diff --git a/doc/src/Howto_bpm.rst b/doc/src/Howto_bpm.rst index 5aa277275d..86e091fcef 100644 --- a/doc/src/Howto_bpm.rst +++ b/doc/src/Howto_bpm.rst @@ -17,6 +17,8 @@ producing fracture. The examples/bpm directory has sample input scripts for simulations of the fragmentation of an impacted plate and the pouring of extended, elastic bodies. See :ref:`(Clemmer) ` for more general information on the approach and the LAMMPS implementation. +Example movies illustrating some of these capabilities are found at +https://www.lammps.org/movies.html#bpmpackage. ---------- diff --git a/doc/src/Howto_rheo.rst b/doc/src/Howto_rheo.rst index 3667d88e3a..90f9ff82d0 100644 --- a/doc/src/Howto_rheo.rst +++ b/doc/src/Howto_rheo.rst @@ -15,7 +15,8 @@ details of the system, or develop new capabilities. For instance, the numerics associated with calculating gradients, reproducing kernels, etc. are separated into distinct classes to simplify the development of new integration schemes which can call these calculations. Additional numerical details can be found in -:ref:`(Clemmer) `. +:ref:`(Clemmer) `. Example movies illustrating some of these +capabilities are found at https://www.lammps.org/movies.html#rheopackage. Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package ` package is likely better suited for your application. It has fewer advanced diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index ccc77bd754..4483601a88 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -350,6 +350,7 @@ models for mesoscale simulations of solids and fracture. See the * :doc:`compute nbond/atom ` * :doc:`fix nve/bpm/sphere ` * :doc:`pair_style bpm/spring ` +* https://www.lammps.org/movies.html#bpmpackage * ``examples/bpm`` ---------- @@ -2658,6 +2659,7 @@ Thomas C. O'Connor (Carnegie Mellon University) * :doc:`fix rheo/viscosity ` * :doc:`pair_style rheo ` * :doc:`pair_style rheo/solid ` +* https://www.lammps.org/movies.html#rheopackage * ``examples/rheo`` ---------- diff --git a/doc/src/fix_add_heat.rst b/doc/src/fix_add_heat.rst index 5b67bd4e15..6d192fd0b6 100644 --- a/doc/src/fix_add_heat.rst +++ b/doc/src/fix_add_heat.rst @@ -18,11 +18,11 @@ Syntax *constant* args = *rate* *rate* = rate of heat flow (energy/time units) - *linear* args = :math:`T_{target}` *k* - :math:`T_{target}` = target temperature (temperature units) + *linear* args = *Ttarget* *k* + *Ttarget* = target temperature (temperature units) *k* = prefactor (energy/(time*temperature) units) - *quartic* args = :math:`T_{target}` *k* - :math:`T_{target}` = target temperature (temperature units) + *quartic* args = *Ttarget* *k* + *Ttarget* = target temperature (temperature units) *k* = prefactor (energy/(time*temperature^4) units) * zero or more keyword/value pairs may be appended to args @@ -45,9 +45,9 @@ Examples Description """"""""""" -This fix adds heat to particles with the temperature attribute every timestep. -Note that this is an internal temperature of a particle intended for use with -non-atomistic models like the discrete element method. +This fix adds heat to particles with the temperature attribute every timestep +at a given rate. Note that this is an internal temperature of a particle intended +for use with non-atomistic models like the discrete element method. For the *constant* style, heat is added at the specified rate. For the *linear* style, heat is added at a rate of :math:`k (T_{target} - T)` where :math:`k` is the @@ -96,7 +96,8 @@ only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. This fix requires that atoms store temperature and heat flow -as defined by the :doc:`fix property/atom ` command. +as