 index 057513d9cf..77584994fc 100644 --- a/examples/min/log.min.1Oct06.linux.1 +++ b/examples/min/log.min.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # 2d Lennard-Jones melt and subsequent energy minimization units lj @@ -6,6 +6,7 @@ dimension 2 atom_style atomic lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 region box block 0 20 0 20 -0.1 0.1 create_box 1 box Created box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) @@ -26,7 +27,6 @@ fix 1 all nve fix 2 all enforce2d dump 1 all atom 100 dump.min -dump_modify 1 scale no thermo 100 @@ -44,13 +44,13 @@ Step Temp E_pair E_mol TotEng Press 800 3.2765414 -0.87172188 0 2.398676 34.272332 900 3.4086632 -1.003472 0 2.3988 32.603903 1000 3.3011881 -0.89596181 0 2.3990365 34.054429 -Loop time of 1.30303 on 1 procs for 1000 steps with 800 atoms +Loop time of 1.20356 on 1 procs for 1000 steps with 800 atoms -Pair time (%) = 0.878404 (67.4122) -Neigh time (%) = 0.219869 (16.8736) -Comm time (%) = 0.035471 (2.72219) -Outpt time (%) = 0.041925 (3.21749) -Other time (%) = 0.127365 (9.7745) +Pair time (%) = 0.766051 (63.649) +Neigh time (%) = 0.224616 (18.6627) +Comm time (%) = 0.040716 (3.38298) +Outpt time (%) = 0.042399 (3.52281) +Other time (%) = 0.129774 (10.7825) Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -80,7 +80,7 @@ Step Temp E_pair E_mol TotEng Press 1030 3.3011881 -2.9246339 0 0.37036444 3.8097613 1035 3.3011881 -2.941932 0 0.35306633 3.6545452 1036 3.3011881 -2.9434242 0 0.3515742 3.6268584 -Loop time of 0.255988 on 1 procs for 36 steps with 800 atoms +Loop time of 0.234251 on 1 procs for 36 steps with 800 atoms Minimization stats: E initial, next-to-last, final = -0.895962 -2.94193 -2.94342 @@ -89,11 +89,11 @@ Minimization stats: Iterations = 36 Force evaluations = 177 -Pair time (%) = 0.182294 (71.2119) -Neigh time (%) = 0.017308 (6.76125) -Comm time (%) = 0.004652 (1.81727) -Outpt time (%) = 0.028575 (11.1626) -Other time (%) = 0.023159 (9.04691) +Pair time (%) = 0.158737 (67.7636) +Neigh time (%) = 0.016951 (7.23626) +Comm time (%) = 0.004804 (2.05079) +Outpt time (%) = 0.029892 (12.7607) +Other time (%) = 0.023867 (10.1886) Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/obstacle/log.obstacle.12Feb07.liberty.4 b/examples/obstacle/log.obstacle.12Feb07.liberty.4 new file mode 100644 index 0000000000..053ee75c41 --- /dev/null +++ b/examples/obstacle/log.obstacle.12Feb07.liberty.4 @@ -0,0 +1,134 @@ +LAMMPS (12 Feb 2007) +# 2d LJ obstacle flow + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 +region box block 0 40 0 10 -0.25 0.25 +create_box 3 box +Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) + 4 by 1 by 1 processor grid +create_atoms 1 +Created 840 atoms + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials + +pair_style lj/cut 1.12246 +pair_coeff * * 1.0 1.0 1.12246 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +120 atoms in group lower +region 2 block INF INF 8.75 INF INF INF +group upper region 2 +120 atoms in group upper +group boundary union lower upper +240 atoms in group boundary +group flow subtract all boundary +600 atoms in group flow + +set lower atom 2 + 120 settings made +set upper atom 3 + 120 settings made + +# initial velocities + +compute mobile flow temp +velocity flow create 1.0 482748 temp mobile +fix 1 all nve +fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 +fix_modify 2 temp mobile + +# Poiselle flow + +velocity boundary set 0.0 0.0 0.0 +fix 3 lower setforce 0.0 0.0 0.0 +fix 4 upper setforce 0.0 NULL 0.0 +fix 5 upper aveforce 0.0 -0.5 0.0 +fix 6 flow addforce 1.0 0.0 0.0 + +# 2 obstacles + +region void1 sphere 10 4 0 3 +delete_atoms region void1 +Deleted 35 atoms, new total = 805 +region void2 sphere 20 7 0 3 +delete_atoms region void2 +Deleted 35 atoms, new total = 770 + +fix 7 flow indent 100 sphere 10 4 0 4 +fix 8 flow indent 100 sphere 20 7 0 4 +fix 9 all enforce2d + +# Run + +timestep 0.003 +thermo 1000 +thermo_modify temp mobile + +dump 1 all atom 100 dump.obstacle +#dump 1 all custom 100 dump.custom tag type x y z vx vy + +run 25000 +Memory usage per processor = 1.44234 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.0006918 0 0 0.68683847 0.48039951 733.92473 + 1000 1 -0.3603446 0 0.32601904 1.5725867 779.90508 + 2000 1 -0.42832732 0 0.25803632 1.3587382 813.11821 + 3000 1 -0.47232806 0 0.21403558 1.4341388 844.88084 + 4000 1 -0.52763648 0 0.15872716 1.5459739 875.13499 + 5000 1 -0.48314311 0 0.20322052 1.4357888 907.02154 + 6000 1 -0.472141 0 0.21422264 1.3030726 924.98416 + 7000 1 -0.44830722 0 0.23805641 1.2882909 928.95817 + 8000 1 -0.43371728 0 0.25264635 1.132775 927.35692 + 9000 1 -0.41463177 0 0.27173186 1.1209309 921.76003 + 10000 1 -0.38315652 0 0.30320712 1.0966664 922.24088 + 11000 1 -0.37156486 0 0.31479878 1.1423804 919.78903 + 12000 1 -0.3742195 0 0.31214414 1.0593775 928.05099 + 13000 1 -0.38124076 0 0.30512288 1.1256769 929.73097 + 14000 1 -0.38555026 0 0.30081337 1.0946739 933.53885 + 15000 1 -0.40703488 0 0.27932876 1.0764066 930.2934 + 16000 1 -0.3725232 0 0.31384044 1.0011147 931.1519 + 17000 1 -0.38470452 0 0.30165912 0.99838577 928.91833 + 18000 1 -0.40199729 0 0.28436634 1.0888096 932.68523 + 19000 1 -0.37259199 0 0.31377165 0.97032094 938.58622 + 20000 1 -0.44719826 0 0.23916537 1.0118322 936.68972 + 21000 1 -0.39518804 0 0.29117559 1.0584198 935.59526 + 22000 1 -0.36368989 0 0.32267374 1.0593392 935.25352 + 23000 1 -0.41084354 0 0.27552009 0.9952792 936.90123 + 24000 1 -0.39025763 0 0.29610601 1.014413 941.44567 + 25000 1 -0.36909647 0 0.31726717 0.9812463 940.90255 +Loop time of 4.94495 on 4 procs for 25000 steps with 770 atoms + +Pair time (%) = 0.416176 (8.41618) +Neigh time (%) = 0.147718 (2.98725) +Comm time (%) = 2.01956 (40.8409) +Outpt time (%) = 0.358058 (7.24087) +Other time (%) = 2.00344 (40.5148) + +Nlocal: 192.5 ave 240 max 158 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Nghost: 42.5 ave 45 max 37 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 401.25 ave 559 max 288 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 1605 +Ave neighs/atom = 2.08442 +Neighbor list builds = 1636 +Dangerous builds = 0 diff --git a/examples/obstacle/log.obstacle.12Feb07.linux.1 b/examples/obstacle/log.obstacle.12Feb07.linux.1 new file mode 100644 index 0000000000..30d944c3c8 --- /dev/null +++ b/examples/obstacle/log.obstacle.12Feb07.linux.1 @@ -0,0 +1,134 @@ +LAMMPS (12 Feb 2007) +# 2d LJ obstacle flow + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 + +# create geometry + +lattice hex 0.7 +Lattice spacing in x,y,z = 1.28436 2.22457 1.28436 +region box block 0 40 0 10 -0.25 0.25 +create_box 3 box +Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) + 1 by 1 by 1 processor grid +create_atoms 1 +Created 840 atoms + +mass 1 1.0 +mass 2 1.0 +mass 3 1.0 + +# LJ potentials + +pair_style lj/cut 1.12246 +pair_coeff * * 1.0 1.0 1.12246 + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +120 atoms in group lower +region 2 block INF INF 8.75 INF INF INF +group upper region 2 +120 atoms in group upper +group boundary union lower upper +240 atoms in group boundary +group flow subtract all boundary +600 atoms in group flow + +set lower atom 2 + 120 settings made +set upper atom 3 + 120 settings made + +# initial velocities + +compute mobile flow temp +velocity flow create 1.0 482748 temp mobile +fix 1 all nve +fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0 +fix_modify 2 temp mobile + +# Poiselle flow + +velocity boundary set 0.0 0.0 0.0 +fix 3 lower setforce 0.0 0.0 0.0 +fix 4 upper setforce 0.0 NULL 0.0 +fix 5 upper aveforce 0.0 -0.5 0.0 +fix 6 flow addforce 1.0 0.0 0.0 + +# 2 obstacles + +region void1 sphere 10 4 0 3 +delete_atoms region void1 +Deleted 35 atoms, new total = 805 +region void2 sphere 20 7 0 3 +delete_atoms region void2 +Deleted 35 atoms, new total = 770 + +fix 7 flow indent 100 sphere 10 4 0 4 +fix 8 flow indent 100 sphere 20 7 0 4 +fix 9 all enforce2d + +# Run + +timestep 0.003 +thermo 1000 +thermo_modify temp mobile + +dump 1 all atom 100 dump.obstacle +#dump 1 all custom 100 dump.custom tag type x y z vx vy + +run 25000 +Memory usage per processor = 1.4637 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.0087541 0 0 0.69237216 0.48426997 733.92473 + 1000 1 -0.37498059 0 0.31138304 1.5619007 780.16609 + 2000 1 -0.42018277 0 0.26618087 1.381975 813.7446 + 3000 1 -0.49158436 0 0.19477928 1.4950838 846.60042 + 4000 1 -0.50974647 0 0.17661717 1.6968335 877.90837 + 5000 1 -0.48739676 0 0.19896688 1.372862 906.72222 + 6000 1 -0.45489776 0 0.23146588 1.1850408 922.1588 + 7000 1 -0.44298261 0 0.24338103 1.2353271 922.55214 + 8000 1 -0.39106076 0 0.29530287 1.2129774 923.79013 + 9000 1 -0.36894699 0 0.31741665 1.1022787 925.88908 + 10000 1 -0.40366483 0 0.28269881 1.0425088 924.55991 + 11000 1 -0.37662826 0 0.30973537 1.0605386 924.15634 + 12000 1 -0.39748408 0 0.28887956 1.1069709 926.1591 + 13000 1 -0.40533845 0 0.28102518 1.0999422 931.71451 + 14000 1 -0.39364952 0 0.29271412 0.98434706 935.98322 + 15000 1 -0.38545757 0 0.30090607 1.0288972 936.10741 + 16000 1 -0.34970581 0 0.33665783 1.0686207 939.12879 + 17000 1 -0.35935376 0 0.32700987 0.96188021 939.41127 + 18000 1 -0.38218429 0 0.30417934 0.97219528 939.42804 + 19000 1 -0.35002145 0 0.33634218 0.96884865 941.93045 + 20000 1 -0.37936966 0 0.30699398 1.0604325 935.73258 + 21000 1 -0.3797544 0 0.30660924 1.0525308 936.59648 + 22000 1 -0.37015981 0 0.31620383 1.0908613 935.05927 + 23000 1 -0.39940438 0 0.28695925 1.0860163 932.28118 + 24000 1 -0.36738604 0 0.3189776 0.97212319 936.04359 + 25000 1 -0.36023241 0 0.32613123 1.0971047 938.21817 +Loop time of 12.2357 on 1 procs for 25000 steps with 770 atoms + +Pair time (%) = 2.69352 (22.0137) +Neigh time (%) = 0.822182 (6.71956) +Comm time (%) = 0.283775 (2.31925) +Outpt time (%) = 3.9804 (32.5312) +Other time (%) = 4.45578 (36.4163) + +Nlocal: 770 ave 770 max 770 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1637 ave 1637 max 1637 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1637 +Ave neighs/atom = 2.12597 +Neighbor list builds = 1632 +Dangerous builds = 0 diff --git a/examples/obstacle/log.obstacle.1Oct06.liberty.4 b/examples/obstacle/log.obstacle.1Oct06.liberty.4 deleted file mode 100644 index 52c50000ae..0000000000 --- a/examples/obstacle/log.obstacle.1Oct06.liberty.4 +++ /dev/null @@ -1,133 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 40 0 10 -0.25 0.25 -create_box 3 box -Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) - 4 by 1 by 1 processor grid -create_atoms 1 -Created 840 atoms - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 - -# LJ potentials - -pair_style lj/cut 1.12246 -pair_coeff * * 1.0 1.0 1.12246 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -120 atoms in group lower -region 2 block INF INF 8.75 INF INF INF -group upper region 2 -120 atoms in group upper -group boundary union lower upper -240 atoms in group boundary -group flow subtract all boundary -600 atoms in group flow - -set lower atom 2 - 120 settings made -set upper atom 3 - 120 settings made - -# initial velocities - -temperature mobile flow full -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 37 atoms, new total = 767 - -fix 7 flow indent 100 sphere 10 4 0 4 -fix 8 flow indent 100 sphere 20 7 0 4 -fix 9 all enforce2d - -# Run - -timestep 0.003 -thermo 1000 -thermo_modify temp mobile - -dump 1 all atom 100 dump.obstacle -#dump 1 all custom 100 dump.custom tag type x y z vx vy - -run 25000 -Memory usage per processor = 1.44234 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.0026027 0 0 0.68692013 0.47858472 733.92473 - 1000 1 -0.37738477 0 0.30775213 1.5583691 784.71717 - 2000 1 -0.41654339 0 0.26859351 1.4383017 811.91076 - 3000 1 -0.457908 0 0.22722889 1.4560268 840.96593 - 4000 1 -0.49703654 0 0.18810036 1.6667159 875.09273 - 5000 1 -0.5036762 0 0.18146069 1.5201858 896.06529 - 6000 1 -0.46146759 0 0.22366931 1.2626363 910.96886 - 7000 1 -0.45319553 0 0.23194137 1.2400164 919.79024 - 8000 1 -0.43703324 0 0.24810365 1.1687124 917.54854 - 9000 1 -0.41944398 0 0.26569292 1.1506946 919.08596 - 10000 1 -0.38212395 0 0.30301294 1.2159701 922.73564 - 11000 1 -0.40131109 0 0.2838258 1.0143617 928.59439 - 12000 1 -0.40729865 0 0.27783825 1.1463534 927.92228 - 13000 1 -0.40247949 0 0.28265741 1.0362177 932.66931 - 14000 1 -0.40708584 0 0.27805106 1.05021 931.20813 - 15000 1 -0.38885172 0 0.29628518 0.97302912 932.47567 - 16000 1 -0.36720972 0 0.31792717 1.0900379 929.29673 - 17000 1 -0.38146707 0 0.30366982 1.0608592 931.83222 - 18000 1 -0.38710515 0 0.29803175 0.91156243 940.47326 - 19000 1 -0.38215507 0 0.30298183 1.049551 937.81127 - 20000 1 -0.33197729 0 0.35315961 0.97020648 938.40346 - 21000 1 -0.33775592 0 0.34738098 1.0035901 932.85086 - 22000 1 -0.38733229 0 0.29780461 1.0175281 926.40207 - 23000 1 -0.35819884 0 0.32693805 1.0468418 927.63479 - 24000 1 -0.36327235 0 0.32186455 1.0859266 930.98575 - 25000 1 -0.41296958 0 0.27216731 1.0157726 929.59365 -Loop time of 4.53299 on 4 procs for 25000 steps with 767 atoms - -Pair time (%) = 0.355299 (7.83807) -Neigh time (%) = 0.1305 (2.87891) -Comm time (%) = 1.82422 (40.2431) -Outpt time (%) = 0.366969 (8.09551) -Other time (%) = 1.856 (40.9444) - -Nlocal: 191.75 ave 243 max 152 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Nghost: 41.75 ave 45 max 40 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Neighs: 405.5 ave 588 max 272 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 1622 -Ave neighs/atom = 2.11473 -Neighbor list builds = 1613 -Dangerous builds = 0 diff --git a/examples/obstacle/log.obstacle.1Oct06.linux.1 b/examples/obstacle/log.obstacle.1Oct06.linux.1 deleted file mode 100644 index 0585ed6911..0000000000 --- a/examples/obstacle/log.obstacle.1Oct06.linux.1 +++ /dev/null @@ -1,133 +0,0 @@ -LAMMPS (1 Oct 2006) -# 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 -region box block 0 40 0 10 -0.25 0.25 -create_box 3 box -Created box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) - 1 by 1 by 1 processor grid -create_atoms 1 -Created 840 atoms - -mass 1 1.0 -mass 2 1.0 -mass 3 1.0 - -# LJ potentials - -pair_style lj/cut 1.12246 -pair_coeff * * 1.0 1.0 1.12246 - -# define groups - -region 1 block INF INF INF 1.25 INF INF -group lower region 1 -120 atoms in group lower -region 2 block INF INF 8.75 INF INF INF -group upper region 2 -120 atoms in group upper -group boundary union lower upper -240 atoms in group boundary -group flow subtract all boundary -600 atoms in group flow - -set lower atom 2 - 120 settings made -set upper atom 3 - 120 settings made - -# initial velocities - -temperature mobile flow full -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 37 atoms, new total = 767 - -fix 7 flow indent 100 sphere 10 4 0 4 -fix 8 flow indent 100 sphere 20 7 0 4 -fix 9 all enforce2d - -# Run - -timestep 0.003 -thermo 1000 -thermo_modify temp mobile - -dump 1 all atom 100 dump.obstacle -#dump 1 all custom 100 dump.custom tag type x y z vx vy - -run 25000 -Memory usage per processor = 1.46358 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.0019297 0 0 0.68645902 0.47826346 733.92473 - 1000 1 -0.35063938 0 0.33449751 1.6522953 783.62722 - 2000 1 -0.4338009 0 0.25133599 1.3442754 814.00845 - 3000 1 -0.48560531 0 0.19953159 1.3851427 842.4322 - 4000 1 -0.52446917 0 0.16066773 1.534073 880.36205 - 5000 1 -0.46416349 0 0.22097341 1.288376 915.89876 - 6000 1 -0.46692642 0 0.21821047 1.2806072 927.05522 - 7000 1 -0.44824027 0 0.23689663 1.1691239 935.06903 - 8000 1 -0.44835316 0 0.23678374 1.0958272 931.19324 - 9000 1 -0.3927248 0 0.2924121 1.1093553 927.69772 - 10000 1 -0.38347162 0 0.30166528 1.0818633 923.32891 - 11000 1 -0.4036644 0 0.28147249 1.1190364 925.22091 - 12000 1 -0.37573271 0 0.30940418 1.0661954 932.99191 - 13000 1 -0.38127169 0 0.30386521 1.0347388 934.82878 - 14000 1 -0.3917136 0 0.2934233 1.0359581 934.76479 - 15000 1 -0.38159291 0 0.30354398 1.1029874 934.15381 - 16000 1 -0.36036528 0 0.32477162 0.98739828 932.69222 - 17000 1 -0.36939144 0 0.31574546 1.1260055 934.51009 - 18000 1 -0.37198742 0 0.31314948 0.95796075 935.53765 - 19000 1 -0.35008405 0 0.33505284 1.0525993 932.71924 - 20000 1 -0.3946193 0 0.2905176 1.0181298 932.72262 - 21000 1 -0.36508116 0 0.32005573 1.0466637 937.18711 - 22000 1 -0.37402575 0 0.31111115 1.0836104 933.86271 - 23000 1 -0.37087569 0 0.3142612 1.0454446 933.85941 - 24000 1 -0.37779474 0 0.30734216 1.1488903 934.78585 - 25000 1 -0.3530395 0 0.3320974 0.9608987 937.57522 -Loop time of 11.2929 on 1 procs for 25000 steps with 767 atoms - -Pair time (%) = 3.08741 (27.3394) -Neigh time (%) = 0.90573 (8.02035) -Comm time (%) = 0.344634 (3.05178) -Outpt time (%) = 0.923682 (8.17932) -Other time (%) = 6.03144 (53.4092) - -Nlocal: 767 ave 767 max 767 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 46 ave 46 max 46 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1643 ave 1643 max 1643 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1643 -Ave neighs/atom = 2.14211 -Neighbor list builds = 1601 -Dangerous builds = 0 diff --git a/examples/peptide/log.peptide.12Feb07.liberty.4 b/examples/peptide/log.peptide.12Feb07.liberty.4 new file mode 100644 index 0000000000..9d577128c3 --- /dev/null +++ b/examples/peptide/log.peptide.12Feb07.liberty.4 @@ -0,0 +1,154 @@ +LAMMPS (12 Feb 2007) +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + 3 = max bonds/atom + 6 = max angles/atom + 14 = max dihedrals/atom + 1 = max impropers/atom + 1 by 2 by 2 processor grid + 2004 atoms + 2004 velocities + 1365 bonds + 786 angles + 207 dihedrals + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style multi +thermo 50 + +fix 1 all nvt 275.0 275.0 100.0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +group peptide type <= 12 +84 atoms in group peptide +dump 1 peptide atom 10 dump.peptide +dump 2 peptide bond 300 dump.bond + +run 300 +PPPM initialization ... + G vector = 0.268725 + grid = 15 15 15 + RMS precision = 4.85953e-05 + brick FFT buffer size/proc = 4312 960 3696 +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Memory usage per processor = 8.89765 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005 +PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726 +E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 +E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771 +---------------- Step 50 ----- CPU = 1.0231 (sec) ---------------- +TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752 +PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365 +E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774 +E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 7.80748e-07 + 6 0.997 1.06201e-06 + 8 1.08 6.20434e-07 + 10 1.111 6.23399e-07 + 12 1.08 2.68045e-07 + 14 0.96 0 + 18 0.957201 5.38002e-06 + 31 104.52 0.000502303 +---------------- Step 100 ----- CPU = 2.0570 (sec) ---------------- +TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656 +PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429 +E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271 +E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634 +---------------- Step 150 ----- CPU = 3.1067 (sec) ---------------- +TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739 +PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594 +E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698 +E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851 +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 2.18831e-07 + 6 0.997 1.50909e-07 + 8 1.08 6.58563e-08 + 10 1.111 5.56695e-07 + 12 1.08 1.99338e-07 + 14 0.96 0 + 18 0.957201 3.59689e-06 + 31 104.52 0.000388134 +---------------- Step 200 ----- CPU = 4.1845 (sec) ---------------- +TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480 +PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035 +E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209 +E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571 +---------------- Step 250 ----- CPU = 5.2516 (sec) ---------------- +TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530 +PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972 +E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340 +E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153 +SHAKE stats (type/ave/delta) on step 300 + 4 1.111 3.78173e-06 + 6 0.997001 3.51761e-06 + 8 1.08 2.09202e-06 + 10 1.111 5.64179e-06 + 12 1.08 2.10252e-06 + 14 0.96 0 + 18 0.957202 7.62675e-06 + 31 104.52 0.00080599 +---------------- Step 300 ----- CPU = 6.3128 (sec) ---------------- +TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484 +PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644 +E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075 +E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013 +Loop time of 6.31307 on 4 procs for 300 steps with 2004 atoms + +Pair time (%) = 3.7478 (59.3657) +Bond time (%) = 0.0190388 (0.301577) +Kspce time (%) = 1.04423 (16.5407) +Neigh time (%) = 0.366191 (5.80052) +Comm time (%) = 0.669456 (10.6043) +Outpt time (%) = 0.0110819 (0.175539) +Other time (%) = 0.455277 (7.21165) + +FFT time (% of Kspce) = 0.219916 (21.0601) +FFT Gflps 3d 1d-only = 0.748076 3.75246 + +Nlocal: 501 ave 508 max 490 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 6586.25 ave 6628 max 6548 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 177008 ave 180559 max 170208 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 708030 +Ave neighs/atom = 353.308 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 26 +Dangerous builds = 0 + diff --git a/examples/peptide/log.peptide.12Feb07.linux.1 b/examples/peptide/log.peptide.12Feb07.linux.1 new file mode 100644 index 0000000000..bbca298400 --- /dev/null +++ b/examples/peptide/log.peptide.12Feb07.linux.1 @@ -0,0 +1,154 @@ +LAMMPS (12 Feb 2007) +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + 3 = max bonds/atom + 6 = max angles/atom + 14 = max dihedrals/atom + 1 = max impropers/atom + 1 by 1 by 1 processor grid + 2004 atoms + 2004 velocities + 1365 bonds + 786 angles + 207 dihedrals + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style multi +thermo 50 + +fix 1 all nvt 275.0 275.0 100.0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +group peptide type <= 12 +84 atoms in group peptide +dump 1 peptide atom 10 dump.peptide +dump 2 peptide bond 300 dump.bond + +run 300 +PPPM initialization ... + G vector = 0.268725 + grid = 15 15 15 + RMS precision = 4.85953e-05 + brick FFT buffer size/proc = 10648 3375 5808 +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Memory usage per processor = 19.9477 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005 +PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726 +E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 +E_coul = 26772.2794 E_long = -33907.9417 Press = -845.4771 +---------------- Step 50 ----- CPU = 7.8161 (sec) ---------------- +TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752 +PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365 +E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774 +E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 7.80748e-07 + 6 0.997 1.06201e-06 + 8 1.08 6.20434e-07 + 10 1.111 6.23399e-07 + 12 1.08 2.68045e-07 + 14 0.96 0 + 18 0.957201 5.38002e-06 + 31 104.52 0.000502303 +---------------- Step 100 ----- CPU = 15.6613 (sec) ---------------- +TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656 +PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429 +E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271 +E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634 +---------------- Step 150 ----- CPU = 23.6754 (sec) ---------------- +TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739 +PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594 +E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698 +E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851 +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 2.18831e-07 + 6 0.997 1.50909e-07 + 8 1.08 6.58563e-08 + 10 1.111 5.56695e-07 + 12 1.08 1.99338e-07 + 14 0.96 0 + 18 0.957201 3.59689e-06 + 31 104.52 0.000388134 +---------------- Step 200 ----- CPU = 31.3970 (sec) ---------------- +TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480 +PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035 +E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209 +E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571 +---------------- Step 250 ----- CPU = 39.4151 (sec) ---------------- +TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530 +PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972 +E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340 +E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153 +SHAKE stats (type/ave/delta) on step 300 + 4 1.111 3.78173e-06 + 6 0.997001 3.51761e-06 + 8 1.08 2.09202e-06 + 10 1.111 5.64179e-06 + 12 1.08 2.10252e-06 + 14 0.96 0 + 18 0.957202 7.62675e-06 + 31 104.52 0.00080599 +---------------- Step 300 ----- CPU = 47.4101 (sec) ---------------- +TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484 +PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644 +E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075 +E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013 +Loop time of 47.4104 on 1 procs for 300 steps with 2004 atoms + +Pair time (%) = 38.771 (81.7773) +Bond time (%) = 0.074676 (0.15751) +Kspce time (%) = 3.46724 (7.31323) +Neigh time (%) = 4.29476 (9.05867) +Comm time (%) = 0.326736 (0.689165) +Outpt time (%) = 0.019285 (0.0406767) +Other time (%) = 0.456781 (0.963461) + +FFT time (% of Kspce) = 1.14174 (32.9294) +FFT Gflps 3d 1d-only = 0.144091 0.210559 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11181 ave 11181 max 11181 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708030 ave 708030 max 708030 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708030 +Ave neighs/atom = 353.308 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 26 +Dangerous builds = 0 + diff --git a/examples/peptide/log.peptide.1Oct06.liberty.4 b/examples/peptide/log.peptide.1Oct06.liberty.4 deleted file mode 100644 index 8d0e3452a4..0000000000 --- a/examples/peptide/log.peptide.1Oct06.liberty.4 +++ /dev/null @@ -1,154 +0,0 @@ -LAMMPS (1 Oct 2006) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - 1 by 2 by 2 processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -thermo_style multi -thermo 50 - -fix 1 all nvt 275.0 275.0 100.0 -fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -group peptide type <= 12 -84 atoms in group peptide -dump 1 peptide atom 10 dump.peptide -dump 2 peptide bond 300 dump.bond - -run 300 -PPPM initialization ... - G vector = 0.268725 - grid = 15 15 15 - RMS precision = 4.85953e-05 - brick FFT buffer size/proc = 4312 960 3696 -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 8.89765 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -5237.4557 KinEng = 1134.9184 Temp = 282.1027 -PotEng = -6372.3741 E_bond = 16.5572 E_angle = 36.3726 -E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 -E_coul = 26772.2705 E_long = -33907.9305 Press = -845.7315 ----------------- Step 50 ----- CPU = 1.4801 (sec) ---------------- -TotEng = -5247.5537 KinEng = 1132.3981 Temp = 281.4762 -PotEng = -6379.9518 E_bond = 12.2118 E_angle = 31.7364 -E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1762 -E_coul = 26804.4518 E_long = -33907.7036 Press = -1332.2322 -SHAKE stats (type/ave/delta) on step 100 - 4 1.111 7.81219e-07 - 6 0.997 1.06269e-06 - 8 1.08 6.20924e-07 - 10 1.111 6.23819e-07 - 12 1.08 2.68216e-07 - 14 0.96 0 - 18 0.957201 5.38162e-06 - 31 104.52 0.000502412 ----------------- Step 100 ----- CPU = 2.9482 (sec) ---------------- -TotEng = -5258.0208 KinEng = 1078.0404 Temp = 267.9647 -PotEng = -6336.0612 E_bond = 14.4827 E_angle = 43.4425 -E_dihed = 15.2568 E_impro = 2.3160 E_vdwl = 708.3258 -E_coul = 26786.6805 E_long = -33906.5655 Press = -648.9282 ----------------- Step 150 ----- CPU = 4.4355 (sec) ---------------- -TotEng = -5287.3158 KinEng = 1098.5907 Temp = 273.0729 -PotEng = -6385.9065 E_bond = 17.4922 E_angle = 32.8590 -E_dihed = 15.1622 E_impro = 1.6521 E_vdwl = 736.9709 -E_coul = 26717.2418 E_long = -33907.2848 Press = -333.3566 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 2.18765e-07 - 6 0.997 1.50571e-07 - 8 1.08 6.57567e-08 - 10 1.111 5.57115e-07 - 12 1.08 1.98908e-07 - 14 0.96 0 - 18 0.957201 3.59647e-06 - 31 104.52 0.000388049 ----------------- Step 200 ----- CPU = 5.8989 (sec) ---------------- -TotEng = -5308.4800 KinEng = 1100.4956 Temp = 273.5463 -PotEng = -6408.9756 E_bond = 18.2711 E_angle = 33.3032 -E_dihed = 16.8153 E_impro = 2.6053 E_vdwl = 686.3176 -E_coul = 26736.1059 E_long = -33902.3940 Press = -1470.9775 ----------------- Step 250 ----- CPU = 7.3982 (sec) ---------------- -TotEng = -5294.1836 KinEng = 1071.1372 Temp = 266.2488 -PotEng = -6365.3209 E_bond = 14.2026 E_angle = 39.1962 -E_dihed = 19.4540 E_impro = 3.1384 E_vdwl = 753.6645 -E_coul = 26713.7437 E_long = -33908.7203 Press = -187.3211 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 3.78222e-06 - 6 0.997001 3.50327e-06 - 8 1.08 2.09306e-06 - 10 1.111 5.643e-06 - 12 1.08 2.10265e-06 - 14 0.96 0 - 18 0.957202 7.61122e-06 - 31 104.52 0.000804522 ----------------- Step 300 ----- CPU = 8.8909 (sec) ---------------- -TotEng = -5251.4247 KinEng = 1123.3204 Temp = 279.2198 -PotEng = -6374.7450 E_bond = 14.2228 E_angle = 38.4702 -E_dihed = 18.1329 E_impro = 2.3701 E_vdwl = 715.7685 -E_coul = 26745.4242 E_long = -33909.1337 Press = -464.7492 -Loop time of 8.89127 on 4 procs for 300 steps with 2004 atoms - -Pair time (%) = 5.43468 (61.1237) -Bond time (%) = 0.0192376 (0.216365) -Kspce time (%) = 1.92633 (21.6654) -Neigh time (%) = 0.360919 (4.05924) -Comm time (%) = 0.683199 (7.68393) -Outpt time (%) = 0.0141159 (0.158762) -Other time (%) = 0.452794 (5.09256) - -FFT time (% of Kspce) = 0.221518 (11.4995) -FFT Gflps 3d 1d-only = 0.742666 3.96667 - -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: 177010 ave 180567 max 170204 min -Histogram: 1 0 0 0 0 0 0 1 1 1 - -Total # of neighbors = 708038 -Ave neighs/atom = 353.312 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 26 -Dangerous builds = 0 - diff --git a/examples/peptide/log.peptide.1Oct06.linux.1 b/examples/peptide/log.peptide.1Oct06.linux.1 deleted file mode 100644 index ccaf3dba36..0000000000 --- a/examples/peptide/log.peptide.1Oct06.linux.1 +++ /dev/null @@ -1,154 +0,0 @@ -LAMMPS (1 Oct 2006) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - 1 by 1 by 1 processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -thermo_style multi -thermo 50 - -fix 1 all nvt 275.0 275.0 100.0 -fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -group peptide type <= 12 -84 atoms in group peptide -dump 1 peptide atom 10 dump.peptide -dump 2 peptide bond 300 dump.bond - -run 300 -PPPM initialization ... - G vector = 0.268725 - grid = 15 15 15 - RMS precision = 4.85953e-05 - brick FFT buffer size/proc = 10648 3375 5808 -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 19.9477 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -5237.4557 KinEng = 1134.9184 Temp = 282.1027 -PotEng = -6372.3741 E_bond = 16.5572 E_angle = 36.3726 -E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 -E_coul = 26772.2705 E_long = -33907.9305 Press = -845.7315 ----------------- Step 50 ----- CPU = 7.8391 (sec) ---------------- -TotEng = -5247.5537 KinEng = 1132.3981 Temp = 281.4762 -PotEng = -6379.9518 E_bond = 12.2118 E_angle = 31.7364 -E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1762 -E_coul = 26804.4518 E_long = -33907.7036 Press = -1332.2322 -SHAKE stats (type/ave/delta) on step 100 - 4 1.111 7.81219e-07 - 6 0.997 1.06269e-06 - 8 1.08 6.20924e-07 - 10 1.111 6.23819e-07 - 12 1.08 2.68216e-07 - 14 0.96 0 - 18 0.957201 5.38162e-06 - 31 104.52 0.000502412 ----------------- Step 100 ----- CPU = 15.6343 (sec) ---------------- -TotEng = -5258.0208 KinEng = 1078.0404 Temp = 267.9647 -PotEng = -6336.0612 E_bond = 14.4827 E_angle = 43.4425 -E_dihed = 15.2568 E_impro = 2.3160 E_vdwl = 708.3258 -E_coul = 26786.6805 E_long = -33906.5655 Press = -648.9282 ----------------- Step 150 ----- CPU = 23.5108 (sec) ---------------- -TotEng = -5287.3158 KinEng = 1098.5907 Temp = 273.0729 -PotEng = -6385.9065 E_bond = 17.4922 E_angle = 32.8590 -E_dihed = 15.1622 E_impro = 1.6521 E_vdwl = 736.9709 -E_coul = 26717.2418 E_long = -33907.2848 Press = -333.3566 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 2.18765e-07 - 6 0.997 1.50571e-07 - 8 1.08 6.57567e-08 - 10 1.111 5.57115e-07 - 12 1.08 1.98908e-07 - 14 0.96 0 - 18 0.957201 3.59647e-06 - 31 104.52 0.000388049 ----------------- Step 200 ----- CPU = 31.1103 (sec) ---------------- -TotEng = -5308.4800 KinEng = 1100.4956 Temp = 273.5463 -PotEng = -6408.9756 E_bond = 18.2711 E_angle = 33.3032 -E_dihed = 16.8153 E_impro = 2.6053 E_vdwl = 686.3176 -E_coul = 26736.1059 E_long = -33902.3940 Press = -1470.9775 ----------------- Step 250 ----- CPU = 39.2012 (sec) ---------------- -TotEng = -5294.1836 KinEng = 1071.1372 Temp = 266.2488 -PotEng = -6365.3209 E_bond = 14.2026 E_angle = 39.1962 -E_dihed = 19.4540 E_impro = 3.1384 E_vdwl = 753.6645 -E_coul = 26713.7437 E_long = -33908.7203 Press = -187.3211 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 3.78222e-06 - 6 0.997001 3.50327e-06 - 8 1.08 2.09306e-06 - 10 1.111 5.643e-06 - 12 1.08 2.10265e-06 - 14 0.96 0 - 18 0.957202 7.61122e-06 - 31 104.52 0.000804522 ----------------- Step 300 ----- CPU = 47.1755 (sec) ---------------- -TotEng = -5251.4247 KinEng = 1123.3204 Temp = 279.2198 -PotEng = -6374.7450 E_bond = 14.2228 E_angle = 38.4702 -E_dihed = 18.1329 E_impro = 2.3701 E_vdwl = 715.7685 -E_coul = 26745.4242 E_long = -33909.1337 Press = -464.7492 -Loop time of 47.1756 on 1 procs for 300 steps with 2004 atoms - -Pair time (%) = 38.5968 (81.8151) -Bond time (%) = 0.077238 (0.163724) -Kspce time (%) = 3.51546 (7.45187) -Neigh time (%) = 4.11099 (8.71422) -Comm time (%) = 0.360056 (0.763225) -Outpt time (%) = 0.017432 (0.0369513) -Other time (%) = 0.497656 (1.0549) - -FFT time (% of Kspce) = 1.1808 (33.5887) -FFT Gflps 3d 1d-only = 0.139324 0.209866 - -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: 708038 ave 708038 max 708038 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708038 -Ave neighs/atom = 353.312 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 26 -Dangerous builds = 0 - diff --git a/examples/pour/log.pour.12Feb07.liberty.4 b/examples/pour/log.pour.12Feb07.liberty.4 new file mode 100644 index 0000000000..de3380da76 --- /dev/null +++ b/examples/pour/log.pour.12Feb07.liberty.4 @@ -0,0 +1,136 @@ +LAMMPS (12 Feb 2007) +# Pour granular particles into chute container, then induce flow + +atom_style granular +boundary p p fm +newton off + +region reg block -10 10 -10 10 -0.5 16 units box +create_box 1 reg +Created box = (-10 -10 -0.5) to (10 10 16) + 2 by 2 by 1 processor grid + +neighbor 0.2 bin +neigh_modify delay 0 + +# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001) +# are used in this example file to produce a quick simulation and movie. +# More appropriate values for realistic simulations would be +# k = 2.0e5 and dt = 0.0001, as in bench/in.chute. + +pair_style gran/history 2000.0 50.0 0.50 0 +timestep 0.001 + +fix 1 all nve/gran +fix 2 all gravity spherical 0.0 -180.0 +fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5 + +region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box +fix ins all pour 3000 1 300719 vol 0.13 50 region slab +Particle insertion: 402 every 3162 steps, 3000 by step 22135 + +thermo_style granular +thermo 1000 +thermo_modify lost ignore +compute_modify thermo_temp dynamic yes + +dump id all atom 125 dump.pour +run 25000 +Memory usage per processor = 0.335693 Mbytes +Step Atoms KinEng RotKEgrn Volume + 0 0 -0 0 6600 + 1000 402 779.98578 0 6600 + 2000 402 1424.4252 0 6600 + 3000 402 1424.6738 13.243803 6600 + 4000 804 1725.4319 47.250762 6600 + 5000 804 1605.2015 60.084404 6600 + 6000 804 1371.3425 69.247899 6600 + 7000 1206 1524.3574 74.071529 6600 + 8000 1206 1418.8997 60.727536 6600 + 9000 1206 1258.0238 52.045974 6600 + 10000 1608 1387.2361 50.17452 6600 + 11000 1608 1226.8131 50.547962 6600 + 12000 1608 1195.97 41.951622 6600 + 13000 2010 1312.7197 51.888514 6600 + 14000 2010 1176.2242 43.086598 6600 + 15000 2010 972.7316 46.053358 6600 + 16000 2412 1040.0907 45.535472 6600 + 17000 2412 1033.3053 37.798831 6600 + 18000 2412 929.20314 37.574869 6600 + 19000 2814 1010.9926 38.716555 6600 + 20000 2814 953.49259 41.76949 6600 + 21000 2814 768.81045 45.76655 6600 + 22000 2814 501.98827 42.18076 6600 + 23000 3000 428.98535 35.914834 6600 + 24000 3000 365.81359 22.320118 6600 + 25000 3000 227.404 23.276402 6600 +Loop time of 13.8863 on 4 procs for 25000 steps with 3000 atoms + +Pair time (%) = 4.97869 (35.8531) +Neigh time (%) = 0.706881 (5.09047) +Comm time (%) = 3.96635 (28.5629) +Outpt time (%) = 0.637875 (4.59354) +Other time (%) = 3.59655 (25.8999) + +Nlocal: 750 ave 766 max 734 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 388.75 ave 395 max 386 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Neighs: 3588.5 ave 3661 max 3520 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 14354 +Ave neighs/atom = 4.78467 +Neighbor list builds = 1154 +Dangerous builds = 0 + +unfix ins +fix 2 all gravity chute 26.0 +run 25000 +Memory usage per processor = 6.82853 Mbytes +Step Atoms KinEng RotKEgrn Volume + 25000 3000 227.404 23.276402 6600 + 26000 3000 106.43826 18.101442 6600 + 27000 3000 113.05348 12.760864 6600 + 28000 3000 205.07328 11.584573 6600 + 29000 3000 358.43804 15.113582 6600 + 30000 3000 598.64933 20.578979 6600 + 31000 3000 873.5316 28.461109 6600 + 32000 3000 1170.5204 31.532882 6600 + 33000 3000 1527.4366 38.434515 6600 + 34000 3000 1984.9084 46.821444 6600 + 35000 3000 2510.0466 50.236977 6600 + 36000 3000 3115.8979 66.529363 6600 + 37000 3000 3828.8672 78.585843 6600 + 38000 3000 4614.202 90.003111 6600 + 39000 3000 5443.9784 97.5867 6600 + 40000 3000 6277.0696 109.40245 6600 + 41000 3000 7205.7543 116.90896 6600 + 42000 3000 8231.9822 123.54846 6600 + 43000 3000 9341.3262 139.91668 6600 + 44000 3000 10540.217 154.5832 6600 + 45000 3000 11634.026 163.89013 6600 + 46000 3000 12939.113 172.01293 6600 + 47000 3000 14117.982 183.04471 6600 + 48000 3000 15405.59 211.29982 6600 + 49000 3000 16780.191 197.48907 6600 + 50000 3000 18147.971 232.52213 6600 +Loop time of 25.2916 on 4 procs for 25000 steps with 3000 atoms + +Pair time (%) = 11.0239 (43.5871) +Neigh time (%) = 1.08584 (4.29328) +Comm time (%) = 6.05157 (23.9272) +Outpt time (%) = 1.07456 (4.24868) +Other time (%) = 6.05576 (23.9438) + +Nlocal: 750 ave 757 max 742 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 401.5 ave 412 max 390 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 3645.75 ave 3775 max 3584 min +Histogram: 1 2 0 0 0 0 0 0 0 1 + +Total # of neighbors = 14583 +Ave neighs/atom = 4.861 +Neighbor list builds = 825 +Dangerous builds = 0 diff --git a/examples/pour/log.pour.12Feb07.linux.1 b/examples/pour/log.pour.12Feb07.linux.1 new file mode 100644 index 0000000000..f72710732e --- /dev/null +++ b/examples/pour/log.pour.12Feb07.linux.1 @@ -0,0 +1,136 @@ +LAMMPS (12 Feb 2007) +# Pour granular particles into chute container, then induce flow + +atom_style granular +boundary p p fm +newton off + +region reg block -10 10 -10 10 -0.5 16 units box +create_box 1 reg +Created box = (-10 -10 -0.5) to (10 10 16) + 1 by 1 by 1 processor grid + +neighbor 0.2 bin +neigh_modify delay 0 + +# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001) +# are used in this example file to produce a quick simulation and movie. +# More appropriate values for realistic simulations would be +# k = 2.0e5 and dt = 0.0001, as in bench/in.chute. + +pair_style gran/history 2000.0 50.0 0.50 0 +timestep 0.001 + +fix 1 all nve/gran +fix 2 all gravity spherical 0.0 -180.0 +fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5 + +region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box +fix ins all pour 3000 1 300719 vol 0.13 50 region slab +Particle insertion: 402 every 3162 steps, 3000 by step 22135 + +thermo_style granular +thermo 1000 +thermo_modify lost ignore +compute_modify thermo_temp dynamic yes + +dump id all atom 125 dump.pour +run 25000 +Memory usage per processor = 0.335693 Mbytes +Step Atoms KinEng RotKEgrn Volume + 0 0 -0 0 6600 + 1000 402 779.98578 0 6600 + 2000 402 1424.4252 0 6600 + 3000 402 1424.6738 13.243803 6600 + 4000 804 1725.9135 47.193854 6600 + 5000 804 1605.9404 61.336034 6600 + 6000 804 1364.6108 67.554058 6600 + 7000 1206 1511.4113 74.376707 6600 + 8000 1206 1418.8901 57.72159 6600 + 9000 1206 1256.2845 48.910044 6600 + 10000 1608 1398.3246 51.447622 6600 + 11000 1608 1247.546 48.387594 6600 + 12000 1608 1182.5307 42.323247 6600 + 13000 2010 1308.4067 48.900862 6600 + 14000 2010 1184.2874 44.83509 6600 + 15000 2010 1005.943 39.943887 6600 + 16000 2412 1031.9872 47.786837 6600 + 17000 2412 1032.5851 40.540687 6600 + 18000 2412 919.78138 36.200329 6600 + 19000 2814 1017.0854 35.573349 6600 + 20000 2814 964.17268 41.63371 6600 + 21000 2814 748.30864 44.884418 6600 + 22000 2814 531.66082 40.886555 6600 + 23000 3000 415.96265 35.009259 6600 + 24000 3000 363.92132 18.910655 6600 + 25000 3000 223.50386 24.163325 6600 +Loop time of 77.9105 on 1 procs for 25000 steps with 3000 atoms + +Pair time (%) = 44.229 (56.769) +Neigh time (%) = 4.82477 (6.19271) +Comm time (%) = 2.59149 (3.32625) +Outpt time (%) = 1.80922 (2.32218) +Other time (%) = 24.456 (31.3899) + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 675 ave 675 max 675 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13637 ave 13637 max 13637 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13637 +Ave neighs/atom = 4.54567 +Neighbor list builds = 1153 +Dangerous builds = 0 + +unfix ins +fix 2 all gravity chute 26.0 +run 25000 +Memory usage per processor = 7.24008 Mbytes +Step Atoms KinEng RotKEgrn Volume + 25000 3000 223.50386 24.163325 6600 + 26000 3000 116.7995 18.613728 6600 + 27000 3000 122.40388 11.057402 6600 + 28000 3000 231.29589 11.189183 6600 + 29000 3000 394.03717 14.367314 6600 + 30000 3000 647.20427 22.016262 6600 + 31000 3000 908.91364 28.607326 6600 + 32000 3000 1271.4653 30.481316 6600 + 33000 3000 1667.4275 41.693229 6600 + 34000 3000 2165.6715 50.388564 6600 + 35000 3000 2742.9875 52.867314 6600 + 36000 3000 3313.9686 64.802217 6600 + 37000 3000 4043.4311 73.963901 6600 + 38000 3000 4826.4345 82.469868 6600 + 39000 3000 5665.19 95.419726 6600 + 40000 3000 6555.0312 105.12519 6600 + 41000 3000 7541.9934 121.4346 6600 + 42000 3000 8632.6663 129.37799 6600 + 43000 3000 9666.568 132.68521 6600 + 44000 3000 10825.138 153.12413 6600 + 45000 3000 12010.686 165.13241 6600 + 46000 3000 13364.225 184.80686 6600 + 47000 3000 14694.757 196.08109 6600 + 48000 3000 16083.771 220.53678 6600 + 49000 3000 17548.113 228.11249 6600 + 50000 3000 19103.087 244.48465 6600 +Loop time of 158.137 on 1 procs for 25000 steps with 3000 atoms + +Pair time (%) = 98.0991 (62.0342) +Neigh time (%) = 7.5106 (4.74943) +Comm time (%) = 5.67871 (3.59101) +Outpt time (%) = 2.85027 (1.8024) +Other time (%) = 43.9984 (27.823) + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 766 ave 766 max 766 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13994 ave 13994 max 13994 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13994 +Ave neighs/atom = 4.66467 +Neighbor list builds = 833 +Dangerous builds = 0 diff --git a/examples/pour/log.pour.1Oct06.liberty.4 b/examples/pour/log.pour.1Oct06.liberty.4 deleted file mode 100644 index 042d9fe707..0000000000 --- a/examples/pour/log.pour.1Oct06.liberty.4 +++ /dev/null @@ -1,135 +0,0 @@ -LAMMPS (1 Oct 2006) -# Pour granular particles into chute container, then induce flow - -atom_style granular -boundary p p fm -newton off - -region reg block -10 10 -10 10 -0.5 16 units box -create_box 1 reg -Created box = (-10 -10 -0.5) to (10 10 16) - 2 by 2 by 1 processor grid - -neighbor 0.2 bin -neigh_modify delay 0 - -# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001) -# are used in this example file to produce a quick simulation and movie. -# More appropriate values for realistic simulations would be -# k = 2.0e5 and dt = 0.0001, as in bench/in.chute. - -pair_style gran/history 2000.0 50.0 0.50 0 -timestep 0.001 - -fix 1 all nve/gran -fix 2 all gravity spherical 0.0 -180.0 -fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5 - -region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box -fix ins all insert 3000 1 300719 vol 0.13 50 region slab -Particle insertion: 402 every 3162 steps, 3000 by step 22135 - -thermo_style granular -thermo 1000 -thermo_modify lost ignore - -dump id all atom 125 dump.pour -run 25000 -Memory usage per processor = 0.335693 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 0 0 0 0 6600 - 1000 402 779.98578 0 6600 - 2000 402 1424.4252 0 6600 - 3000 402 1425.2447 14.149848 6600 - 4000 804 1717.4634 46.771706 6600 - 5000 804 1600.9045 53.21935 6600 - 6000 804 1351.6492 60.760589 6600 - 7000 1206 1565.6473 62.669488 6600 - 8000 1206 1417.1737 62.758562 6600 - 9000 1206 1258.9904 51.005212 6600 - 10000 1608 1399.1287 49.839456 6600 - 11000 1608 1243.873 48.930454 6600 - 12000 1608 1195.4479 43.545487 6600 - 13000 2010 1306.9138 54.570296 6600 - 14000 2010 1157.9021 43.330935 6600 - 15000 2010 983.9019 43.615315 6600 - 16000 2412 1034.6442 42.147002 6600 - 17000 2412 1031.4629 40.030993 6600 - 18000 2412 893.29609 38.534882 6600 - 19000 2814 1016.6024 38.562892 6600 - 20000 2814 957.40159 41.423471 6600 - 21000 2814 761.01108 38.191827 6600 - 22000 2814 522.65734 42.380196 6600 - 23000 3000 441.50278 37.280492 6600 - 24000 3000 364.60716 19.154219 6600 - 25000 3000 226.05523 23.102252 6600 -Loop time of 13.6809 on 4 procs for 25000 steps with 3000 atoms - -Pair time (%) = 4.87714 (35.6493) -Neigh time (%) = 0.748691 (5.47254) -Comm time (%) = 3.72672 (27.2403) -Outpt time (%) = 0.640552 (4.6821) -Other time (%) = 3.68778 (26.9557) - -Nlocal: 750 ave 765 max 733 min -Histogram: 1 0 0 0 1 0 0 1 0 1 -Nghost: 392 ave 402 max 382 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 3573.5 ave 3638 max 3540 min -Histogram: 1 2 0 0 0 0 0 0 0 1 - -Total # of neighbors = 14294 -Ave neighs/atom = 4.76467 -Neighbor list builds = 1151 -Dangerous builds = 0 - -unfix ins -fix 2 all gravity chute 26.0 -run 25000 -Memory usage per processor = 6.82785 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 25000 3000 226.05523 23.102252 6600 - 26000 3000 107.00196 18.375396 6600 - 27000 3000 63.99827 10.996141 6600 - 28000 3000 85.164329 8.8173571 6600 - 29000 3000 117.92934 7.75666 6600 - 30000 3000 163.87863 8.7138337 6600 - 31000 3000 233.20236 10.329617 6600 - 32000 3000 342.53254 13.898474 6600 - 33000 3000 468.44696 15.99158 6600 - 34000 3000 621.87103 19.886939 6600 - 35000 3000 815.39747 20.705882 6600 - 36000 3000 1057.2229 26.571307 6600 - 37000 3000 1328.8595 30.123382 6600 - 38000 3000 1657.3423 36.114002 6600 - 39000 3000 1981.1213 41.318004 6600 - 40000 3000 2391.9019 45.046643 6600 - 41000 3000 2831.3144 50.549127 6600 - 42000 3000 3235.6137 57.512833 6600 - 43000 3000 3747.9079 62.890502 6600 - 44000 3000 4178.1452 59.476683 6600 - 45000 3000 4594.1909 70.420341 6600 - 46000 3000 5147.6655 72.299465 6600 - 47000 3000 5677.574 81.275593 6600 - 48000 3000 6300.6258 81.736559 6600 - 49000 3000 6911.4189 87.717341 6600 - 50000 3000 7539.698 94.03491 6600 -Loop time of 25.886 on 4 procs for 25000 steps with 3000 atoms - -Pair time (%) = 11.7344 (45.331) -Neigh time (%) = 0.916894 (3.54205) -Comm time (%) = 5.79871 (22.401) -Outpt time (%) = 1.08395 (4.18742) -Other time (%) = 6.35205 (24.5386) - -Nlocal: 750 ave 761 max 733 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 409.75 ave 418 max 405 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Neighs: 3583 ave 3665 max 3470 min -Histogram: 1 0 0 0 0 0 2 0 0 1 - -Total # of neighbors = 14332 -Ave neighs/atom = 4.77733 -Neighbor list builds = 653 -Dangerous builds = 0 diff --git a/examples/pour/log.pour.1Oct06.linux.1 b/examples/pour/log.pour.1Oct06.linux.1 deleted file mode 100644 index dc69ad9c52..0000000000 --- a/examples/pour/log.pour.1Oct06.linux.1 +++ /dev/null @@ -1,135 +0,0 @@ -LAMMPS (1 Oct 2006) -# Pour granular particles into chute container, then induce flow - -atom_style granular -boundary p p fm -newton off - -region reg block -10 10 -10 10 -0.5 16 units box -create_box 1 reg -Created box = (-10 -10 -0.5) to (10 10 16) - 1 by 1 by 1 processor grid - -neighbor 0.2 bin -neigh_modify delay 0 - -# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001) -# are used in this example file to produce a quick simulation and movie. -# More appropriate values for realistic simulations would be -# k = 2.0e5 and dt = 0.0001, as in bench/in.chute. - -pair_style gran/history 2000.0 50.0 0.50 0 -timestep 0.001 - -fix 1 all nve/gran -fix 2 all gravity spherical 0.0 -180.0 -fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5 - -region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box -fix ins all insert 3000 1 300719 vol 0.13 50 region slab -Particle insertion: 402 every 3162 steps, 3000 by step 22135 - -thermo_style granular -thermo 1000 -thermo_modify lost ignore - -dump id all atom 125 dump.pour -run 25000 -Memory usage per processor = 0.335693 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 0 0 0 0 6600 - 1000 402 779.98578 0 6600 - 2000 402 1424.4252 0 6600 - 3000 402 1425.2447 14.149848 6600 - 4000 804 1717.5445 46.833537 6600 - 5000 804 1602.4038 53.613557 6600 - 6000 804 1344.3882 61.238792 6600 - 7000 1206 1551.5556 61.093446 6600 - 8000 1206 1403.0526 59.960391 6600 - 9000 1206 1235.4923 50.748092 6600 - 10000 1608 1363.3275 53.312989 6600 - 11000 1608 1240.0576 51.060525 6600 - 12000 1608 1181.29 41.956851 6600 - 13000 2010 1305.2234 48.405298 6600 - 14000 2010 1184.9666 43.407539 6600 - 15000 2010 982.48676 46.414299 6600 - 16000 2412 1039.3552 40.73208 6600 - 17000 2412 1021.9131 40.24246 6600 - 18000 2412 918.39685 36.6021 6600 - 19000 2814 1008.0642 40.503982 6600 - 20000 2814 969.92049 46.359854 6600 - 21000 2814 742.83883 45.261311 6600 - 22000 2814 535.51412 35.78601 6600 - 23000 3000 422.4646 36.018166 6600 - 24000 3000 369.01471 20.276832 6600 - 25000 3000 222.8011 25.262721 6600 -Loop time of 78.181 on 1 procs for 25000 steps with 3000 atoms - -Pair time (%) = 43.4696 (55.6012) -Neigh time (%) = 5.03235 (6.4368) -Comm time (%) = 2.47885 (3.17066) -Outpt time (%) = 1.71796 (2.19742) -Other time (%) = 25.4822 (32.5939) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 673 ave 673 max 673 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 13554 ave 13554 max 13554 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 13554 -Ave neighs/atom = 4.518 -Neighbor list builds = 1150 -Dangerous builds = 0 - -unfix ins -fix 2 all gravity chute 26.0 -run 25000 -Memory usage per processor = 7.23976 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 25000 3000 222.8011 25.262721 6600 - 26000 3000 99.759326 19.389504 6600 - 27000 3000 74.30069 10.522988 6600 - 28000 3000 95.90836 8.0897997 6600 - 29000 3000 136.21033 7.1058765 6600 - 30000 3000 202.52399 9.2690664 6600 - 31000 3000 282.02475 11.360363 6600 - 32000 3000 375.70421 12.925874 6600 - 33000 3000 501.43635 15.872649 6600 - 34000 3000 656.34183 20.080962 6600 - 35000 3000 859.69119 23.330343 6600 - 36000 3000 1124.0709 27.369289 6600 - 37000 3000 1402.6834 32.467711 6600 - 38000 3000 1755.6508 36.236793 6600 - 39000 3000 2127.602 43.307008 6600 - 40000 3000 2514.5587 41.763683 6600 - 41000 3000 2894.3174 50.043024 6600 - 42000 3000 3375.7464 58.443129 6600 - 43000 3000 3927.7147 63.466029 6600 - 44000 3000 4361.4566 67.176165 6600 - 45000 3000 4990.8433 72.328717 6600 - 46000 3000 5538.4251 76.231574 6600 - 47000 3000 6148.7886 82.989651 6600 - 48000 3000 6759.9046 86.32529 6600 - 49000 3000 7398.1553 93.870085 6600 - 50000 3000 8060.7836 93.818377 6600 -Loop time of 163.879 on 1 procs for 25000 steps with 3000 atoms - -Pair time (%) = 104.425 (63.7212) -Neigh time (%) = 5.99224 (3.65651) -Comm time (%) = 5.51156 (3.3632) -Outpt time (%) = 2.83083 (1.72739) -Other time (%) = 45.1186 (27.5317) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 779 ave 779 max 779 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 13636 ave 13636 max 13636 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 13636 -Ave neighs/atom = 4.54533 -Neighbor list builds = 641 -Dangerous builds = 0 diff --git a/examples/pour/log.pour.2d.1Oct06.liberty.4 b/examples/pour/log.pour.2d.12Feb07.liberty.4 similarity index 84% rename from examples/pour/log.pour.2d.1Oct06.liberty.4 rename to examples/pour/log.pour.2d.12Feb07.liberty.4 index e3a6881261..1bc37d394c 100644 --- a/examples/pour/log.pour.2d.1Oct06.liberty.4 +++ b/examples/pour/log.pour.2d.