defined by the :doc:`fix property/atom ` command or +included in certain atom styles, such as atom_style rheo/thermal. Related commands """""""""""""""" diff --git a/examples/rheo/oxidation/in.rheo.oxidation b/examples/rheo/oxidation/in.rheo.oxidation index 57bd71b917..37a34bae9d 100644 --- a/examples/rheo/oxidation/in.rheo.oxidation +++ b/examples/rheo/oxidation/in.rheo.oxidation @@ -80,7 +80,7 @@ fix 5 rbar rheo/oxidation 1.5 2 1.0 fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0 fix 7 all gravity 5e-5 vector 0 -1 0 fix 8 floor setforce 0.0 0.0 0.0 -fix 9 surf add/heat linear 1.1 0.05 +fix 9 surf add/heat linear 1.1 0.5 fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor fix 11 all enforce2d diff --git a/examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4 b/examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4 deleted file mode 100644 index 92eb4aa94a..0000000000 --- a/examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4 +++ /dev/null @@ -1,488 +0,0 @@ -LAMMPS (17 Apr 2024 - Development - patch_5May2020-18508-g3c0eaf6870-modified) -# ------ 2D oxidizing bar ------ # - -dimension 2 -units lj -atom_style hybrid rheo/thermal bond -boundary m m p -comm_modify vel yes -newton off - -region box block -60 60 0 80 -0.01 0.01 units box -create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 -Created orthogonal box = (-60 0 -0.01) to (60 80 0.01) - 2 by 2 by 1 MPI processor grid - -region lbar block -15 0 3 80 EDGE EDGE units box -region rbar block 0 15 3 80 EDGE EDGE units box -region bar union 2 lbar rbar -region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box - -lattice hex 1.0 -Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699 -create_atoms 1 region bar -Created 2255 atoms - using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01) - create_atoms CPU = 0.001 seconds -create_atoms 3 region floor -Created 446 atoms - using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01) - create_atoms CPU = 0.000 seconds - -set region rbar type 2 -Setting atom values ... - 1148 settings made for type -group bar type 1 2 -2255 atoms in group bar -group rbar type 2 -1148 atoms in group rbar -group floor type 3 -446 atoms in group floor - -set group all sph/e 0.0 -Setting atom values ... - 2701 settings made for sph/e -set group all rheo/status 1 -Setting atom values ... - 2701 settings made for rheo/status - -# ------ Model parameters ------# - -variable cut equal 3.0 -variable n equal 1.0 -variable rho0 equal 1.0 -variable cs equal 1.0 -variable mp equal ${rho0}/${n} -variable mp equal 1/${n} -variable mp equal 1/1 -variable zeta equal 0.05 -variable kappa equal 0.1*${rho0}/${mp} -variable kappa equal 0.1*1/${mp} -variable kappa equal 0.1*1/1 -variable dt_max equal 0.1*${cut}/${cs}/3 -variable dt_max equal 0.1*3/${cs}/3 -variable dt_max equal 0.1*3/1/3 -variable eta equal 0.05 -variable Cv equal 1.0 -variable L equal 0.1 -variable Tf equal 1.0 - -mass * ${mp} -mass * 1 -timestep 0.1 - -pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid -pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid -pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid -pair_coeff * * rheo -pair_coeff * * rheo/solid 1.0 1.0 1.0 - -special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 0 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.000 seconds -create_bonds many bar bar 1 0 1.5 -Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3 - ghost atom cutoff = 3.3 - binsize = 1.65, bins = 73 49 1 - 3 neighbor lists, perpetual/occasional/extra = 2 1 0 - (1) command create_bonds, occasional - attributes: full, newton off - pair build: full/bin - stencil: full/bin/2d - bin: standard - (2) pair rheo, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: full/bin/2d - bin: standard - (3) pair rheo/solid, perpetual, trim from (2) - attributes: half, newton off, cut 1.3 - pair build: trim - stencil: none - bin: none -Added 6547 bonds, new total = 6547 -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 1 1 - special bond factors coul: 0 1 1 - 6 = max # of 1-2 neighbors - 101 = max # of special neighbors - special bonds CPU = 0.000 seconds -special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 - -bond_style hybrid bpm/spring rheo/shell t/form 100 -bond_coeff 1 bpm/spring 1.0 1.0 1.0 -bond_coeff 2 rheo/shell 0.2 0.2 0.1 - -# ------ Apply dynamics ------# - -# Note: surface detection is not performed on solid bodies, so cannot use surface property -compute coord all rheo/property/atom coordination -variable surf atom c_coord<22 -group surf dynamic all var surf every 10 -dynamic group surf defined - -fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8 -fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8 -fix 2 all rheo/viscosity * constant ${eta} -fix 2 all rheo/viscosity * constant 0.05 -fix 3 all rheo/pressure * linear -fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 -fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 -fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 -fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1 -fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1 - -fix 5 rbar rheo/oxidation 1.5 2 1.0 -fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0 -fix 7 all gravity 5e-5 vector 0 -1 0 -fix 8 floor setforce 0.0 0.0 0.0 -fix 9 surf add/heat linear 1.1 0.05 -fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor -fix 11 all enforce2d - -compute surf all rheo/property/atom surface -compute rho all rheo/property/atom rho -compute phase all rheo/property/atom phase -compute status all rheo/property/atom status -compute temp all rheo/property/atom temperature -compute eng all rheo/property/atom energy -compute nbond_shell all rheo/property/atom nbond/shell -compute nbond_solid all nbond/atom bond/type 1 - -# ------ Output & Run ------ # - -thermo 200 -thermo_style custom step time ke press atoms - -dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf c_status - -run 40000 - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Your simulation uses code contributions which should be cited: - -- BPM bond style: doi:10.1039/D3SM01373A - -@Article{Clemmer2024, - author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, - title = {A soft departure from jamming: the compaction of deformable - granular matter under high pressures}, - journal = {Soft Matter}, - year = 2024, - volume = 20, - number = 8, - pages = {1702--1718} -} - -- @article{PalermoInPrep, - journal = {in prep}, - title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows}, - year = {2024}, - author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor}, -} - -- @article{ApplMathModel.130.310, - title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum}, - journal = {Applied Mathematical Modelling}, - volume = {130}, - pages = {310-326}, - year = {2024}, - issn = {0307-904X}, - doi = {https://doi.org/10.1016/j.apm.2024.02.027}, - author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer}, -} - -CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE - -Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 3.3 - ghost atom cutoff = 3.3 - binsize = 1.65, bins = 73 49 1 - 8 neighbor lists, perpetual/occasional/extra = 7 1 0 - (1) pair rheo, perpetual, half/full from (3) - attributes: half, newton off - pair build: halffull/newtoff - stencil: none - bin: none - (2) pair rheo/solid, perpetual, trim from (4) - attributes: half, newton off, cut 1.3 - pair build: trim - stencil: none - bin: none - (3) compute RHEO/KERNEL, perpetual - attributes: full, newton off - pair build: full/bin - stencil: full/bin/2d - bin: standard - (4) compute RHEO/GRAD, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) compute RHEO/VSHIFT, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) compute RHEO/SURFACE, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (7) fix rheo/thermal, occasional, trim from (4) - attributes: half, newton off, cut 3 - pair build: trim - stencil: none - bin: none - (8) fix rheo/oxidation, perpetual, trim from (3) - attributes: full, newton off, cut 1.8 - pair build: trim - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes - Step Time KinEng Press Atoms - 0 0 0 0 2701 - 200 20 4.1743799e-07 1.1743617e-07 2701 - 400 40 1.6697519e-06 4.6974469e-07 2701 - 600 60 3.7127333e-06 1.0646825e-05 2701 - 800 80 4.6683656e-06 0.00015182605 2701 - 1000 100 4.7368707e-06 0.00028128761 2701 - 1200 120 3.4384322e-06 0.00045913378 2701 - 1400 140 1.4119866e-06 0.00055627091 2701 - 1600 160 4.4114517e-07 0.00058247308 2701 - 1800 180 4.8289229e-07 0.0005510948 2701 - 2000 200 1.8494183e-06 0.00048386222 2701 - 2200 220 3.3319816e-06 0.00037903264 2701 - 2400 240 3.8128922e-06 0.00024115906 2701 - 2600 260 3.1943401e-06 9.727407e-05 2701 - 2800 280 1.6172816e-06 -2.632162e-05 2701 - 3000 300 3.6100709e-07 -8.5761867e-05 2701 - 3200 320 1.4745502e-07 -5.9204127e-05 2701 - 3400 340 8.3369782e-07 8.8312464e-07 2701 - 3600 360 2.0484052e-06 5.8521477e-05 2701 - 3800 380 3.1639387e-06 0.0001685663 2701 - 4000 400 3.1692907e-06 0.00026875988 2701 - 4200 420 2.391933e-06 0.00038621787 2701 - 4400 440 1.1964404e-06 0.00048901286 2701 - 4600 460 4.0508824e-07 0.00051863639 2701 - 4800 480 5.4908507e-07 0.00049263754 2701 - 5000 500 1.3139665e-06 0.00041984264 2701 - 5200 520 2.1939161e-06 0.00033095351 2701 - 5400 540 2.3687031e-06 0.00022422981 2701 - 5600 560 1.8280882e-06 0.00011544328 2701 - 5800 580 8.8610517e-07 2.9307791e-05 2701 - 6000 600 2.0989359e-07 -1.7340941e-05 2701 - 6200 620 2.8658301e-07 -8.1237835e-06 2701 - 6400 640 9.7636239e-07 4.3755922e-05 2701 - 6600 660 1.891303e-06 0.0001185719 2701 - 6800 680 2.4149904e-06 0.00020830273 2701 - 7000 700 2.3174953e-06 0.00030114767 2701 - 7200 720 1.7918612e-06 0.00037821537 2701 - 7400 740 1.2114987e-06 0.0004233475 2701 - 7600 760 9.9661553e-07 0.00042958263 2701 - 7800 780 1.1552559e-06 0.00039944618 2701 - 8000 800 1.5249138e-06 0.00034034478 2701 - 8200 820 1.7453861e-06 0.00026826463 2701 - 8400 840 1.6259021e-06 0.00019131768 2701 - 8600 860 1.2612805e-06 0.0001162957 2701 - 8800 880 8.6964518e-07 7.1771506e-05 2701 - 9000 900 7.6892472e-07 5.6170687e-05 2701 - 9200 920 1.0780045e-06 7.1925995e-05 2701 - 9400 940 1.6514902e-06 0.00011635293 2701 - 9600 960 2.1891377e-06 0.00017599885 2701 - 9800 980 2.4551701e-06 0.00024127934 2701 - 10000 1000 2.4277051e-06 0.00029918622 2701 - 10200 1020 2.2655987e-06 0.00034067996 2701 - 10400 1040 2.1767207e-06 0.00035598133 2701 - 10600 1060 2.2796719e-06 0.00034359076 2701 - 10800 1080 2.4884225e-06 0.00030749714 2701 - 11000 1100 2.6387215e-06 0.00025725198 2701 - 11200 1120 2.5968908e-06 0.00020170699 2701 - 11400 1140 2.4108931e-06 0.00015185858 2701 - 11600 1160 2.2375166e-06 0.00011800349 2701 - 11800 1180 2.2407196e-06 0.00010646971 2701 - 12000 1200 2.4845263e-06 0.00011817498 2701 - 12200 1220 2.8733204e-06 0.00015013186 2701 - 12400 1240 3.2437087e-06 0.00019211975 2701 - 12600 1260 3.4732728e-06 0.00023620276 2701 - 12800 1280 3.5836611e-06 0.00027352269 2701 - 13000 1300 3.6592211e-06 0.00029533734 2701 - 13200 1320 3.782506e-06 0.00030032559 2701 - 13400 1340 3.9807086e-06 0.00028395722 2701 - 13600 1360 4.2023176e-06 0.00025390325 2701 - 13800 1380 4.3559781e-06 0.00021794236 2701 - 14000 1400 4.4273371e-06 0.00018026034 2701 - 14200 1420 4.49867e-06 0.0001526569 2701 - 14400 1440 4.6591574e-06 0.00013707051 2701 - 14600 1460 4.9589583e-06 0.00013803875 2701 - 14800 1480 5.3859375e-06 0.00015455425 2701 - 15000 1500 5.8639557e-06 0.00017954785 2701 - 15200 1520 6.3075561e-06 0.0002084257 2701 - 15400 1540 6.7022179e-06 0.0002347669 2701 - 15600 1560 7.0789688e-06 0.00025020766 2701 - 15800 1580 7.4734777e-06 0.00025394845 2701 - 16000 1600 7.8884743e-06 0.00024571725 2701 - 16200 1620 8.3224059e-06 0.00022706648 2701 - 16400 1640 8.7337783e-06 0.00020320706 2701 - 16600 1660 9.1454649e-06 0.00017824346 2701 - 16800 1680 9.5948793e-06 0.00015961835 2701 - 17000 1700 1.0106407e-05 0.00015135471 2701 - 17200 1720 1.0707273e-05 0.00015166884 2701 - 17400 1740 1.1392597e-05 0.0001645916 2701 - 17600 1760 1.2118829e-05 0.00018119729 2701 - 17800 1780 1.2846056e-05 0.0002003616 2701 - 18000 1800 1.3555288e-05 0.00021585952 2701 - 18200 1820 1.4301024e-05 0.00022290158 2701 - 18400 1840 1.5089217e-05 0.00021970192 2701 - 18600 1860 1.5902351e-05 0.00020911128 2701 - 18800 1880 1.6753175e-05 0.00019278718 2701 - 19000 1900 1.7602996e-05 0.00017584076 2701 - 19200 1920 1.8479378e-05 0.00016206226 2701 - 19400 1940 1.9421603e-05 0.00015575677 2701 - 19600 1960 2.0477421e-05 0.00015687558 2701 - 19800 1980 2.1617288e-05 0.00016424998 2701 - 20000 2000 2.2814347e-05 0.00017466664 2701 - 20200 2020 2.4029097e-05 0.00018647149 2701 - 20400 2040 2.5255953e-05 0.00019516077 2701 - 20600 2060 2.649418e-05 0.00019906384 2701 - 20800 2080 2.7755897e-05 0.00019630586 2701 - 21000 2100 2.9067854e-05 0.00018674721 2701 - 21200 2120 3.0396477e-05 0.0001758048 2701 - 21400 2140 3.1759719e-05 0.00016782801 2701 - 21600 2160 3.3193597e-05 0.00016324138 2701 - 21800 2180 3.4729384e-05 0.00016124274 2701 - 22000 2200 3.6367594e-05 0.00016437457 2701 - 22200 2220 3.8095131e-05 0.00017015573 2701 - 22400 2240 3.9867003e-05 0.00017649465 2701 - 22600 2260 4.169511e-05 0.00018111374 2701 - 22800 2280 4.3566134e-05 0.00018104136 2701 - 23000 2300 4.5461538e-05 0.00017822707 2701 - 23200 2320 4.7377333e-05 0.00017285066 2701 - 23400 2340 4.9354403e-05 0.00016826524 2701 - 23600 2360 5.1399791e-05 0.00016517913 2701 - 23800 2380 5.3510931e-05 0.00016299649 2701 - 24000 2400 5.5681048e-05 0.00016256674 2701 - 24200 2420 5.7902429e-05 0.00016513449 2701 - 24400 2440 6.0216049e-05 0.00016895109 2701 - 24600 2460 6.270982e-05 0.00016946227 2701 - 24800 2480 6.5390117e-05 0.00016589426 2701 - 25000 2500 6.8121899e-05 0.00016241676 2701 - 25200 2520 7.0947331e-05 0.00015624292 2701 - 25400 2540 7.4304148e-05 0.0001449537 2701 - 25600 2560 7.7745077e-05 0.00013179658 2701 - 25800 2580 8.0739829e-05 0.00013098838 2701 - 26000 2600 8.3827874e-05 0.00014278841 2701 - 26200 2620 8.7060677e-05 0.00015381649 2701 - 26400 2640 9.0266508e-05 0.00016130999 2701 - 26600 2660 9.3339049e-05 0.00016908268 2701 - 26800 2680 9.6347013e-05 0.00016771087 2701 - 27000 2700 9.9294711e-05 0.00016577315 2701 - 27200 2720 0.00010230007 0.0001670893 2701 - 27400 2740 0.00010547172 0.00016569077 2701 - 27600 2760 0.00010872426 0.00016506303 2701 - 27800 2780 0.00011201844 0.00016482702 2701 - 28000 2800 0.00011532129 0.00016694886 2701 - 28200 