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Pour 2d granular particles into container dimension 2 @@ -28,7 +28,7 @@ fix xwalls all wall/gran xplane 0 100 50 0 fix ywalls all wall/gran yplane 0 NULL 50 0 region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box -fix ins all insert 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab +fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab Particle insertion: 224 every 3000 steps, 1000 by step 12001 fix 3 all enforce2d @@ -36,12 +36,13 @@ fix 3 all enforce2d thermo_style granular thermo 1000 thermo_modify lost ignore +compute_modify thermo_temp dynamic yes -dump id all atom 100 dump.pour.2d +dump id all atom 100 dump.pour run 25000 Memory usage per processor = 0.335693 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 0 0 0 0 5000 +Step Atoms KinEng RotKEgrn Volume + 0 0 -0 0 5000 1000 224 348.20549 0 5000 2000 224 650.98655 0 5000 3000 224 1056.0039 0 5000 @@ -67,13 +68,13 @@ Step Atoms Trans-KE Rot-KE Volume 23000 1000 38.365449 0 5000 24000 1000 27.535477 0 5000 25000 1000 16.082932 0 5000 -Loop time of 7.35198 on 4 procs for 25000 steps with 1000 atoms +Loop time of 7.63049 on 4 procs for 25000 steps with 1000 atoms -Pair time (%) = 1.18859 (16.167) -Neigh time (%) = 0.289227 (3.934) -Comm time (%) = 1.58685 (21.584) -Outpt time (%) = 0.418018 (5.68578) -Other time (%) = 3.8693 (52.6293) +Pair time (%) = 1.21044 (15.8632) +Neigh time (%) = 0.267945 (3.51151) +Comm time (%) = 1.8156 (23.794) +Outpt time (%) = 0.418886 (5.48963) +Other time (%) = 3.91762 (51.3417) Nlocal: 250 ave 502 max 0 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/pour/log.pour.2d.1Oct06.linux.1 b/examples/pour/log.pour.2d.12Feb07.linux.1 similarity index 84% rename from examples/pour/log.pour.2d.1Oct06.linux.1 rename to examples/pour/log.pour.2d.12Feb07.linux.1 index c8777e9124..3a42f98f80 100644 --- a/examples/pour/log.pour.2d.1Oct06.linux.1 +++ b/examples/pour/log.pour.2d.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Pour 2d granular particles into container dimension 2 @@ -28,7 +28,7 @@ fix xwalls all wall/gran xplane 0 100 50 0 fix ywalls all wall/gran yplane 0 NULL 50 0 region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box -fix ins all insert 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab +fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab Particle insertion: 224 every 3000 steps, 1000 by step 12001 fix 3 all enforce2d @@ -36,12 +36,13 @@ fix 3 all enforce2d thermo_style granular thermo 1000 thermo_modify lost ignore +compute_modify thermo_temp dynamic yes -dump id all atom 100 dump.pour.2d +dump id all atom 100 dump.pour run 25000 Memory usage per processor = 0.328064 Mbytes -Step Atoms Trans-KE Rot-KE Volume - 0 0 0 0 5000 +Step Atoms KinEng RotKEgrn Volume + 0 0 -0 0 5000 1000 224 348.20549 0 5000 2000 224 650.98655 0 5000 3000 224 1056.0039 0 5000 @@ -67,13 +68,13 @@ Step Atoms Trans-KE Rot-KE Volume 23000 1000 32.615049 0 5000 24000 1000 25.853047 0 5000 25000 1000 17.216223 0 5000 -Loop time of 22.8255 on 1 procs for 25000 steps with 1000 atoms +Loop time of 22.8967 on 1 procs for 25000 steps with 1000 atoms -Pair time (%) = 9.2328 (40.4494) -Neigh time (%) = 2.19741 (9.627) -Comm time (%) = 0.301715 (1.32183) -Outpt time (%) = 0.97282 (4.26198) -Other time (%) = 10.1208 (44.3398) +Pair time (%) = 9.27836 (40.5226) +Neigh time (%) = 2.03788 (8.90029) +Comm time (%) = 0.293353 (1.2812) +Outpt time (%) = 1.06686 (4.65942) +Other time (%) = 10.2203 (44.6364) Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/rigid/log.rigid.1Oct06.liberty.4 b/examples/rigid/log.rigid.12Feb07.liberty.4 similarity index 98% rename from examples/rigid/log.rigid.1Oct06.liberty.4 rename to examples/rigid/log.rigid.12Feb07.liberty.4 index f64d5ed158..6ee9d6725e 100644 --- a/examples/rigid/log.rigid.1Oct06.liberty.4 +++ b/examples/rigid/log.rigid.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Simple rigid body system units lj @@ -284,13 +284,13 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984559 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 1.69721 on 4 procs for 10000 steps with 81 atoms +Loop time of 1.86143 on 4 procs for 10000 steps with 81 atoms -Pair time (%) = 0.0132074 (0.77818) -Neigh time (%) = 0.023569 (1.38869) -Comm time (%) = 1.089 (64.164) -Outpt time (%) = 0.0916764 (5.40158) -Other time (%) = 0.479761 (28.2676) +Pair time (%) = 0.0128456 (0.690097) +Neigh time (%) = 0.0243435 (1.30779) +Comm time (%) = 1.21756 (65.4102) +Outpt time (%) = 0.102895 (5.52778) +Other time (%) = 0.503778 (27.0641) Nlocal: 20.25 ave 38 max 3 min Histogram: 1 0 1 0 0 0 1 0 0 1 diff --git a/examples/rigid/log.rigid.1Oct06.linux.1 b/examples/rigid/log.rigid.12Feb07.linux.1 similarity index 98% rename from examples/rigid/log.rigid.1Oct06.linux.1 rename to examples/rigid/log.rigid.12Feb07.linux.1 index 634bf39fe8..dd1f16ad77 100644 --- a/examples/rigid/log.rigid.1Oct06.linux.1 +++ b/examples/rigid/log.rigid.12Feb07.linux.1 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Simple rigid body system units lj @@ -284,13 +284,13 @@ Step Temp E_pair E_mol TotEng Press 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.887339 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.851031 on 1 procs for 10000 steps with 81 atoms -Pair time (%) = 0.076566 (8.62872) -Neigh time (%) = 0.130989 (14.762) -Comm time (%) = 0.105157 (11.8508) -Outpt time (%) = 0.116808 (13.1639) -Other time (%) = 0.457819 (51.5946) +Pair time (%) = 0.071532 (8.40533) +Neigh time (%) = 0.117486 (13.8051) +Comm time (%) = 0.108591 (12.7599) +Outpt time (%) = 0.133537 (15.6912) +Other time (%) = 0.419885 (49.3384) Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/rigid/log.rigid.poems.1Oct06.liberty.4 b/examples/rigid/log.rigid.poems.12Feb07.liberty.4 similarity index 98% rename from examples/rigid/log.rigid.poems.1Oct06.liberty.4 rename to examples/rigid/log.rigid.poems.12Feb07.liberty.4 index 54f2a8bea5..9320f9008b 100644 --- a/examples/rigid/log.rigid.poems.1Oct06.liberty.4 +++ b/examples/rigid/log.rigid.poems.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Simple rigid body system units lj @@ -284,13 +284,13 @@ Step Temp E_pair E_mol TotEng Press 9900 19393.195 452.88226 0 3685.0814 1.4304574 9950 17226.824 814.05288 0 3685.1902 19.353254 10000 20630.15 245.97222 0 3684.3306 0.61583151 -Loop time of 16.5532 on 4 procs for 10000 steps with 81 atoms +Loop time of 16.4503 on 4 procs for 10000 steps with 81 atoms -Pair time (%) = 0.12595 (0.760878) -Neigh time (%) = 0.0543506 (0.328338) -Comm time (%) = 1.67897 (10.1428) -Outpt time (%) = 0.0939289 (0.567436) -Other time (%) = 14.6 (88.2005) +Pair time (%) = 0.123495 (0.750712) +Neigh time (%) = 0.0552313 (0.335746) +Comm time (%) = 1.68884 (10.2663) +Outpt time (%) = 0.101621 (0.617742) +Other time (%) = 14.4811 (88.0295) Nlocal: 20.25 ave 74 max 0 min Histogram: 3 0 0 0 0 0 0 0 0 1 diff --git a/examples/rigid/log.rigid.poems.12Feb07.linux.1 b/examples/rigid/log.rigid.poems.12Feb07.linux.1 new file mode 100644 index 0000000000..d5de690eef --- /dev/null +++ b/examples/rigid/log.rigid.poems.12Feb07.linux.1 @@ -0,0 +1,305 @@ +LAMMPS (12 Feb 2007) +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + 1 by 1 by 1 processor grid + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 +dump 1 all atom 50 dump.rigid + +timestep 0.0001 +thermo 50 +run 10000 +Memory usage per processor = 1.50473 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699156 + 1200 21815.003 45.317415 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064077 + 1300 20780.781 217.36506 0 3680.8286 6.053862 + 1350 20558.972 254.36481 0 3680.8601 -3.6773966 + 1400 21485.029 99.812935 0 3680.6511 -16.185472 + 1450 21771.107 52.159605 0 3680.6775 -2.4756675 + 1500 21520.948 93.503934 0 3680.3286 2.1023577 + 1550 21351.418 121.68138 0 3680.2511 5.5159957 + 1600 20778.805 216.92176 0 3680.0559 15.089186 + 1650 21477.638 100.2183 0 3679.8247 -1.1045812 + 1700 18501.341 596.47889 0 3680.0357 -15.67966 + 1750 18563.642 587.34786 0 3681.2882 33.532195 + 1800 19110.187 494.82315 0 3679.8543 18.024044 + 1850 21364.193 119.2351 0 3679.9339 2.5291255 + 1900 20146.632 322.14766 0 3679.9197 5.7312569 + 1950 20692.671 231.25335 0 3680.0319 4.2977718 + 2000 20943.904 189.1123 0 3679.7629 -22.645328 + 2050 19668.094 401.82367 0 3679.8394 3.625351 + 2100 20280.495 299.75279 0 3679.8352 7.4808501 + 2150 19181.964 483.50484 0 3680.4989 22.618437 + 2200 21300.002 130.73207 0 3680.7324 4.7107204 + 2250 20487.278 266.58364 0 3681.13 -8.6436788 + 2300 18653.922 572.11506 0 3681.102 -5.2650803 + 2350 21513.162 95.675284 0 3681.2022 -9.358275 + 2400 21466.87 103.46516 0 3681.2768 -29.576898 + 2450 20098.852 332.48096 0 3682.2896 35.802574 + 2500 20763.224 221.86356 0 3682.401 -12.492465 + 2550 20425.308 278.04709 0 3682.265 -22.360414 + 2600 21467.742 104.32441 0 3682.2815 -10.062558 + 2650 20774.17 220.00066 0 3682.3623 5.2193436 + 2700 18569.233 587.73881 0 3682.6109 22.145192 + 2750 20654.466 239.78519 0 3682.1961 -6.9106068 + 2800 20814.792 213.06343 0 3682.1954 -6.9316614 + 2850 16353.471 956.9648 0 3682.5433 34.229058 + 2900 19519.089 429.00752 0 3682.189 8.7072031 + 2950 20171.665 320.18684 0 3682.1309 2.7223515 + 3000 20470.108 270.26106 0 3681.9457 -8.2674499 + 3050 20359.511 288.83368 0 3682.0856 -4.69092 + 3100 19856.099 372.69336 0 3682.0432 9.3653131 + 3150 20561.401 254.89391 0 3681.794 6.7807193 + 3200 18974.717 519.59328 0 3682.0462 14.028207 + 3250 17201.03 816.05668 0 3682.895 30.827229 + 3300 21032.748 176.57229 0 3682.0304 -8.8776478 + 3350 17299.203 798.82174 0 3682.0222 -6.5474977 + 3400 16871.128 870.67484 0 3682.5295 -23.235008 + 3450 19319.303 462.06051 0 3681.9443 -11.811901 + 3500 17860.126 705.48294 0 3682.1705 -15.992033 + 3550 21874.357 36.186306 0 3681.9124 -2.4098493 + 3600 21393.595 116.22067 0 3681.8199 -10.262929 + 3650 20544.718 257.71089 0 3681.8306 0.55484185 + 3700 20330.417 293.63761 0 3682.0404 16.661746 + 3750 21244.461 141.09081 0 3681.8343 4.9615754 + 3800 19958.592 355.64853 0 3682.0806 13.979713 + 3850 21497.423 98.927167 0 3681.8309 -6.621684 + 3900 21769.359 53.67612 0 3681.9026 -1.926207 + 3950 19975.772 352.52452 0 3681.8198 9.245817 + 4000 21113.483 163.03078 0 3681.9446 2.7569744 + 4050 19709.067 397.27579 0 3682.1202 -3.0811456 + 4100 21815.578 46.077634 0 3682.0073 -12.520188 + 4150 21642.428 74.997052 0 3682.0685 -1.1460009 + 4200 19928.01 360.19492 0 3681.53 8.857095 + 4250 17863.117 703.82283 0 3681.009 33.346649 + 4300 20382.848 284.9686 0 3682.1099 -7.0563493 + 4350 21589.546 83.691599 0 3681.9492 -6.3466935 + 4400 21561.341 88.259907 0 3681.8167 -0.05858595 + 4450 19016.303 512.39829 0 3681.7821 43.125503 + 4500 20065.798 337.40858 0 3681.7083 1.7677159 + 4550 19263.771 471.03594 0 3681.6644 -23.462523 + 4600 20845.688 207.74162 0 3682.023 0.16598388 + 4650 19646.643 407.84353 0 3682.2841 11.884842 + 4700 20692.329 233.43094 0 3682.1524 -14.265029 + 4750 17999.182 682.2895 0 3682.1531 -25.09426 + 4800 20585.117 251.43776 0 3682.2906 10.111397 + 4850 19368.488 453.98051 0 3682.0618 6.199069 + 4900 20416.868 279.66263 0 3682.474 7.5050136 + 4950 21376.045 119.55597 0 3682.2302 -9.6343892 + 5000 21346.337 124.42913 0 3682.1519 -3.6930357 + 5050 19787.72 384.70087 0 3682.6542 -5.855159 + 5100 20440.061 275.27592 0 3681.9528 1.7528745 + 5150 15625.189 1079.1543 0 3683.3525 19.539205 + 5200 20308.779 297.80498 0 3682.6014 8.9223119 + 5250 21044.849 175.43646 0 3682.9113 5.2785373 + 5300 20543.584 258.744 0 3682.6747 1.2007699 + 5350 21171.39 154.69163 0 3683.2566 -12.896011 + 5400 19626.405 409.45045 0 3680.518 16.150799 + 5450 20550.071 258.26489 0 3683.2766 -21.262685 + 5500 19104.84 499.01387 0 3683.1539 11.949545 + 5550 19559.267 422.41448 0 3682.2923 3.8829356 + 5600 20044.332 342.61709 0 3683.3391 -1.7700503 + 5650 21953.27 25.016694 0 3683.8951 -22.754979 + 5700 21639.986 77.352619 0 3684.017 -15.578393 + 5750 21144.414 159.81932 0 3683.8884 -9.0956708 + 5800 19267.59 472.68582 0 3683.9509 12.517057 + 5850 21221.184 146.53726 0 3683.4012 -0.35975116 + 5900 21141.226 159.83342 0 3683.371 0.79471018 + 5950 20417.806 280.84037 0 3683.808 -4.380384 + 6000 15946.467 1025.7528 0 3683.4973 -2.9233738 + 6050 20307.785 299.10545 0 3683.7362 -7.6865743 + 6100 18110.389 663.98174 0 3682.3799 4.1591862 + 6150 19958.364 357.9562 0 3684.3502 0.64161306 + 6200 18283.091 637.04273 0 3684.2246 1.3409324 + 6250 17081.956 837.9693 0 3684.962 -6.7113704 + 6300 21382.883 120.98513 0 3684.7989 -13.987822 + 6350 19952.702 359.01391 0 3684.4642 6.3550454 + 6400 20832.557 212.50673 0 3684.5995 -1.5787609 + 6450 18646.002 577.10671 0 3684.7738 7.7299342 + 6500 18261.033 641.30218 0 3684.8076 17.386854 + 6550 18426.877 613.53329 0 3684.6794 -3.3462219 + 6600 20349.993 293.18762 0 3684.8531 -12.422327 + 6650 21112.2 166.06059 0 3684.7606 -6.7451773 + 6700 20046.245 343.52129 0 3684.5621 -4.0057021 + 6750 20834.1 212.52233 0 3684.8724 -1.5556583 + 6800 21150.619 159.68754 0 3684.7908 -1.5850612 + 6850 20008.249 350.12255 0 3684.8308 6.4872768 + 6900 18654.888 575.51473 0 3684.6627 -17.992304 + 6950 19708.289 400.17932 0 3684.8942 7.0106327 + 7000 20437.426 278.17876 0 3684.4164 6.2019137 + 7050 19604.082 416.96446 0 3684.3114 -3.924055 + 7100 18301.87 633.03111 0 3683.3428 19.029745 + 7150 18558.782 591.49191 0 3684.6222 25.690348 + 7200 16746.788 894.4891 0 3685.6204 9.3897347 + 7250 19956.035 358.65844 0 3684.6642 2.9307876 + 7300 21612.74 82.596669 0 3684.7199 -6.0761772 + 7350 21082.361 170.97104 0 3684.6979 -1.6531911 + 7400 21447.623 110.03038 0 3684.6342 -9.6680921 + 7450 21815.262 48.645261 0 3684.5222 -2.4194461 + 7500 21586.807 86.513539 0 3684.3147 0.80475725 + 7550 21432.021 112.08344 0 3684.087 3.7213279 + 7600 18765.76 557.30844 0 3684.9351 25.566982 + 7650 19237.591 477.51887 0 3683.784 -0.93181342 + 7700 20058.61 340.75274 0 3683.8544 4.1984966 + 7750 21689.282 69.4903 0 3684.3707 -8.0484797 + 7800 21149.046 159.71259 0 3684.5537 7.1881243 + 7850 19334.412 461.23349 0 3683.6355 14.066324 + 7900 21263.983 140.83705 0 3684.8343 -14.739146 + 7950 20871.691 206.2356 0 3684.8508 -11.575259 + 8000 18916.496 531.93786 0 3684.6872 -20.395653 + 8050 20703.238 233.97858 0 3684.5183 4.2191304 + 8100 19544.399 426.74441 0 3684.1442 15.563275 + 8150 17578.916 755.02603 0 3684.8454 23.23474 + 8200 18121.828 663.35414 0 3683.6588 -23.277149 + 8250 19000.859 515.63274 0 3682.4425 8.1499185 + 8300 16312.856 965.20527 0 3684.0147 69.340264 + 8350 17908.285 699.50533 0 3684.2195 -13.64631 + 8400 19971.59 355.22033 0 3683.8187 6.2163041 + 8450 13617.129 1415.4014 0 3684.9229 -9.1829017 + 8500 20374.985 288.34097 0 3684.1719 1.0194401 + 8550 21452.212 108.96717 0 3684.3359 -8.0882838 + 8600 17196.613 818.7652 0 3684.8674 -2.1874477 + 8650 21510.389 99.326067 0 3684.3909 -3.5449392 + 8700 21446.623 109.76972 0 3684.2068 -0.76115037 + 8750 20700.162 234.50311 0 3684.5301 2.0551713 + 8800 21686.769 69.759974 0 3684.2215 -3.6322891 + 8850 20892.916 201.69594 0 3683.8486 0.57163157 + 8900 18095.714 668.44418 0 3684.3965 19.055292 + 8950 21325.044 129.56368 0 3683.7377 2.2916549 + 9000 20739.771 227.15562 0 3683.7842 -6.4759144 + 9050 20683.885 235.94003 0 3683.2543 1.8163478 + 9100 21432.386 111.08386 0 3683.1483 -9.5573949 + 9150 21686.43 69.315468 0 3683.7205 2.1854565 + 9200 16916.728 864.20897 0 3683.6636 7.2632357 + 9250 20122.374 329.80422 0 3683.5332 6.2589988 + 9300 20621.693 246.58967 0 3683.5386 -20.210043 + 9350 20343.792 292.92921 0 3683.5612 0.47974589 + 9400 20334.062 294.47957 0 3683.4899 -5.5269222 + 9450 20971.669 188.26826 0 3683.5464 1.5825497 + 9500 20948.938 191.99574 0 3683.4855 1.7294775 + 9550 21557.149 90.697719 0 3683.5559 4.5248095 + 9600 21121.109 162.83027 0 3683.0151 -3.8673505 + 9650 21306.551 132.27859 0 3683.3704 -0.05028404 + 9700 21064.24 172.82072 0 3683.5273 1.7248916 + 9750 18962.129 523.71798 0 3684.0729 17.93568 + 9800 21192.894 151.77036 0 3683.9193 -0.2514556 + 9850 20585.229 252.91402 0 3683.7855 9.2033197 + 9900 21584.165 86.429361 0 3683.7902 -5.4686156 + 9950 21190.652 151.98402 0 3683.7593 -3.5815764 + 10000 20061.072 340.24042 0 3683.7525 -2.2008049 +Loop time of 25.7955 on 1 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.950715 (3.68559) +Neigh time (%) = 0.339646 (1.31669) +Comm time (%) = 0.113344 (0.439395) +Outpt time (%) = 0.168425 (0.652924) +Other time (%) = 24.2234 (93.9054) + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 60 ave 60 max 60 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 721 ave 721 max 721 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 721 +Ave neighs/atom = 8.90123 +Neighbor list builds = 989 +Dangerous builds = 911 diff --git a/examples/rigid/log.rigid.poems.1Oct06.linux.1 b/examples/rigid/log.rigid.poems.1Oct06.linux.1 deleted file mode 100644 index e3151f1263..0000000000 --- a/examples/rigid/log.rigid.poems.1Oct06.linux.1 +++ /dev/null @@ -1,305 +0,0 @@ -LAMMPS (1 Oct 2006) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - 1 by 1 by 1 processor grid - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 -dump 1 all atom 50 dump.rigid - -timestep 0.0001 -thermo 50 -run 10000 -Memory usage per processor = 1.50473 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384278 - 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 -0.86699147 - 1200 21815.003 45.317414 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064078 - 1300 20780.781 217.36507 0 3680.8286 6.0538618 - 1350 20558.971 254.36483 0 3680.8601 -3.6773945 - 1400 21485.029 99.812915 0 3680.6511 -16.185473 - 1450 21771.107 52.159616 0 3680.6775 -2.4756671 - 1500 21520.948 93.503919 0 3680.3286 2.1023577 - 1550 21351.418 121.68136 0 3680.2511 5.5159939 - 1600 20778.805 216.92179 0 3680.0559 15.08919 - 1650 21477.638 100.21841 0 3679.8247 -1.1045676 - 1700 18501.338 596.47934 0 3680.0357 -15.679693 - 1750 18563.641 587.34802 0 3681.2882 33.532224 - 1800 19110.184 494.82361 0 3679.8543 18.024052 - 1850 21364.189 119.23567 0 3679.9339 2.5290982 - 1900 20146.623 322.14928 0 3679.9197 5.7313631 - 1950 20692.672 231.25329 0 3680.0319 4.2977763 - 2000 20943.904 189.11224 0 3679.7629 -22.644967 - 2050 19668.032 401.83413 0 3679.8394 3.6250579 - 2100 20280.405 299.76781 0 3679.8353 7.4807458 - 2150 19181.776 483.53587 0 3680.4986 22.622025 - 2200 21300.275 130.68616 0 3680.732 4.7099237 - 2250 20486.714 266.67751 0 3681.1298 -8.6469998 - 2300 18652.596 572.33559 0 3681.1016 -5.2628292 - 2350 21513.777 95.572407 0 3681.202 -9.3648592 - 2400 21465.849 103.63471 0 3681.2763 -29.550454 - 2450 20100.961 332.12793 0 3682.2881 35.70449 - 2500 20765.206 221.53187 0 3682.3996 -12.452833 - 2550 20442.965 275.09622 0 3682.2571 -22.450229 - 2600 21465.612 104.67793 0 3682.2799 -10.089769 - 2650 20840.301 208.97723 0 3682.3607 5.0962323 - 2700 18566.291 588.29119 0 3682.6731 22.314898 - 2750 20859.619 205.61533 0 3682.2184 -8.4111045 - 2800 21152.619 156.74913 0 3682.1856 -7.0841069 - 2850 17034.124 843.41557 0 3682.4362 31.940811 - 2900 19433.377 443.20884 0 3682.105 8.154109 - 2950 20759.601 222.07863 0 3682.0121 0.94860156 - 3000 20639.898 242.09747 0 3682.0805 -5.0441986 - 3050 18165.856 654.36056 0 3682.0032 2.0390617 - 3100 20352.11 290.03669 0 3682.055 -6.4787936 - 3150 20081.761 335.00558 0 3681.9657 12.403377 - 3200 20312.335 296.00002 0 3681.3892 6.6521722 - 3250 20715.141 228.97633 0 3681.4998 0.29254419 - 3300 21033.583 176.05884 0 3681.656 -0.82749027 - 3350 20555.686 255.51202 0 3681.4596 -2.6224778 - 3400 20517.425 261.8331 0 3681.404 5.7965799 - 3450 21550.686 89.629485 0 3681.4104 1.7369192 - 3500 18213.776 648.60728 0 3684.2366 25.179084 - 3550 20181.817 317.95514 0 3681.5914 12.030205 - 3600 20064.929 336.99155 0 3681.1464 0.46703252 - 3650 20548.763 256.74258 0 3681.5364 5.6316258 - 3700 21695.436 65.821167 0 3681.7272 -4.046094 - 3750 20339.586 291.86983 0 3681.8009 -6.9843488 - 3800 20556.293 255.92096 0 3681.9698 -2.4803781 - 3850 20446.56 274.11342 0 3681.8735 -4.7609085 - 3900 19011.276 513.44779 0 3681.9938 17.583808 - 3950 20584.829 250.52631 0 3681.3311 2.2444895 - 4000 20971.029 185.41558 0 3680.5871 -20.990511 - 4050 18377.385 617.09077 0 3679.9882 7.178804 - 4100 16844.266 873.0443 0 3680.4219 8.8851101 - 4150 21182.287 149.12309 0 3679.5043 -5.7838368 - 4200 20081.816 332.50466 0 3679.4741 11.141881 - 4250 16039.426 1006.3467 0 3679.5845 19.421993 - 4300 21194.532 147.15003 0 3679.572 6.1066469 - 4350 18629.518 575.11052 0 3680.0302 -2.7680889 - 4400 20141.896 323.11764 0 3680.1004 -12.100591 - 4450 19515.022 427.59265 0 3680.0963 -11.941524 - 4500 20713.779 227.58503 0 3679.8816 -2.0762411 - 4550 20534.825 257.13203 0 3679.6029 3.9506072 - 4600 16110.778 995.49492 0 3680.6245 39.113403 - 4650 20050.377 337.60184 0 3679.3313 4.0339243 - 4700 20714.3 226.37364 0 3678.757 1.6928839 - 4750 20397.838 278.68649 0 3678.3261 0.72631759 - 4800 21090.67 163.3683 0 3678.4799 -7.4766616 - 4850 20410.173 276.47646 0 3678.1719 -0.48404227 - 4900 17341.87 787.80944 0 3678.1212 4.7714063 - 4950 20335.7 289.09005 0 3678.3734 -10.795568 - 5000 20001.497 344.2494 0 3677.8322 14.312823 - 5050 17359.581 784.91275 0 3678.1762 -15.0609 - 5100 17595.237 745.73589 0 3678.2753 -8.3672887 - 5150 17097.012 827.91859 0 3677.4206 15.446196 - 5200 18757.137 552.19192 0 3678.3814 -6.9635082 - 5250 20388.016 279.39834 0 3677.401 20.142181 - 5300 19965.35 350.31245 0 3677.8707 -17.821737 - 5350 18436.118 605.83431 0 3678.5207 0.84914232 - 5400 20415.986 276.61546 0 3679.2799 -0.0037894847 - 5450 20973.245 184.18908 0 3679.73 1.5256563 - 5500 21320.183 126.74576 0 3680.1096 2.2287329 - 5550 20328.455 292.4549 0 3680.5307 4.674135 - 5600 19512.862 428.45854 0 3680.6021 2.2858232 - 5650 15118.355 1162.6262 0 3682.352 66.775105 - 5700 21062.257 171.98221 0 3682.3583 -0.20268203 - 5750 21441.233 109.32963 0 3682.8684 -12.340852 - 5800 21012.806 181.33239 0 3683.4666 -7.1699728 - 5850 21023.089 179.80114 0 3683.6494 3.8101095 - 5900 21015.077 181.14388 0 3683.6567 -1.176308 - 5950 18343.926 626.46055 0 3683.7815 15.79278 - 6000 20984.465 186.52409 0 3683.935 -6.1829013 - 6050 20941.64 193.97543 0 3684.2488 1.2909073 - 6100 19546.675 426.86545 0 3684.6447 -0.41477554 - 6150 21264.032 140.55982 0 3684.5651 -4.953571 - 6200 20343.321 293.92487 0 3684.4784 -4.8781976 - 6250 20109.575 333.08805 0 3684.6839 -0.23986631 - 6300 19589.511 419.53578 0 3684.4543 18.387721 - 6350 20331.681 295.43346 0 3684.0469 -2.6072047 - 6400 21210.3 148.28185 0 3683.3319 -13.224448 - 6450 19636.964 407.42287 0 3680.2503 26.945373 - 6500 21158.461 156.82542 0 3683.2355 -5.558554 - 6550 21937.478 26.931715 0 3683.1781 -5.8148489 - 6600 20716.445 229.76043 0 3682.5013 -5.4893734 - 6650 20349.273 291.61535 0 3683.1609 -4.7078762 - 6700 20397.246 281.10262 0 3680.6437 6.1633541 - 6750 17336.761 793.781 0 3683.2412 16.830799 - 6800 21708.663 65.02598 0 3683.1366 -13.06689 - 6850 20710.866 231.36429 0 3683.1752 1.1238222 - 6900 20882.087 202.43759 0 3682.7855 -11.177831 - 6950 21045.002 175.62221 0 3683.1225 -3.9647121 - 7000 21170.606 154.92601 0 3683.3603 -3.0075479 - 7050 17340.245 793.0154 0 3683.0563 18.709167 - 7100 20454.586 274.19282 0 3683.2905 4.359508 - 7150 19292.634 470.28091 0 3685.72 23.379394 - 7200 20398.407 283.80225 0 3683.5367 -8.1595888 - 7250 19860.856 374.83326 0 3684.9759 4.3995323 - 7300 21399.991 116.79899 0 3683.4642 -14.69253 - 7350 18469.477 605.76977 0 3684.016 9.072211 - 7400 21246.811 142.508 0 3683.6431 -2.6286469 - 7450 21606.727 82.490537 0 3683.6116 -2.193408 - 7500 20758.001 223.13996 0 3682.8068 3.9337703 - 7550 21529.182 95.699054 0 3683.896 -2.7652731 - 7600 20810.859 215.29662 0 3683.7731 -3.4678516 - 7650 21441.965 109.96162 0 3683.6224 2.8688092 - 7700 21393.02 117.71951 0 3683.2229 -2.0199004 - 7750 21261.451 139.46728 0 3683.0424 -2.351181 - 7800 20994.936 184.15383 0 3683.3099 -1.9007711 - 7850 20956.664 190.40367 0 3683.1811 -4.9029478 - 7900 21318.654 129.90109 0 3683.0101 -7.7655435 - 7950 19343.389 458.65739 0 3682.5556 5.0414528 - 8000 21252.522 140.54793 0 3682.6349 1.7604951 - 8050 21323.878 128.7032 0 3682.6829 -0.66125431 - 8100 20832.414 210.30335 0 3682.3724 -2.6680938 - 8150 17550.263 757.30848 0 3682.3522 1.416445 - 8200 20762.307 222.30426 0 3682.6887 7.061507 - 8250 21016.153 180.1793 0 3682.8714 2.1107236 - 8300 20995.135 183.00069 0 3682.1899 -10.79355 - 8350 19663.825 405.47578 0 3682.7799 10.9075 - 8400 20234.71 310.31036 0 3682.7621 -1.612016 - 8450 21745.345 58.858829 0 3683.083 -3.880159 - 8500 20836.685 210.48891 0 3683.2698 2.5161282 - 8550 18481.486 602.92686 0 3683.1746 4.7767422 - 8600 20149.663 325.20466 0 3683.4819 1.7540149 - 8650 20416.882 280.56681 0 3683.3806 -5.3074807 - 8700 17276.182 803.72341 0 3683.087 3.9552683 - 8750 21629.427 78.173566 0 3683.0781 -1.1208261 - 8800 16461.211 941.11509 0 3684.6503 58.708816 - 8850 20826.403 212.13566 0 3683.2028 -3.6779809 - 8900 21043.766 176.04074 0 3683.335 3.2840745 - 8950 18551.011 591.38957 0 3683.2248 -15.766551 - 9000 17588.62 751.70197 0 3683.1387 -0.79416225 - 9050 18598.429 582.45011 0 3682.1882 -7.8121328 - 9100 17574.963 755.1499 0 3684.3105 23.521269 - 9150 16789.177 884.58607 0 3682.7823 28.62529 - 9200 21059.662 173.26532 0 3683.209 -6.2449386 - 9250 21358.259 123.53455 0 3683.2445 -25.726367 - 9300 20926.413 195.70771 0 3683.4433 -10.230702 - 9350 20863.621 205.86722 0 3683.1373 -1.4396828 - 9400 20440.979 275.97483 0 3682.8047 -10.029174 - 9450 21412.619 114.29156 0 3683.0614 1.8521419 - 9500 18120.95 662.26385 0 3682.4221 23.552524 - 9550 19931.385 360.93428 0 3682.8317 1.8081452 - 9600 19663.03 406.00051 0 3683.1722 11.177455 - 9650 19534.402 427.35484 0 3683.0885 5.3754448 - 9700 20291.266 300.91321 0 3682.7908 -14.76683 - 9750 17786.971 718.21275 0 3682.708 -16.653312 - 9800 21065.368 171.3061 0 3682.2008 -6.6147323 - 9850 19611.141 413.59775 0 3682.1213 2.9925904 - 9900 20735.244 226.23444 0 3682.1084 0.29229058 - 9950 18050.1 673.94746 0 3682.2975 6.6859551 - 10000 19913.432 363.4788 0 3682.3842 -5.8860431 -Loop time of 33.1043 on 1 procs for 10000 steps with 81 atoms - -Pair time (%) = 1.07997 (3.26231) -Neigh time (%) = 0.32972 (0.996002) -Comm time (%) = 0.104371 (0.315279) -Outpt time (%) = 0.145776 (0.440353) -Other time (%) = 31.4445 (94.9861) - -Nlocal: 81 ave 81 max 81 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: 857 ave 857 max 857 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 857 -Ave neighs/atom = 10.5802 -Neighbor list builds = 992 -Dangerous builds = 944 diff --git a/examples/rigid/log.rigid.poems2.1Oct06.liberty.4 b/examples/rigid/log.rigid.poems2.12Feb07.liberty.4 similarity index 98% rename from examples/rigid/log.rigid.poems2.1Oct06.liberty.4 rename to examples/rigid/log.rigid.poems2.12Feb07.liberty.4 index 20c15350f5..f6258c4bdb 100644 --- a/examples/rigid/log.rigid.poems2.1Oct06.liberty.4 +++ b/examples/rigid/log.rigid.poems2.12Feb07.liberty.4 @@ -1,4 +1,4 @@ -LAMMPS (1 Oct 2006) +LAMMPS (12 Feb 2007) # Simple rigid body system units lj @@ -285,13 +285,13 @@ Step Temp E_pair E_mol TotEng Press 9900 19542.173 142.22929 0 3761.1503 7.6623836 9950 19794.356 96.034607 0 3761.6561 2.4218049 10000 19058.563 232.34496 0 3761.7085 -1.2298428 -Loop time of 16.9577 on 4 procs for 10000 steps with 81 atoms +Loop time of 17.5626 on 4 procs for 10000 steps with 81 atoms -Pair time (%) = 0.0940045 (0.554347) -Neigh time (%) = 0.04158 (0.245198) -Comm time (%) = 1.38353 (8.15873) -Outpt time (%) = 0.0951915 (0.561347) -Other time (%) = 15.3434 (90.4804) +Pair time (%) = 0.0920856 (0.524327) +Neigh time (%) = 0.0420477 (0.239415) +Comm time (%) = 1.61713 (9.20777) +Outpt time (%) = 0.101673 (0.578917) +Other time (%) = 15.7097 (89.4496) Nlocal: 20.25 ave 42 max 0 min Histogram: 2 0 0 0 0 0 0 0 1 1 diff --git a/examples/rigid/log.rigid.poems2.12Feb07.linux.1 b/examples/rigid/log.rigid.poems2.12Feb07.linux.1 new file mode 100644 index 0000000000..9b2ea90ad5 --- /dev/null +++ b/examples/rigid/log.rigid.poems2.12Feb07.linux.1 @@ -0,0 +1,306 @@ +LAMMPS (12 Feb 2007) +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + 1 by 1 by 1 processor grid + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 +1 clusters, 4 bodies, 3 joints, 36 atoms +fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +1 clusters, 5 bodies, 4 joints, 45 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 +dump 1 all atom 50 dump.rigid + +timestep 0.0001 +thermo 50 +run 10000 +Memory usage per processor = 1.85083 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -49.218825 + 50 12167.633 1505.5478 0 3758.8133 33.574274 + 100 17556.978 512.66277 0 3763.9549 7.6047451 + 150 19579.586 138.04942 0 3763.8987 -16.463506 + 200 19757.51 105.30542 0 3764.1036 7.5942941 + 250 18218.374 390.10747 0 3763.8804 19.672945 + 300 19383.039 174.40688 0 3763.8586 10.032093 + 350 20125.986 36.972611 0 3764.0071 6.0125969 + 400 18888.816 266.10975 0 3764.0386 8.3046039 + 450 19307.656 188.2511 0 3763.743 7.8887976 + 500 16331.197 738.56392 0 3762.8597 13.456852 + 550 19318.722 186.16172 0 3763.7027 8.2282227 + 600 19455.268 161.20621 0 3764.0336 7.7732896 + 650 18487.011 340.03216 0 3763.5528 3.9255991 + 700 17321.201 556.32471 0 3763.9545 -6.4011523 + 750 18979.187 249.04389 0 3763.7082 2.1939314 + 800 19342.456 181.85552 0 3763.7918 12.876517 + 850 19070.641 232.19342 0 3763.7936 8.2159078 + 900 19478.873 156.65987 0 3763.8586 7.4568244 + 950 19912.415 76.437437 0 3763.9216 5.8486682 + 1000 16003.749 802.39753 0 3766.0548 55.191187 + 1050 19859.583 86.64176 0 3764.3424 8.7977394 + 1100 19229.575 203.61488 0 3764.6473 -4.0979799 + 1150 18821.6 279.15861 0 3764.64 1.5304912 + 1200 19392.695 173.59744 0 3764.8373 10.841959 + 1250 16459.624 717.32104 0 3765.3995 40.93 + 1300 19343.863 182.59043 0 3764.7874 9.4801222 + 1350 20019.643 57.503573 0 3764.8448 8.041765 + 1400 18549.582 329.31436 0 3764.4221 13.151345 + 1450 15163.926 957.47582 0 3765.6103 -7.3048396 + 1500 19223.689 204.15156 0 3764.0939 6.5539037 + 1550 18147.996 404.12674 0 3764.8668 13.092194 + 1600 18615.043 317.42458 0 3764.6548 5.910153 + 1650 20120.654 38.887996 0 3764.935 0.38927147 + 1700 19450.903 162.98348 0 3765.0025 7.9275404 + 1750 19374.636 177.37893 0 3765.2744 8.7907115 + 1800 19424.402 167.93995 0 3765.0514 5.6664351 + 1850 17936.625 442.77274 0 3764.3699 14.100683 + 1900 19982.599 64.405428 0 3764.8868 3.845421 + 1950 16216.44 761.80238 0 3764.8469 19.871956 + 2000 18584.234 322.15493 0 3763.6798 12.138618 + 2050 20107.969 41.025039 0 3764.723 5.3930845 + 2100 20002.411 60.57861 0 3764.7288 0.25780472 + 2150 16948.844 626.76647 0 3765.4413 12.955652 + 2200 20010.946 58.809564 0 3764.5403 -1.2241058 + 2250 18982.703 247.01388 0 3762.3292 8.9782072 + 2300 18401.642 354.81637 0 3762.5279 7.00181 + 2350 19390.361 172.97181 0 3763.7793 1.8204299 + 2400 16086.125 785.40108 0 3764.3132 -12.43145 + 2450 18872.351 268.39211 0 3763.2718 14.60112 + 2500 19684.688 118.25055 0 3763.5632 8.3452435 + 2550 18878.925 267.2853 0 3763.3825 -0.4776104 + 2600 17005.407 614.29162 0 3763.441 11.648752 + 2650 18827.389 277.31059 0 3763.8641 8.0646841 + 2700 19715.461 112.12451 0 3763.1358 6.611501 + 2750 19319.449 185.79269 0 3763.4684 7.0469373 + 2800 18120.942 406.44184 0 3762.1719 34.017493 + 2850 19401.627 170.17075 0 3763.0647 6.6156058 + 2900 20106.157 39.874788 0 3763.2371 3.9356029 + 2950 16814.814 649.4335 0 3763.288 19.866275 + 3000 16200.577 761.45184 0 3761.5588 24.481639 + 3050 18396.676 356.11264 0 3762.9044 11.886991 + 3100 17582.958 506.67523 0 3762.7786 -8.4420604 + 3150 18362.109 362.43838 0 3762.8289 20.848538 + 3200 17008.785 613.88943 0 3763.6645 17.861071 + 3250 19614.194 130.81389 0 3763.072 6.9309301 + 3300 18995.955 245.31261 0 3763.0821 -3.0930246 + 3350 18215.815 389.87474 0 3763.1737 7.0361215 + 3400 18068.71 417.08655 0 3763.144 9.961669 + 3450 19352.914 179.0126 0 3762.8855 13.271847 + 3500 18738.818 292.55665 0 3762.7082 8.7182296 + 3550 19469.912 157.36508 0 3762.9044 9.8811856 + 3600 18431.706 349.41269 0 3762.6916 9.8972814 + 3650 18819.962 277.76095 0 3762.9392 10.602006 + 3700 19813.675 93.945731 0 3763.1449 5.3804999 + 3750 18075.078 415.77801 0 3763.0146 6.6699336 + 3800 19422.14 166.53886 0 3763.2315 6.5699764 + 3850 18013.209 427.44475 0 3763.2243 0.47129141 + 3900 19193.889 208.87526 0 3763.2991 2.2645534 + 3950 16568.188 695.64549 0 3763.8284 18.270973 + 4000 17993.623 430.51008 0 3762.6626 10.839154 + 4050 19625.511 128.63837 0 3762.9922 5.7391383 + 4100 19069.298 231.35736 0 3762.7088 6.8146572 + 4150 18033.877 424.02231 0 3763.6292 2.7693427 + 4200 19950.626 68.482279 0 3763.0426 9.5547662 + 4250 18786.19 284.10677 0 3763.0309 14.089513 + 4300 19526.067 146.81821 0 3762.7565 3.5904061 + 4350 16343.335 736.72783 0 3763.2714 39.410491 + 4400 18759.668 288.81939 0 3762.8319 12.975401 + 4450 18633.251 312.20135 0 3762.8033 10.199762 + 4500 18079.31 414.80535 0 3762.8256 7.6705765 + 4550 18288.498 376.11039 0 3762.8693 12.253044 + 4600 18315.887 371.16083 0 3762.9918 5.0242317 + 4650 18901.901 262.59396 0 3762.9459 2.7293238 + 4700 19311.704 186.85051 0 3763.092 4.5926473 + 4750 19426.54 165.69302 0 3763.2005 -1.3847183 + 4800 18347.933 365.43611 0 3763.2015 7.9755076 + 4850 19952.067 68.477491 0 3763.3047 8.9724781 + 4900 19224.549 203.14962 0 3763.2513 8.0785966 + 4950 19857.322 85.89601 0 3763.1779 6.7304247 + 5000 19592.925 134.86246 0 3763.182 7.6141401 + 5050 19472.16 157.37877 0 3763.3343 9.2091755 + 5100 19814.831 93.787624 0 3763.2008 11.330509 + 5150 18211.407 390.82193 0 3763.3047 13.81542 + 5200 18828.994 276.3271 0 3763.1778 11.34844 + 5250 20121.332 37.261735 0 3763.4344 6.7338019 + 5300 17755.337 475.75071 0 3763.7761 14.167064 + 5350 20033.05 53.761483 0 3763.5855 5.3749453 + 5400 19332.059 183.54479 0 3763.5557 7.4674926 + 5450 19964.421 66.56191 0 3763.677 6.1167743 + 5500 19838.257 89.969443 0 3763.7207 3.3591427 + 5550 19202.804 207.40212 0 3763.4769 16.351587 + 5600 19855.825 86.760789 0 3763.7654 8.0189044 + 5650 19060.478 234.22396 0 3763.9421 6.1572157 + 5700 20124.587 37.161564 0 3763.937 7.5696918 + 5750 19304.489 189.01672 0 3763.9221 5.7150756 + 5800 18516.206 335.07659 0 3764.0036 3.5806069 + 5850 18093.127 413.01533 0 3763.5945 7.8629917 + 5900 17303.637 559.08088 0 3763.458 2.7072615 + 5950 19818.733 93.796285 0 3763.932 8.9805512 + 6000 18162.182 400.57864 0 3763.9457 13.263234 + 6050 18439.177 349.30792 0 3763.9703 6.4756606 + 6100 18899.456 263.84185 0 3763.741 10.898781 + 6150 17317.004 556.71789 0 3763.5704 11.704857 + 6200 18991.81 246.89696 0 3763.8989 3.2286864 + 6250 19868.798 84.388048 0 3763.795 5.9103508 + 6300 18989.135 247.26992 0 3763.7763 18.604444 + 6350 15978.578 804.89 0 3763.8858 12.169877 + 6400 18967.47 251.22915 0 3763.7236 6.8735765 + 6450 19294.369 190.87058 0 3763.9019 -1.5455507 + 6500 19826.451 92.014872 0 3763.5798 7.2553554 + 6550 17480.845 526.28717 0 3763.4807 5.5505499 + 6600 17806.087 465.8384 0 3763.262 26.481782 + 6650 17942.192 439.48981 0 3762.118 11.35985 + 6700 16468.094 712.95472 0 3762.6018 14.069858 + 6750 19305.119 188.34815 0 3763.3703 7.052136 + 6800 19988.201 62.004452 0 3763.5231 6.5334797 + 6850 20193.079 24.117041 0 3763.5761 3.4827497 + 6900 20011.596 57.729546 0 3763.5806 3.4890214 + 6950 18419.577 352.48285 0 3763.5157 0.47973678 + 7000 19178.531 212.01179 0 3763.5917 8.9488095 + 7050 18754.875 289.8693 0 3762.9942 15.271004 + 7100 19179.381 211.26035 0 3762.9975 7.7065367 + 7150 18221.392 388.75188 0 3763.0837 -5.5870803 + 7200 19508.765 150.73861 0 3763.4729 0.86924221 + 7250 16779.268 656.19712 0 3763.4689 9.6537749 + 7300 19184.405 210.6069 0 3763.2744 1.3949529 + 7350 17914.948 445.90458 0 3763.4876 8.5105795 + 7400 14040.559 1164.2709 0 3764.3744 -18.733631 + 7450 17680.643 489.04226 0 3763.2354 7.7465943 + 7500 15575.048 879.11471 0 3763.3829 11.73774 + 7550 16738.339 663.36831 0 3763.0607 19.071113 + 7600 18927.126 258.2804 0 3763.3038 8.7575196 + 7650 17033.929 610.18818 0 3764.6195 20.103976 + 7700 17800.589 463.84003 0 3760.2454 -0.58664763 + 7750 18337.643 367.47891 0 3763.3388 3.0646364 + 7800 20102.521 40.465427 0 3763.1544 5.890522 + 7850 18854.307 271.72975 0 3763.2681 21.40115 + 7900 18769.869 287.08151 0 3762.9832 13.873827 + 7950 19530.556 146.69214 0 3763.4618 6.9677806 + 8000 17967.757 436.48149 0 3763.8439 -8.7686357 + 8050 19995.451 60.489084 0 3763.3503 -0.16755556 + 8100 17668.554 491.39156 0 3763.346 5.2085894 + 8150 17041.937 607.0112 0 3762.9255 32.910713 + 8200 19634.282 127.02828 0 3763.0064 10.156284 + 8250 19464.43 158.26891 0 3762.7929 4.6092644 + 8300 18262.088 380.75171 0 3762.6199 -2.8465886 + 8350 19154.678 214.95549 0 3762.118 7.9411401 + 8400 18631.904 312.04844 0 3762.4011 8.5365875 + 8450 17326.79 552.9849 0 3761.6497 5.5282777 + 8500 18262.986 380.59746 0 3762.6319 4.5328455 + 8550 16355.636 733.37813 0 3762.1995 -0.081116392 + 8600 17652.805 494.50385 0 3763.5419 7.9532832 + 8650 16589.75 690.94159 0 3763.1175 5.9389722 + 8700 18767.632 287.52175 0 3763.0091 8.5339813 + 8750 19530.676 145.40209 0 3762.194 13.700999 + 8800 16209.935 760.89243 0 3762.7323 -3.8758006 + 8850 19909.854 75.790768 0 3762.8008 7.227949 + 8900 19162.868 213.40033 0 3762.0797 13.090144 + 8950 17996.377 429.38719 0 3762.0496 11.184399 + 9000 17366.686 545.41384 0 3761.4667 1.1354401 + 9050 16976.454 618.54424 0 3762.332 2.9998911 + 9100 19419.965 166.18943 0 3762.4793 9.2514375 + 9150 17900.022 448.30981 0 3763.1287 1.7569818 + 9200 18662.637 306.89813 0 3762.942 9.9910386 + 9250 19806.478 95.487105 0 3763.3534 1.7132635 + 9300 19065.731 233.31844 0 3764.0093 5.8910882 + 9350 15347.66 921.21669 0 3763.3759 8.8446349 + 9400 18056.449 416.32084 0 3760.1078 19.958532 + 9450 19104.743 225.75045 0 3763.6658 6.8595588 + 9500 18193.488 394.55096 0 3763.7154 5.7859475 + 9550 17005.07 614.383 0 3763.4701 26.389911 + 9600 18956.557 253.26137 0 3763.7349 9.313651 + 9650 18278.345 379.38464 0 3764.2634 -5.9106259 + 9700 19791.354 98.864736 0 3763.9303 7.4991305 + 9750 19840.264 89.82519 0 3763.9482 3.3775783 + 9800 19120.304 222.91513 0 3763.7122 -2.4237742 + 9850 15643.719 866.53246 0 3763.5175 4.7456523 + 9900 16998.456 616.53609 0 3764.3983 -1.5467682 + 9950 19670.981 121.07532 0 3763.8496 8.7750881 + 10000 16544.589 699.98952 0 3763.8022 -7.723777 +Loop time of 26.9527 on 1 procs for 10000 steps with 81 atoms + +Pair time (%) = 0.688746 (2.55539) +Neigh time (%) = 0.27122 (1.00628) +Comm time (%) = 0.133495 (0.495294) +Outpt time (%) = 0.140981 (0.523068) +Other time (%) = 25.7183 (95.42) + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 528 ave 528 max 528 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 528 +Ave neighs/atom = 6.51852 +Neighbor list builds = 993 +Dangerous builds = 946 diff --git a/examples/rigid/log.rigid.poems2.1Oct06.linux.1 b/examples/rigid/log.rigid.poems2.1Oct06.linux.1 deleted file mode 100644 index 6a6433994b..0000000000 --- a/examples/rigid/log.rigid.poems2.1Oct06.linux.1 +++ /dev/null @@ -1,306 +0,0 @@ -LAMMPS (1 Oct 2006) -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - 1 by 1 by 1 processor grid - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 -dump 1 all atom 50 dump.rigid - -timestep 0.0001 -thermo 50 -run 10000 -Memory usage per processor = 1.85083 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -49.218825 - 50 12167.633 1505.5478 0 3758.8133 33.574274 - 100 17556.978 512.66277 0 3763.9549 7.6047451 - 150 19579.586 138.04942 0 3763.8987 -16.463506 - 200 19757.51 105.30542 0 3764.1036 7.5942941 - 250 18218.374 390.10747 0 3763.8804 19.672945 - 300 19383.039 174.40688 0 3763.8586 10.032093 - 350 20125.986 36.972611 0 3764.0071 6.0125969 - 400 18888.816 266.10975 0 3764.0386 8.3046039 - 450 19307.656 188.2511 0 3763.743 7.8887976 - 500 16331.197 738.56392 0 3762.8597 13.456852 - 550 19318.722 186.16172 0 3763.7027 8.2282227 - 600 19455.268 161.20621 0 3764.0336 7.7732896 - 650 18487.011 340.03216 0 3763.5528 3.9255991 - 700 17321.201 556.32471 0 3763.9545 -6.4011523 - 750 18979.187 249.04389 0 3763.7082 2.1939314 - 800 19342.456 181.85552 0 3763.7918 12.876517 - 850 19070.641 232.19342 0 3763.7936 8.2159078 - 900 19478.873 156.65987 0 3763.8586 7.4568244 - 950 19912.415 76.437437 0 3763.9216 5.8486682 - 1000 16003.749 802.39753 0 3766.0548 55.191187 - 1050 19859.583 86.64176 0 3764.3424 8.7977394 - 1100 19229.575 203.61488 0 3764.6473 -4.0979799 - 1150 18821.6 279.15861 0 3764.64 1.5304912 - 1200 19392.695 173.59744 0 3764.8373 10.841959 - 1250 16459.624 717.32104 0 3765.3995 40.93 - 1300 19343.863 182.59043 0 3764.7874 9.4801222 - 1350 20019.643 57.503573 0 3764.8448 8.041765 - 1400 18549.582 329.31436 0 3764.4221 13.151345 - 1450 15163.926 957.47582 0 3765.6103 -7.3048397 - 1500 19223.689 204.1516 0 3764.0939 6.5539043 - 1550 18147.996 404.12674 0 3764.8668 13.092195 - 1600 18615.043 317.4246 0 3764.6548 5.9101558 - 1650 20120.654 38.887979 0 3764.935 0.38926746 - 1700 19450.904 162.98332 0 3765.0025 7.9275434 - 1750 19374.635 177.37908 0 3765.2744 8.790711 - 1800 19424.402 167.93989 0 3765.0514 5.6664303 - 1850 17936.547 442.78706 0 3764.3699 14.100896 - 1900 19982.599 64.405586 0 3764.8868 3.8454569 - 1950 16216.319 761.8251 0 3764.8472 19.872541 - 2000 18584.273 322.14785 0 3763.6798 12.138511 - 2050 20107.968 41.025185 0 3764.723 5.3931166 - 2100 20002.395 60.581572 0 3764.7288 0.2577697 - 2150 16949.033 626.73148 0 3765.4413 12.955 - 2200 20010.947 58.809301 0 3764.5403 -1.2240041 - 2250 18982.708 247.01284 0 3762.3292 8.9780528 - 2300 18401.571 354.8294 0 3762.5278 7.0019831 - 2350 19390.394 172.9656 0 3763.7793 1.8206136 - 2400 16085.032 785.60385 0 3764.3135 -12.434917 - 2450 18871.953 268.46552 0 3763.2716 14.607919 - 2500 19685.428 118.11323 0 3763.5629 8.3387285 - 2550 18877.269 267.59235 0 3763.3828 -0.48341735 - 2600 17008.289 613.75762 0 3763.4407 11.639259 - 2650 18812.576 280.05888 0 3763.8693 8.0841903 - 2700 19721.109 111.09615 0 3763.1533 6.5832394 - 2750 19385.826 173.49011 0 3763.4578 6.9477448 - 2800 18261.265 380.36977 0 3762.0854 31.328975 - 2850 19262.504 195.91155 0 3763.042 7.1306245 - 2900 20108.917 39.360683 0 3763.2342 4.2051073 - 2950 16520.273 703.73173 0 3763.0416 20.666642 - 3000 17721.082 480.84673 0 3762.5286 10.889353 - 3050 18281.378 377.38446 0 3762.8248 12.727107 - 3100 17813.119 464.33179 0 3763.0575 -5.9033506 - 3150 17848.794 456.92067 0 3762.253 24.280682 - 3200 16283.244 747.77931 0 3763.1949 -34.084455 - 3250 17775.99 470.52364 0 3762.3736 31.744378 - 3300 18920.688 258.84248 0 3762.6735 9.8437551 - 3350 18374.481 358.89272 0 3761.5744 3.5475689 - 3400 18147.71 402.29354 0 3762.9806 11.829727 - 3450 19446.951 161.38162 0 3762.6688 -0.25609588 - 3500 18586.947 320.84226 0 3762.8695 4.4386085 - 3550 19739.703 107.24051 0 3762.7411 6.7843088 - 3600 18020.123 425.86788 0 3762.9277 32.692211 - 3650 17703.685 484.51122 0 3762.9715 18.888689 - 3700 18571.567 323.53862 0 3762.7177 -2.5479026 - 3750 19747.937 105.29513 0 3762.3204 6.9264561 - 3800 19055.305 233.61597 0 3762.3762 10.269813 - 3850 19390.879 171.45465 0 3762.3582 8.5051872 - 3900 17669.249 489.45512 0 3761.5382 28.590013 - 3950 18309.837 371.37486 0 3762.0854 17.457093 - 4000 17913.77 444.38412 0 3761.7489 11.054563 - 4050 19357.4 177.36212 0 3762.0659 -2.7100501 - 4100 19601.584 132.10663 0 3762.0297 7.7432662 - 4150 19468.348 156.55912 0 3761.8087 7.9494045 - 4200 18791.279 282.08385 0 3761.9502 8.0141814 - 4250 17932.214 440.54317 0 3761.3236 8.6775437 - 4300 19854.413 85.385328 0 3762.1285 2.6399285 - 4350 18753.885 289.43762 0 3762.3792 -3.348463 - 4400 19497.1 151.47714 0 3762.0512 8.2129692 - 4450 18881.054 265.79896 0 3762.2904 15.717461 - 4500 19483 154.31774 0 3762.2806 4.5428504 - 4550 18372.304 359.93631 0 3762.2148 2.1598549 - 4600 18538.653 329.1277 0 3762.2117 9.8161015 - 4650 19561.941 139.74654 0 3762.3281 10.249049 - 4700 18772.917 286.03706 0 3762.5032 21.326885 - 4750 19574.986 137.31432 0 3762.3117 7.4877085 - 4800 18707.43 297.96418 0 3762.303 3.5977275 - 4850 19084.263 228.13574 0 3762.2584 4.8620306 - 4900 19256.565 196.41485 0 3762.4453 7.1493737 - 4950 19692.391 115.536 0 3762.2751 9.4402989 - 5000 19540.996 143.5732 0 3762.2761 8.2081649 - 5050 18653.131 308.51184 0 3762.7953 12.668618 - 5100 19633.591 126.5541 0 3762.4043 5.7938001 - 5150 18621.364 313.78864 0 3762.1894 24.57491 - 5200 19688.937 116.08545 0 3762.185 12.477508 - 5250 18410.54 353.19966 0 3762.559 12.976514 - 5300 19950.659 67.914691 0 3762.4811 5.8022194 - 5350 20096.327 40.899907 0 3762.4419 6.0410733 - 5400 19919.818 73.467027 0 3762.3221 2.2220049 - 5450 19300.983 185.34644 0 3759.6026 8.1383036 - 5500 19800.648 95.498164 0 3762.2848 2.3885829 - 5550 20056.731 48.009231 0 3762.2186 4.3782978 - 5600 19844.923 87.14203 0 3762.1277 7.7533964 - 5650 17129.848 590.16296 0 3762.3571 17.511751 - 5700 19711.052 111.82109 0 3762.0159 11.77834 - 5750 19617.414 129.29781 0 3762.1523 7.8333492 - 5800 20036.44 51.792528 0 3762.2443 1.2142201 - 5850 19666.587 120.39539 0 3762.356 2.9059895 - 5900 19270.785 193.72474 0 3762.3887 8.5521132 - 5950 18570.273 323.50997 0 3762.4494 7.917873 - 6000 19639.926 125.31297 0 3762.3363 7.8943644 - 6050 19170.13 212.17653 0 3762.2006 11.073748 - 6100 19477.33 155.36998 0 3762.2829 9.7741577 - 6150 19489.538 153.13138 0 3762.3051 10.490838 - 6200 15767.031 842.38404 0 3762.2046 17.502671 - 6250 18412.418 352.52257 0 3762.2297 6.5373659 - 6300 17972.252 434.26055 0 3762.4554 13.704085 - 6350 18918.499 258.81778 0 3762.2436 1.9382232 - 6400 18849.088 271.35964 0 3761.9315 6.6707881 - 6450 18253.5 381.84702 0 3762.1248 11.492891 - 6500 19249.208 197.34439 0 3762.0126 8.5573923 - 6550 17155.467 584.92475 0 3761.863 10.220904 - 6600 19820.303 91.781334 0 3762.2078 3.1199949 - 6650 16832.666 643.9692 0 3761.1296 3.1224873 - 6700 19043.731 235.36302 0 3761.9799 9.0582649 - 6750 18893.629 263.25929 0 3762.0794 7.2472883 - 6800 17109.53 593.22372 0 3761.6553 4.3802066 - 6850 16744.117 662.34545 0 3763.1078 12.922567 - 6900 19458.193 158.37115 0 3761.7402 11.006662 - 6950 18725.976 294.25915 0 3762.0326 3.2140093 - 7000 16598.724 687.82474 0 3761.6624 -3.6835942 - 7050 18730.073 293.30419 0 3761.8363 10.884579 - 7100 20018.967 54.77727 0 3761.9935 6.0028598 - 7150 17113.843 592.9644 0 3762.1945 6.7236396 - 7200 17196.345 575.20975 0 3759.7181 22.617984 - 7250 19441.447 161.79318 0 3762.0612 8.6790347 - 7300 18425.176 348.35362 0 3760.4232 1.2239447 - 7350 15831.334 830.07877 0 3761.8073 12.989722 - 7400 15760.367 843.93147 0 3762.5179 20.330489 - 7450 19887.01 78.958802 0 3761.7384 3.9771783 - 7500 17074.502 600.07806 0 3762.0229 0.40604401 - 7550 19498.422 151.10349 0 3761.9224 4.5520709 - 7600 19185.257 208.81514 0 3761.6406 4.2379441 - 7650 18265.566 379.07997 0 3761.5921 6.3803024 - 7700 18874.852 266.08897 0 3761.432 12.40484 - 7750 18129.668 404.32772 0 3761.6736 10.569077 - 7800 18203.274 390.12247 0 3761.0991 9.6842762 - 7850 18194.832 391.87893 0 3761.2922 5.4796988 - 7900 16807.558 648.88314 0 3761.3938 0.29076345 - 7950 18084.122 412.78207 0 3761.6935 6.8841109 - 8000 17981.757 431.92518 0 3761.8801 6.6592835 - 8050 19355.253 177.54899 0 3761.855 5.5142333 - 8100 20025.877 53.385491 0 3761.8812 6.9839182 - 8150 18845.855 271.98132 0 3761.9544 12.093316 - 8200 16272.215 748.48475 0 3761.8579 3.2379236 - 8250 19924.961 72.016182 0 3761.8237 7.4249536 - 8300 17765.452 471.72154 0 3761.6201 7.703297 - 8350 18716.949 295.72885 0 3761.8305 3.9378764 - 8400 18669.341 304.5313 0 3761.8167 6.5183661 - 8450 17588.96 504.87172 0 3762.0864 10.603189 - 8500 19416.561 166.00525 0 3761.6647 4.9012003 - 8550 17856.962 455.50215 0 3762.347 32.77813 - 8600 19538.533 143.63236 0 3761.8792 7.9996791 - 8650 19155.813 213.86669 0 3761.2394 10.276167 - 8700 19069.24 230.4574 0 3761.7982 3.9102709 - 8750 19365.473 175.51172 0 3761.7105 11.362372 - 8800 19133.09 218.25828 0 3761.4231 9.9797495 - 8850 18259.293 380.39561 0 3761.7461 7.7607448 - 8900 18775.775 284.73679 0 3761.7321 -1.8279748 - 8950 15941.533 809.54243 0 3761.6782 20.457951 - 9000 19525.004 145.86783 0 3761.6092 6.7957307 - 9050 17956.771 435.7506 0 3761.0786 7.3335578 - 9100 19258.953 195.12617 0 3761.5989 9.5389589 - 9150 18891.927 262.8519 0 3761.357 9.7974291 - 9200 17804.066 464.97231 0 3762.0215 14.446215 - 9250 18975.048 247.6467 0 3761.5445 10.681583 - 9300 19242.636 198.11698 0 3761.5681 1.1630841 - 9350 19037.441 236.19188 0 3761.644 8.4873411 - 9400 17398.22 539.36333 0 3761.2559 23.119633 - 9450 18636.737 310.27156 0 3761.5192 4.5578491 - 9500 19979.365 61.813877 0 3761.6963 6.4995321 - 9550 18886.37 264.32082 0 3761.7967 4.2159993 - 9600 18374.874 359.07673 0 3761.8312 -0.87552165 - 9650 19927.34 71.462667 0 3761.7108 6.3897422 - 9700 16594.729 688.47459 0 3761.5725 21.040463 - 9750 19520.395 146.32272 0 3761.2106 9.4824852 - 9800 17066.423 600.32957 0 3760.7782 10.240849 - 9850 18262.057 379.95673 0 3761.8191 45.222639 - 9900 19261.074 194.37227 0 3761.2378 -1.6957956 - 9950 19695.741 113.67141 0 3761.0308 8.0826867 - 10000 19798.388 94.785163 0 3761.1534 9.0475616 -Loop time of 33.9032 on 1 procs for 10000 steps with 81 atoms - -Pair time (%) = 0.816388 (2.40799) -Neigh time (%) = 0.259492 (0.76539) -Comm time (%) = 0.132266 (0.390128) -Outpt time (%) = 0.142545 (0.420446) -Other time (%) = 32.5526 (96.016) - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 60 ave 60 max 60 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 626 ave 626 max 626 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 626 -Ave neighs/atom = 7.7284 -Neighbor list builds = 994 -Dangerous builds = 954 diff --git a/examples/shear/log.shear.12Feb07.liberty.4 b/examples/shear/log.shear.12Feb07.liberty.4 new file mode 100644 index 0000000000..be604f3911 --- /dev/null +++ b/examples/shear/log.shear.12Feb07.liberty.4 @@ -0,0 +1,159 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 2 by 2 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style eam +pair_coeff * * niu3.eam + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 1.68686 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346 + 25 220.91849 -8272.7063 0 -8233.2134 5171.0015 19539.346 + 50 300 -8239.0761 0 -8185.446 13404.703 19669.87 + 75 295.11708 -8231.4059 0 -8178.6488 13741.993 19743.549 + 100 300 -8250.5856 0 -8196.9555 6735.754 19818.526 +Loop time of 0.213186 on 4 procs for 100 steps with 1912 atoms + +Pair time (%) = 0.175801 (82.4637) +Neigh time (%) = 0.00498581 (2.33871) +Comm time (%) = 0.0236108 (11.0752) +Outpt time (%) = 0.000816882 (0.383177) +Other time (%) = 0.00797158 (3.73926) + +Nlocal: 478 ave 490 max 468 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1033.75 ave 1043 max 1021 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Neighs: 11508.8 ave 12218 max 10874 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 46035 +Ave neighs/atom = 24.0769 +Neighbor list builds = 4 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 1.70559 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781 + 100 297.48776 -8255.7637 0 -8220.3225 1519.5936 19869.252 + 200 300 -8259.5191 0 -8223.7786 407.14026 19843.233 + 300 306.85093 -8252.9546 0 -8216.3979 -1452.8459 19987.791 + 400 303.87074 -8246.296 0 -8210.0945 1276.3308 20128.061 + 500 299.00581 -8241.6473 0 -8206.0253 943.44685 20226.281 + 600 300 -8228.0773 0 -8192.3369 3740.0009 20307.41 + 700 302.55478 -8222.4773 0 -8186.4325 6034.1752 20412.441 + 800 291.55934 -8208.4477 0 -8173.7129 9870.4071 20534.96 + 900 300.04405 -8197.8106 0 -8162.0649 11858.874 20635.988 + 1000 303.4363 -8185.1721 0 -8149.0223 15860.089 20755.666 + 1100 300 -8172.7372 0 -8136.9967 19064.863 20868.017 + 1200 300 -8163.6948 0 -8127.9543 20503.74 20997.464 + 1300 300 -8157.774 0 -8122.0336 19017.48 21108.594 + 1400 301.23169 -8148.1245 0 -8112.2373 19838.433 21245.369 + 1500 300 -8137.0376 0 -8101.2972 19618.234 21361.383 + 1600 300 -8129.5673 0 -8093.8269 17832.316 21493.274 + 1700 300 -8131.9086 0 -8096.1682 15651.56 21609.288 + 1800 300 -8154.2629 0 -8118.5225 9602.8973 21725.302 + 1900 300 -8166.6747 0 -8130.9342 7079.4166 21855.971 + 2000 297.56913 -8164.1963 0 -8128.7455 6008.7168 21970.765 + 2100 307.18117 -8162.4989 0 -8125.903 5339.1594 22100.212 + 2200 307.91443 -8165.8526 0 -8129.1693 4903.917 22218.669 + 2300 307.29809 -8166.6561 0 -8130.0463 4057.1866 22343.232 + 2400 306.14212 -8165.725 0 -8129.2529 4381.5236 22462.91 + 2500 306.62123 -8166.8443 0 -8130.3151 2924.8251 22583.809 + 2600 300 -8166.6003 0 -8130.8598 2179.9998 22701.045 + 2700 309.89171 -8168.2224 0 -8131.3035 3044.4626 22836.599 + 2800 305.74412 -8166.2652 0 -8129.8404 1099.7498 22952.613 + 2900 301.2671 -8170.7739 0 -8134.8825 -2699.4417 23073.512 + 3000 300 -8171.8299 0 -8136.0895 -3656.4591 23189.527 +Loop time of 8.00391 on 4 procs for 3000 steps with 1912 atoms + +Pair time (%) = 5.24986 (65.5912) +Neigh time (%) = 0.275418 (3.44104) +Comm time (%) = 0.891668 (11.1404) +Outpt time (%) = 0.975094 (12.1827) +Other time (%) = 0.611869 (7.64463) + +Nlocal: 478 ave 508 max 449 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1006.75 ave 1064 max 959 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 11284 ave 12171 max 10415 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 45136 +Ave neighs/atom = 23.6067 +Neighbor list builds = 216 +Dangerous builds = 0 diff --git a/examples/shear/log.shear.12Feb07.linux.1 b/examples/shear/log.shear.12Feb07.linux.1 new file mode 100644 index 0000000000..949cf67bf0 --- /dev/null +++ b/examples/shear/log.shear.12Feb07.linux.1 @@ -0,0 +1,159 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 1 by 1 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style eam +pair_coeff * * niu3.eam + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 1.92854 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8317.4367 0 -8263.8067 -7103.5557 19539.346 + 25 220.34459 -8272.5701 0 -8233.1798 5170.6956 19539.346 + 50 300 -8237.7876 0 -8184.1576 13746.642 19678.792 + 75 292.67269 -8229.8093 0 -8177.4891 14324.984 19737.233 + 100 300 -8245.8191 0 -8192.189 9038.4055 19770.872 +Loop time of 1.256 on 1 procs for 100 steps with 1912 atoms + +Pair time (%) = 1.16738 (92.9443) +Neigh time (%) = 0.03633 (2.89252) +Comm time (%) = 0.012652 (1.00733) +Outpt time (%) = 0.002018 (0.160669) +Other time (%) = 0.03762 (2.99523) + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2122 ave 2122 max 2122 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45975 ave 45975 max 45975 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45975 +Ave neighs/atom = 24.0455 +Neighbor list builds = 4 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 2.00339 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399 + 100 300 -8263.5777 0 -8227.8373 2795.3643 19788.083 + 200 295.48797 -8257.8787 0 -8222.6759 2179.0845 19913.732 + 300 292.48667 -8250.5584 0 -8215.7131 2.9847512 20043.736 + 400 304.93883 -8245.9033 0 -8209.5745 179.50544 20125.384 + 500 294.27283 -8241.2854 0 -8206.2272 829.41012 20145.713 + 600 302.25208 -8230.3821 0 -8194.3734 4273.5024 20285.46 + 700 300 -8223.3443 0 -8187.6038 6565.4269 20406.893 + 800 303.62781 -8211.0391 0 -8174.8665 8116.0638 20515.088 + 900 297.87427 -8197.7869 0 -8162.2997 10317.159 20621.333 + 1000 300 -8181.081 0 -8145.3406 13621.801 20748.339 + 1100 307.26338 -8166.9162 0 -8130.3105 17420.976 20877.786 + 1200 300.29796 -8153.8084 0 -8118.0325 20385.904 20986.474 + 1300 300 -8147.0071 0 -8111.2667 21178.857 21115.921 + 1400 300 -8137.1276 0 -8101.3872 21423.889 21246.59 + 1500 308.75316 -8131.6139 0 -8094.8306 20067.792 21365.047 + 1600 300 -8133.2906 0 -8097.5501 16682.824 21477.398 + 1700 308.52741 -8149.3473 0 -8112.5909 11697.908 21599.518 + 1800 300 -8152.6978 0 -8116.9573 9550.2281 21737.514 + 1900 308.57591 -8146.2494 0 -8109.4873 9662.4382 21859.635 + 2000 308.26812 -8146.4139 0 -8109.6884 9661.2057 21976.871 + 2100 302.17107 -8146.0627 0 -8110.0636 8521.2058 22094.106 + 2200 305.08447 -8151.7703 0 -8115.4241 4427.9711 22218.669 + 2300 300 -8166.2097 0 -8130.4693 -1334.8828 22346.896 + 2400 304.42128 -8165.4861 0 -8129.219 -931.52307 22464.131 + 2500 291.59698 -8160.1078 0 -8125.3684 2248.0287 22592.358 + 2600 304.33702 -8161.3244 0 -8125.0673 3566.8213 22704.709 + 2700 308.4539 -8163.6628 0 -8126.9152 1887.5801 22825.608 + 2800 309.42404 -8163.7723 0 -8126.9092 -395.06508 22946.507 + 2900 307.81471 -8165.3682 0 -8128.6967 -3460.652 23077.176 + 3000 299.7731 -8165.3688 0 -8129.6554 -5437.2745 23191.969 +Loop time of 41.2714 on 1 procs for 3000 steps with 1912 atoms + +Pair time (%) = 34.9492 (84.6813) +Neigh time (%) = 1.98951 (4.82056) +Comm time (%) = 0.404728 (0.98065) +Outpt time (%) = 2.83924 (6.87944) +Other time (%) = 1.08875 (2.63802) + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2089 ave 2089 max 2089 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45088 ave 45088 max 45088 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45088 +Ave neighs/atom = 23.5816 +Neighbor list builds = 216 +Dangerous builds = 0 diff --git a/examples/shear/log.shear.1Oct06.liberty.4 b/examples/shear/log.shear.1Oct06.liberty.4 deleted file mode 100644 index 215c422377..0000000000 --- a/examples/shear/log.shear.1Oct06.liberty.4 +++ /dev/null @@ -1,160 +0,0 @@ -LAMMPS (1 Oct 2006) -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created box = (0 0 0) to (56.32 35.2 9.95606) - 2 by 2 by 1 processor grid - -orient x 1 0 0 -orient y 0 1 1 -orient z 0 -1 1 -origin 0.5 0 0 -create_atoms 1 -Created 1912 atoms - -pair_style eam -pair_coeff * * niu3.eam - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 1.4 INF INF -region upper block INF INF 8.6 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set lower atom 2 - 264 settings made -set upper atom 3 - 264 settings made - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -temperature new3d mobile full -temperature new2d mobile partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 -Memory usage per processor = 1.68686 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -8317.4367 0 -8263.8088 -7102.8898 19539.346 - 25 220.9212 -8272.7102 0 -8233.2184 5169.2532 19539.346 - 50 300 -8239.0788 0 -8185.4509 13402.59 19669.861 - 75 295.11304 -8231.409 0 -8178.6547 13739.709 19743.536 - 100 300 -8250.5854 0 -8196.9575 6735.3894 19818.51 -Loop time of 0.20501 on 4 procs for 100 steps with 1912 atoms - -Pair time (%) = 0.170366 (83.1014) -Neigh time (%) = 0.00511163 (2.49336) -Comm time (%) = 0.0205901 (10.0434) -Outpt time (%) = 0.000730455 (0.356302) -Other time (%) = 0.00821161 (4.00547) - -Nlocal: 478 ave 490 max 468 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 1033.75 ave 1043 max 1021 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Neighs: 11509 ave 12218 max 10874 min -Histogram: 1 0 0 0 2 0 0 0 0 1 - -Total # of neighbors = 46036 -Ave neighs/atom = 24.0774 -Neighbor list builds = 4 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -dump 1 all atom 10 dump.shear -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 -Memory usage per processor = 1.70559 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 292.46935 -8250.5854 0 -8215.7435 5714.5932 19847.768 - 100 297.59499 -8256.7106 0 -8221.2581 1294.1819 19860.892 - 200 292.19816 -8260.283 0 -8225.4734 299.28813 19869.393 - 300 302.96848 -8254.8033 0 -8218.7107 -1931.9374 19978.005 - 400 306.09958 -8249.231 0 -8212.7654 435.17823 20093.509 - 500 296.82499 -8244.0101 0 -8208.6494 646.75953 20198.763 - 600 300 -8230.1411 0 -8194.4021 3590.0541 20277.909 - 700 299.5264 -8222.6973 0 -8187.0147 6328.7718 20385.21 - 800 295.07726 -8207.5484 0 -8172.3958 10476.661 20524.637 - 900 305.7088 -8197.6454 0 -8161.2263 12349.102 20621.333 - 1000 297.84421 -8183.9807 0 -8148.4985 16146.327 20741.011 - 1100 307.99301 -8170.1977 0 -8133.5065 19739.24 20871.68 - 1200 300 -8162.0163 0 -8126.2773 21326.406 20996.243 - 1300 300 -8151.4476 0 -8115.7086 21185.942 21118.364 - 1400 304.51892 -8143.3645 0 -8107.0871 21474.828 21234.378 - 1500 307.86659 -8134.7063 0 -8098.0302 21789.168 21361.383 - 1600 300 -8126.473 0 -8090.734 20673.353 21484.725 - 1700 300 -8129.42 0 -8093.681 17751.243 21606.846 - 1800 300 -8146.0891 0 -8110.3501 12858.826 21737.514 - 1900 301.48058 -8160.3481 0 -8124.4327 10026.088 21854.75 - 2000 303.13886 -8159.9363 0 -8123.8233 10035.576 21979.313 - 2100 302.43445 -8158.993 0 -8122.964 8142.9832 22089.221 - 2200 305.6122 -8159.3597 0 -8122.9521 5981.3934 22216.227 - 2300 307.57806 -8154.583 0 -8117.9413 7603.355 22333.462 - 2400 303.24127 -8162.4278 0 -8126.3027 6097.2511 22469.016 - 2500 305.61941 -8164.9775 0 -8128.5691 3543.4308 22585.031 - 2600 309.10168 -8168.3336 0 -8131.5103 -691.16472 22701.045 - 2700 307.75507 -8168.189 0 -8131.5261 -5684.463 22836.599 - 2800 301.01957 -8164.8783 0 -8129.0178 -9335.7848 22947.728 - 2900 305.43054 -8164.2448 0 -8127.8589 -11554.582 23075.955 - 3000 303.62558 -8162.2789 0 -8126.1079 -12622.002 23199.297 -Loop time of 7.89757 on 4 procs for 3000 steps with 1912 atoms - -Pair time (%) = 5.18402 (65.6407) -Neigh time (%) = 0.282387 (3.57562) -Comm time (%) = 0.885845 (11.2167) -Outpt time (%) = 0.95221 (12.057) -Other time (%) = 0.593105 (7.50997) - -Nlocal: 478 ave 518 max 439 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 1008 ave 1048 max 973 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 11229 ave 12551 max 10264 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 44916 -Ave neighs/atom = 23.4916 -Neighbor list builds = 217 -Dangerous builds = 0 diff --git a/examples/shear/log.shear.1Oct06.linux.1 b/examples/shear/log.shear.1Oct06.linux.1 deleted file mode 100644 index 4fa5075e91..0000000000 --- a/examples/shear/log.shear.1Oct06.linux.1 +++ /dev/null @@ -1,160 +0,0 @@ -LAMMPS (1 Oct 2006) -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created box = (0 0 0) to (56.32 35.2 9.95606) - 1 by 1 by 1 processor grid - -orient x 1 0 0 -orient y 0 1 1 -orient z 0 -1 1 -origin 0.5 0 0 -create_atoms 1 -Created 1912 atoms - -pair_style eam -pair_coeff * * niu3.eam - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 1.4 INF INF -region upper block INF INF 8.6 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set lower atom 2 - 264 settings made -set upper atom 3 - 264 settings made - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -temperature new3d mobile full -temperature new2d mobile partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 -Memory usage per processor = 1.92854 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -8317.4367 0 -8263.8088 -7102.8898 19539.346 - 25 220.34739 -8272.574 0 -8233.1848 5168.9424 19539.346 - 50 300 -8237.7904 0 -8184.1625 13744.474 19678.783 - 75 292.66971 -8229.8128 0 -8177.4952 14322.493 19737.223 - 100 300 -8245.8192 0 -8192.1914 9037.5551 19770.863 -Loop time of 1.32784 on 1 procs for 100 steps with 1912 atoms - -Pair time (%) = 1.24155 (93.5014) -Neigh time (%) = 0.037302 (2.80923) -Comm time (%) = 0.013245 (0.997488) -Outpt time (%) = 0.000552 (0.0415714) -Other time (%) = 0.035192 (2.65033) - -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: 45974 ave 45974 max 45974 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 45974 -Ave neighs/atom = 24.045 -Neighbor list builds = 4 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -dump 1 all atom 10 dump.shear -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 -Memory usage per processor = 2.00339 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 298.53461 -8245.8192 0 -8210.2548 8058.7181 19778.392 - 100 300 -8264.0486 0 -8228.3096 2691.7558 19826.894 - 200 294.32149 -8259.4812 0 -8224.4187 1849.8688 19915.639 - 300 293.23673 -8253.0529 0 -8218.1196 -568.76065 20023.531 - 400 300.89492 -8248.1925 0 -8212.3469 -317.08468 20091.777 - 500 293.55594 -8243.3219 0 -8208.3506 406.7293 20171.198 - 600 301.16216 -8232.0523 0 -8196.1748 4289.0467 20256.193 - 700 300 -8222.1995 0 -8186.4604 7361.3269 20388.083 - 800 297.68439 -8211.4622 0 -8175.999 8573.6353 20512.646 - 900 300.09026 -8197.39 0 -8161.6402 10797.992 20638.43 - 1000 293.3388 -8182.0987 0 -8147.1532 13912.802 20747.117 - 1100 305.0194 -8169.078 0 -8132.741 16871.039 20882.671 - 1200 295.62571 -8154.0757 0 -8118.8578 20598.322 20993.801 - 1300 300 -8143.9231 0 -8108.1841 21781.691 21117.142 - 1400 300 -8130.6475 0 -8094.9085 24186.109 21245.369 - 1500 309.0526 -8127.5064 0 -8090.6889 21858.969 21367.489 - 1600 300 -8128.5701 0 -8092.8311 18560.503 21474.955 - 1700 300 -8147.5253 0 -8111.7862 12751.805 21606.846 - 1800 305.83763 -8164.2172 0 -8127.7828 8040.3799 21732.63 - 1900 301.4629 -8160.2306 0 -8124.3173 8616.0354 21858.414 - 2000 304.26807 -8152.1587 0 -8115.9112 10071.784 21973.207 - 2100 305.08538 -8154.2603 0 -8117.9154 7911.69 22090.443 - 2200 300 -8151.5205 0 -8115.7815 7821.2573 22215.006 - 2300 300 -8154.9943 0 -8119.2553 6744.5955 22338.347 - 2400 300 -8154.8809 0 -8119.1419 6094.8065 22460.468 - 2500 306.30502 -8153.0721 0 -8116.582 6168.5479 22585.031 - 2600 300 -8155.5915 0 -8119.8525 3322.6468 22713.257 - 2700 299.94465 -8155.1357 0 -8119.4033 3475.705 22835.378 - 2800 304.48054 -8154.675 0 -8118.4023 -230.17514 22946.507 - 2900 299.98768 -8154.2556 0 -8118.518 -2933.046 23077.176 - 3000 301.75583 -8148.8621 0 -8112.914 -2858.4431 23195.633 -Loop time of 42.2848 on 1 procs for 3000 steps with 1912 atoms - -Pair time (%) = 36.2138 (85.6426) -Neigh time (%) = 1.93158 (4.56802) -Comm time (%) = 0.410137 (0.96994) -Outpt time (%) = 2.71704 (6.42558) -Other time (%) = 1.01224 (2.39386) - -Nlocal: 1912 ave 1912 max 1912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2083 ave 2083 max 2083 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 45144 ave 45144 max 45144 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 45144 -Ave neighs/atom = 23.6109 -Neighbor list builds = 214 -Dangerous builds = 0 diff --git a/examples/shear/log.shear.void.12Feb07.liberty.4 b/examples/shear/log.shear.void.12Feb07.liberty.4 new file mode 100644 index 0000000000..878a712c36 --- /dev/null +++ b/examples/shear/log.shear.void.12Feb07.liberty.4 @@ -0,0 +1,160 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 2 by 2 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style eam +pair_coeff * * niu3.eam + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +region void cylinder z 8 3.535534 2.5 INF INF +delete_atoms region void +Deleted 204 atoms, new total = 1708 + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 1.67464 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346 + 25 221.73981 -7320.8381 0 -7287.0455 1130.0476 19599.582 + 50 300 -7293.1759 0 -7247.4566 8052.1835 19662.062 + 75 293.25753 -7287.1687 0 -7242.4769 7429.1313 19732.777 + 100 300 -7300.0537 0 -7254.3344 1198.4581 19807.395 +Loop time of 0.183477 on 4 procs for 100 steps with 1708 atoms + +Pair time (%) = 0.149475 (81.468) +Neigh time (%) = 0.00532675 (2.90322) +Comm time (%) = 0.0207931 (11.3328) +Outpt time (%) = 0.000882387 (0.480925) +Other time (%) = 0.00699979 (3.81507) + +Nlocal: 427 ave 435 max 419 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Nghost: 780.25 ave 792 max 769 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 9878.75 ave 10203 max 9534 min +Histogram: 1 0 0 0 1 0 1 0 0 1 + +Total # of neighbors = 39515 +Ave neighs/atom = 23.1352 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 1.69123 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521 + 100 307.23986 -7307.219 0 -7276.0171 -5006.3499 19862.724 + 200 300 -7309.7515 0 -7279.2849 -9319.6187 19862.401 + 300 298.46847 -7303.3937 0 -7273.0826 -9727.416 20012.256 + 400 298.27255 -7299.2458 0 -7268.9546 -7916.7896 20056.15 + 500 297.5947 -7299.7495 0 -7269.5271 -6499.9287 20136.515 + 600 299.11571 -7294.7189 0 -7264.342 -4738.4592 20278.808 + 700 299.12204 -7285.1912 0 -7254.8138 -1900.5818 20396.287 + 800 300 -7279.6074 0 -7249.1408 -601.56409 20516.31 + 900 300 -7272.2062 0 -7241.7396 372.01695 20624.997 + 1000 297.17814 -7265.7734 0 -7235.5934 -1620.5152 20750.781 + 1100 300 -7257.7175 0 -7227.2509 -1422.3295 20870.459 + 1200 300 -7254.9538 0 -7224.4872 -2924.6246 20990.137 + 1300 300 -7257.9757 0 -7227.5091 -4069.1414 21123.248 + 1400 300 -7265.0693 0 -7234.6027 -6549.1146 21249.033 + 1500 305.40659 -7268.4 0 -7237.3844 -9980.0284 21360.162 + 1600 307.73328 -7272.8967 0 -7241.6447 -12845.156 21479.84 + 1700 308.89481 -7272.8308 0 -7241.4609 -14742.73 21599.518 + 1800 301.22537 -7272.7599 0 -7242.1688 -15363.965 21736.293 + 1900 294.08915 -7269.2219 0 -7239.3555 -17918.885 21854.75 + 2000 300 -7267.3723 0 -7236.9057 -22110.158 21970.765 + 2100 303.71749 -7266.6269 0 -7235.7828 -24452.593 22103.876 + 2200 305.09813 -7260.5568 0 -7229.5724 -22990.432 22219.89 + 2300 302.38637 -7258.8153 0 -7228.1063 -21646.154 22335.905 + 2400 305.66165 -7262.3039 0 -7231.2623 -21131.332 22458.025 + 2500 298.90421 -7257.9905 0 -7227.6352 -21269.206 22592.358 + 2600 300.16888 -7256.8469 0 -7226.3631 -23698.687 22699.824 + 2700 296.33302 -7251.3734 0 -7221.2792 -26655.74 22826.829 + 2800 296.22091 -7248.3427 0 -7218.2599 -30008.453 22947.728 + 2900 301.32756 -7250.3222 0 -7219.7207 -28370.97 23080.84 + 3000 300 -7252.9148 0 -7222.4482 -28938.171 23201.739 +Loop time of 6.9145 on 4 procs for 3000 steps with 1708 atoms + +Pair time (%) = 4.49671 (65.033) +Neigh time (%) = 0.231831 (3.35283) +Comm time (%) = 0.760524 (10.999) +Outpt time (%) = 0.882937 (12.7693) +Other time (%) = 0.5425 (7.84583) + +Nlocal: 427 ave 441 max 415 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 784 ave 845 max 718 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 9597.25 ave 10151 max 9269 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 38389 +Ave neighs/atom = 22.476 +Neighbor list builds = 211 +Dangerous builds = 0 diff --git a/examples/shear/log.shear.void.12Feb07.linux.1 b/examples/shear/log.shear.void.12Feb07.linux.1 new file mode 100644 index 0000000000..459c35cc56 --- /dev/null +++ b/examples/shear/log.shear.void.12Feb07.linux.1 @@ -0,0 +1,160 @@ +LAMMPS (12 Feb 2007) +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created box = (0 0 0) to (56.32 35.2 9.95606) + 1 by 1 by 1 processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 +Created 1912 atoms + +pair_style eam +pair_coeff * * niu3.eam + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set lower atom 2 + 264 settings made +set upper atom 3 + 264 settings made + +# void + +region void cylinder z 8 3.535534 2.5 INF INF +delete_atoms region void +Deleted 204 atoms, new total = 1708 + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 +Memory usage per processor = 1.91124 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -7358.6159 0 -7312.8966 -9604.6063 19539.346 + 25 222.66197 -7321.4403 0 -7287.5071 562.50939 19539.346 + 50 300 -7292.2273 0 -7246.508 7558.4629 19680.84 + 75 292.67603 -7286.2016 0 -7241.5984 6828.0763 19738.503 + 100 300 -7297.4174 0 -7251.698 1627.881 19767.928 +Loop time of 1.075 on 1 procs for 100 steps with 1708 atoms + +Pair time (%) = 1.00034 (93.0552) +Neigh time (%) = 0.032266 (3.00149) +Comm time (%) = 0.011465 (1.06651) +Outpt time (%) = 0.001237 (0.11507) +Other time (%) = 0.029688 (2.76168) + +Nlocal: 1708 ave 1708 max 1708 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1898 ave 1898 max 1898 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 39444 ave 39444 max 39444 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39444 +Ave neighs/atom = 23.0937 +Neighbor list builds = 4 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +dump 1 all atom 10 dump.shear +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 +Memory usage per processor = 1.97639 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704 + 100 300 -7311.9184 0 -7281.4518 -5944.573 19791.679 + 200 298.46333 -7306.5409 0 -7276.2304 -6669.0732 19903.341 + 300 298.05646 -7303.4774 0 -7273.2081 -10334.9 20033.654 + 400 297.71277 -7298.5998 0 -7268.3655 -7644.8753 20112.791 + 500 300 -7301.3145 0 -7270.8479 -6327.722 20143.842 + 600 306.29328 -7291.192 0 -7260.0863 -1482.3063 20281.66 + 700 308.44794 -7289.4349 0 -7258.1103 -3026.5046 20394.034 + 800 300 -7282.5733 0 -7252.1067 -3555.2034 20513.867 + 900 300 -7273.9966 0 -7243.53 -1850.9526 20622.554 + 1000 300 -7266.6095 0 -7236.1429 -1119.6046 20741.011 + 1100 301.26482 -7261.9024 0 -7231.3073 -1647.8612 20874.123 + 1200 299.17066 -7259.2281 0 -7228.8457 -1938.4437 20998.686 + 1300 300 -7263.9553 0 -7233.4887 -3376.9235 21112.258 + 1400 300 -7270.1139 0 -7239.6473 -5846.3511 21249.033 + 1500 307.98903 -7273.6991 0 -7242.4211 -6121.5944 21366.268 + 1600 300 -7278.9972 0 -7248.5306 -9389.2139 21484.725 + 1700 300 -7279.8403 0 -7249.3737 -14440.631 21615.394 + 1800 309.55921 -7284.1875 0 -7252.7501 -14795.954 21727.745 + 1900 299.29406 -7282.5749 0 -7252.18 -15392.232 21848.644 + 2000 299.964 -7271.7156 0 -7241.2526 -19451.05 21968.322 + 2100 308.54552 -7272.2334 0 -7240.8989 -23685.178 22100.212 + 2200 308.49102 -7271.1314 0 -7239.8025 -20630.136 22219.89 + 2300 290.31543 -7268.9828 0 -7239.4997 -19028.307 22342.011 + 2400 299.15433 -7259.7686 0 -7229.3878 -14272.769 22459.246 + 2500 299.15088 -7260.7963 0 -7230.4159 -14923.448 22576.482 + 2600 301.27999 -7258.5805 0 -7227.9839 -15706.203 22702.266 + 2700 307.83121 -7254.9828 0 -7223.7209 -19761.07 22830.493 + 2800 300 -7254.6086 0 -7224.142 -23849.892 22944.065 + 2900 303.23126 -7256.0886 0 -7225.2938 -23451.705 23080.84 + 3000 290.86402 -7255.5292 0 -7225.9904 -20678.136 23202.96 +Loop time of 35.8098 on 1 procs for 3000 steps with 1708 atoms + +Pair time (%) = 30.3044 (84.6259) +Neigh time (%) = 1.63803 (4.57426) +Comm time (%) = 0.359993 (1.00529) +Outpt time (%) = 2.61713 (7.30842) +Other time (%) = 0.890292 (2.48617) + +Nlocal: 1708 ave 1708 max 1708 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1882 ave 1882 max 1882 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 38801 ave 38801 max 38801 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 38801 +Ave neighs/atom = 22.7172 +Neighbor list builds = 205 +Dangerous builds = 0 diff --git a/examples/shear/log.shear.void.1Oct06.liberty.4 b/examples/shear/log.shear.void.1Oct06.liberty.4 deleted file mode 100644 index 645497e7c4..0000000000 --- a/examples/shear/log.shear.void.1Oct06.liberty.4 +++ /dev/null @@ -1,161 +0,0 @@ -LAMMPS (1 Oct 2006) -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created box = (0 0 0) to (56.32 35.2 9.95606) - 2 by 2 by 1 processor grid - -orient x 1 0 0 -orient y 0 1 1 -orient z 0 -1 1 -origin 0.5 0 0 -create_atoms 1 -Created 1912 atoms - -pair_style eam -pair_coeff * * niu3.eam - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 1.4 INF INF -region upper block INF INF 8.6 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set lower atom 2 - 264 settings made -set upper atom 3 - 264 settings made - -# void - -region void cylinder z 8 5 2.5 INF INF -delete_atoms region void -Deleted 204 atoms, new total = 1708 - -# temp controllers - -temperature new3d mobile full -temperature new2d mobile partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 -Memory usage per processor = 1.67464 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -7358.6159 0 -7312.8984 -9603.6477 19539.346 - 25 221.74248 -7320.8414 0 -7287.0497 1128.9116 19599.578 - 50 300 -7293.1781 0 -7247.4606 8050.8209 19662.054 - 75 293.25457 -7287.1715 0 -7242.482 7427.7697 19732.766 - 100 300 -7300.054 0 -7254.3365 1198.8155 19807.388 -Loop time of 0.178373 on 4 procs for 100 steps with 1708 atoms - -Pair time (%) = 0.147011 (82.4179) -Neigh time (%) = 0.00538623 (3.01965) -Comm time (%) = 0.0185187 (10.382) -Outpt time (%) = 0.000659287 (0.369611) -Other time (%) = 0.00679743 (3.8108) - -Nlocal: 427 ave 435 max 419 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 780.25 ave 792 max 769 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 9878.75 ave 10203 max 9534 min -Histogram: 1 0 0 0 1 0 1 0 0 1 - -Total # of neighbors = 39515 -Ave neighs/atom = 23.1352 -Neighbor list builds = 5 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -dump 1 all atom 10 dump.shear -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 -Memory usage per processor = 1.69123 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 303.6848 -7300.054 0 -7269.2144 396.60777 19807.514 - 100 306.67967 -7308.1308 0 -7276.9871 -5243.0172 19880.2 - 200 300 -7311.1514 0 -7280.686 -9605.7539 19886.803 - 300 294.96872 -7306.3327 0 -7276.3782 -10520.452 20001.558 - 400 299.02699 -7301.2595 0 -7270.8929 -7900.8177 20054.29 - 500 303.7645 -7300.5234 0 -7269.6757 -6471.8824 20147.506 - 600 307.21531 -7295.4331 0 -7264.235 -4590.3963 20259.857 - 700 306.22567 -7286.1068 0 -7255.0091 -1875.6399 20394.189 - 800 308.41851 -7280.8206 0 -7249.5003 -648.51488 20511.425 - 900 308.81304 -7274.5973 0 -7243.2369 -422.10864 20631.103 - 1000 293.20428 -7267.7783 0 -7238.003 -3459.2985 20745.896 - 1100 307.19333 -7261.032 0 -7229.8362 -4059.2658 20882.671 - 1200 300 -7255.0675 0 -7224.6021 -4495.7756 20998.686 - 1300 300 -7259.4244 0 -7228.959 -5500.7167 21109.815 - 1400 300 -7266.3342 0 -7235.8688 -6996.9268 21249.033 - 1500 309.14664 -7276.5521 0 -7245.1579 -9854.0088 21365.047 - 1600 306.72473 -7276.827 0 -7245.6787 -11618.775 21489.61 - 1700 304.2066 -7275.7234 0 -7244.8308 -13977.049 21603.182 - 1800 300 -7275.8145 0 -7245.3491 -16910.13 21731.408 - 1900 292.59665 -7280.2143 0 -7250.5007 -20332.035 21858.414 - 2000 300.50593 -7275.6944 0 -7245.1776 -21045.085 21969.543 - 2100 293.80834 -7272.8027 0 -7242.966 -20752.104 22101.433 - 2200 300 -7272.9169 0 -7242.4515 -18905.895 22222.333 - 2300 292.33116 -7272.1269 0 -7242.4403 -18279.22 22339.568 - 2400 308.8105 -7269.1775 0 -7237.8174 -13554.606 22458.025 - 2500 307.8757 -7270.3785 0 -7239.1133 -13783.192 22581.367 - 2600 300 -7273.1821 0 -7242.7167 -13842.925 22708.372 - 2700 295.48445 -7269.0293 0 -7239.0225 -14868.543 22834.156 - 2800 302.07467 -7264.7268 0 -7234.0507 -13561.346 22948.95 - 2900 304.03422 -7260.7326 0 -7229.8575 -11126.104 23068.628 - 3000 300 -7264.6327 0 -7234.1673 -12265.417 23193.191 -Loop time of 6.74849 on 4 procs for 3000 steps with 1708 atoms - -Pair time (%) = 4.44794 (65.9102) -Neigh time (%) = 0.228236 (3.38204) -Comm time (%) = 0.691189 (10.2421) -Outpt time (%) = 0.861094 (12.7598) -Other time (%) = 0.520027 (7.70582) - -Nlocal: 427 ave 440 max 419 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 782.25 ave 832 max 731 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 9691.75 ave 10205 max 9345 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 38767 -Ave neighs/atom = 22.6973 -Neighbor list builds = 210 -Dangerous builds = 0 diff --git a/examples/shear/log.shear.void.1Oct06.linux.1 b/examples/shear/log.shear.void.1Oct06.linux.1 deleted file mode 100644 index 684bfb66d0..0000000000 --- a/examples/shear/log.shear.void.1Oct06.linux.1 +++ /dev/null @@ -1,161 +0,0 @@ -LAMMPS (1 Oct 2006) -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created box = (0 0 0) to (56.32 35.2 9.95606) - 1 by 1 by 1 processor grid - -orient x 1 0 0 -orient y 0 1 1 -orient z 0 -1 1 -origin 0.5 0 0 -create_atoms 1 -Created 1912 atoms - -pair_style eam -pair_coeff * * niu3.eam - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 1.4 INF INF -region upper block INF INF 8.6 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set lower atom 2 - 264 settings made -set upper atom 3 - 264 settings made - -# void - -region void cylinder z 8 5 2.5 INF INF -delete_atoms region void -Deleted 204 atoms, new total = 1708 - -# temp controllers - -temperature new3d mobile full -temperature new2d mobile partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d - -timestep 0.001 -run 100 -Memory usage per processor = 1.91124 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -7358.6159 0 -7312.8984 -9603.6477 19539.346 - 25 222.66472 -7321.4436 0 -7287.5114 561.45929 19539.346 - 50 300 -7292.2296 0 -7246.5121 7557.1546 19680.831 - 75 292.67374 -7286.2045 0 -7241.6035 6826.7501 19738.494 - 100 300 -7297.4178 0 -7251.7003 1628.0506 19767.92 -Loop time of 1.14216 on 1 procs for 100 steps with 1708 atoms - -Pair time (%) = 1.06278 (93.0502) -Neigh time (%) = 0.032721 (2.86484) -Comm time (%) = 0.012319 (1.07857) -Outpt time (%) = 0.000515 (0.04509) -Other time (%) = 0.033823 (2.96132) - -Nlocal: 1708 ave 1708 max 1708 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1898 ave 1898 max 1898 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 39444 ave 39444 max 39444 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 39444 -Ave neighs/atom = 23.0937 -Neighbor list builds = 4 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -dump 1 all atom 10 dump.shear -thermo 100 -thermo_modify temp new2d - -reset_timestep 0 -run 3000 -Memory usage per processor = 1.97639 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 296.81571 -7297.4178 0 -7267.2757 786.4061 19771.698 - 100 300 -7312.4709 0 -7282.0055 -6070.7176 19830.015 - 200 298.24057 -7308.4037 0 -7278.117 -7075.3624 19911.227 - 300 298.67627 -7306.0737 0 -7275.7427 -10959.707 20012.463 - 400 295.45281 -7300.8028 0 -7270.7991 -8138.7479 20049.688 - 500 293.51166 -7302.0379 0 -7272.2314 -6169.1551 20160.975 - 600 306.56214 -7292.914 0 -7261.7822 -1497.9662 20264.741 - 700 300 -7288.1794 0 -7257.714 -1694.6598 20394.189 - 800 292.30303 -7280.2273 0 -7250.5436 -2492.6249 20510.204 - 900 294.01762 -7273.2472 0 -7243.3893 -1408.0826 20623.776 - 1000 306.33035 -7266.6178 0 -7235.5095 -1332.1587 20745.896 - 1100 305.42715 -7259.4415 0 -7228.425 -1532.7103 20880.229 - 1200 298.81462 -7252.7391 0 -7222.3941 -84.819805 20992.58 - 1300 305.34821 -7256.2234 0 -7225.2149 -2051.4783 21117.142 - 1400 300 -7261.6324 0 -7231.167 -5225.385 21249.033 - 1500 304.1211 -7270.8198 0 -7239.9359 -6745.2264 21361.383 - 1600 304.0601 -7268.8039 0 -7237.9262 -8095.0839 21479.84 - 1700 300 -7275.418 0 -7244.9526 -12662.853 21614.173 - 1800 300 -7276.2011 0 -7245.7357 -12987.776 21730.187 - 1900 300 -7281.3333 0 -7250.8679 -16149.771 21851.087 - 2000 300 -7272.4857 0 -7242.0203 -19420.269 21978.092 - 2100 300.83156 -7266.7776 0 -7236.2278 -21604.366 22091.664 - 2200 307.68394 -7267.2822 0 -7236.0365 -22271.78 22217.448 - 2300 300 -7267.5846 0 -7237.1192 -18486.541 22344.453 - 2400 306.73936 -7264.0905 0 -7232.9407 -15349.104 22465.353 - 2500 295.97063 -7261.0612 0 -7231.005 -16523.792 22577.703 - 2600 302.58731 -7260.6552 0 -7229.927 -21518.407 22713.257 - 2700 300.8664 -7260.95 0 -7230.3966 -24032.38 22836.599 - 2800 297.95224 -7251.7372 0 -7221.4798 -22569.009 22945.286 - 2900 304.36782 -7254.3093 0 -7223.4003 -23462.932 23071.07 - 3000 293.99223 -7249.0183 0 -7219.163 -23263.342 23199.297 -Loop time of 37.342 on 1 procs for 3000 steps with 1708 atoms - -Pair time (%) = 31.7703 (85.0792) -Neigh time (%) = 1.71104 (4.58208) -Comm time (%) = 0.391151 (1.04748) -Outpt time (%) = 2.45624 (6.57769) -Other time (%) = 1.01328 (2.71351) - -Nlocal: 1708 ave 1708 max 1708 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1877 ave 1877 max 1877 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 38584 ave 38584 max 38584 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 38584 -Ave neighs/atom = 22.5902 -Neighbor list builds = 211 -Dangerous builds = 0 diff --git a/examples/shear/niu3.eam b/examples/shear/niu3.eam new file mode 100755 index 0000000000..b5f2176f00 --- /dev/null +++ b/examples/shear/niu3.eam @@ -0,0 +1,304 @@ +Ni function (universal 3) + 28 58.710 3.5200 FCC + 500 5.0100200400801306e-04 500 9.6969696969697039e-03 4.8000000000000114e+00 + 0. -5.0517016048996766e-01 -7.9317853848267106e-01 -1.0217438587039425e+00 -1.2174805690269395e+00 + -1.3915708504375530e+00 -1.5499932328286121e+00 -1.6963954974188340e+00 -1.8332004716104038e+00 -1.9621160791940611e+00 + -2.0843760483513876e+00 -2.1992938880209749e+00 -2.3093396176347341e+00 -2.4151048342909860e+00 -2.5170730411782927e+00 + -2.6156455313181937e+00 -2.7111597934241303e+00 -2.8039029250035838e+00 -2.8941216165036252e+00 -2.9820297219149694e+00 + -3.0678140937243796e+00 -3.1516391457178798e+00 -3.2336504675375721e+00 -3.3139777215379382e+00 -3.3927369891350594e+00 + -3.4700326894515854e+00 -3.5459591620359561e+00 -3.6206019830134863e+00 -3.6940390674917722e+00 -3.7663415995091469e+00 + -3.8375748211898610e+00 -3.9077987065080180e+00 -3.9770685396213423e+00 -4.0454354138360316e+00 -4.1129466641100976e+00 + -4.1796462436871593e+00 -4.2455750533765979e+00 -4.3107712306517953e+00 -4.3752704043257609e+00 -4.4391059197901370e+00 + -4.5023090387655884e+00 -4.5649091171416387e+00 -4.6269337636658463e+00 -4.6884089819903636e+00 -4.7493592982170298e+00 + -4.8098078755955100e+00 -4.8697766180438862e+00 -4.9292862637278461e+00 -4.9883564698644989e+00 -5.0470058897358570e+00 + -5.1052522427840188e+00 -5.1623072179650649e+00 -5.2189018510607639e+00 -5.2751350144308446e+00 -5.3310209820086811e+00 + -5.3865733770414863e+00 -5.4418052123181724e+00 -5.4967289272545088e+00 -5.5513564221275828e+00 -5.6056990897199057e+00 + -5.6597678446140094e+00 -5.7135731503426257e+00 -5.7671250445876296e+00 -5.8204331625956058e+00 -5.8735067589604455e+00 + -5.9263547279134343e+00 -5.9789856222417370e+00 -6.0314076709491928e+00 -6.0836287957580453e+00 -6.1356566265451704e+00 + -6.1874985157960793e+00 -6.2391615521814003e+00 -6.2906525731472414e+00 -6.3419781770271015e+00 -6.3931447341185503e+00 + -6.4441583972792955e+00 -6.4950251118515041e+00 -6.5457506250122037e+00 -6.5963404945961486e+00 -6.6468000974149675e+00 + -6.6971346371185234e+00 -6.7473491516179536e+00 -6.7974485201119705e+00 -6.8474374697293854e+00 -6.8973205818230383e+00 + -6.9471022979348334e+00 -6.9967869254475659e+00 -7.0463786429507991e+00 -7.0958815053338640e+00 -7.1452994486230068e+00 + -7.1946362945806470e+00 -7.2438957550783698e+00 -7.2930814362578644e+00 -7.3421968424935073e+00 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