2820 0.00011869854 0.00016163005 2701 - 28400 2840 0.00012209747 0.00015339281 2701 - 28600 2860 0.00012549322 0.00014765883 2701 - 28800 2880 0.00012898685 0.00014241765 2701 - 29000 2900 0.00013259039 0.00014215724 2701 - 29200 2920 0.00013628209 0.00014881155 2701 - 29400 2940 0.00014001213 0.00015671333 2701 - 29600 2960 0.00014379216 0.00016446215 2701 - 29800 2980 0.00014764687 0.0001639602 2701 - 30000 3000 0.00015142301 0.00015664816 2701 - 30200 3020 0.00015496407 0.00015545099 2701 - 30400 3040 0.00015797338 0.00015368625 2701 - 30600 3060 0.00016042141 0.00015679918 2701 - 30800 3080 0.00016244716 0.00016093678 2701 - 31000 3100 0.00016202247 0.00016066954 2701 - 31200 3120 0.0001613312 0.00015932059 2701 - 31400 3140 0.00016274961 0.00015988567 2701 - 31600 3160 0.00016541518 0.00015724809 2701 - 31800 3180 0.00016809362 0.00015498827 2701 - 32000 3200 0.00017067801 0.00014830489 2701 - 32200 3220 0.00017333906 0.00014371345 2701 - 32400 3240 0.0001759011 0.00014421259 2701 - 32600 3260 0.00017849952 0.00014228443 2701 - 32800 3280 0.00017801812 0.00014117391 2701 - 33000 3300 0.00017718857 0.00014644675 2701 - 33200 3320 0.00017833666 0.0001291286 2701 - 33400 3340 0.000178576 0.00014878558 2701 - 33600 3360 0.00017846711 0.00013905481 2701 - 33800 3380 0.00017822937 0.00015535996 2701 - 34000 3400 0.00017899663 0.00016094303 2701 - 34200 3420 0.00017924661 0.00015017553 2701 - 34400 3440 0.00018024855 0.00014723549 2701 - 34600 3460 0.00018143865 0.00013903131 2701 - 34800 3480 0.00018258173 0.00013722112 2701 - 35000 3500 0.00018404873 0.00014675949 2701 - 35200 3520 0.00018538521 0.00015108242 2701 - 35400 3540 0.00018669649 0.00014564852 2701 - 35600 3560 0.00018814608 0.00013762161 2701 - 35800 3580 0.00018967415 0.00014602307 2701 - 36000 3600 0.00019146735 0.000126909 2701 - 36200 3620 0.00019414036 0.00012384379 2701 - 36400 3640 0.00019613057 0.00011059573 2701 - 36600 3660 0.00019897104 0.00013621801 2701 - 36800 3680 0.00020169688 0.00013665462 2701 - 37000 3700 0.00020447655 0.00013929258 2701 - 37200 3720 0.00020711105 0.0001363895 2701 - 37400 3740 0.00021077854 0.00013610672 2701 - 37600 3760 0.00021303084 0.00015051235 2701 - 37800 3780 0.00021619561 0.00012664801 2701 - 38000 3800 0.0002194018 0.00012808247 2701 - 38200 3820 0.00022242646 0.0001360174 2701 - 38400 3840 0.00022531568 0.00013311221 2701 - 38600 3860 0.00022821731 0.00013523939 2701 - 38800 3880 0.000231228 0.00014090695 2701 - 39000 3900 0.00023404038 0.00013661835 2701 - 39200 3920 0.00023755044 0.00013659469 2701 - 39400 3940 0.00024009059 0.00012097907 2701 - 39600 3960 0.0002432098 9.7877876e-05 2701 - 39800 3980 0.00024475294 0.0001164688 2701 - 40000 4000 0.00024171274 0.00012432219 2701 -Loop time of 192.659 on 4 procs for 40000 steps with 2701 atoms - -Performance: 1793840.118 tau/day, 207.620 timesteps/s, 560.783 katom-step/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 16.881 | 24.402 | 30.74 | 114.6 | 12.67 -Bond | 1.1126 | 1.8917 | 2.6935 | 43.3 | 0.98 -Neigh | 35.387 | 35.508 | 35.625 | 1.5 | 18.43 -Comm | 1.5499 | 1.6694 | 1.8006 | 7.4 | 0.87 -Output | 0.99755 | 1.0072 | 1.0165 | 0.8 | 0.52 -Modify | 120.6 | 127.43 | 135.54 | 54.8 | 66.14 -Other | | 0.7553 | | | 0.39 - -Nlocal: 675.25 ave 1373 max 7 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 103 ave 163 max 50 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 10509 ave 21592 max 126 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -FullNghs: 20367 ave 41981 max 141 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 81468 -Ave neighs/atom = 30.162162 -Ave special neighs/atom = 1.6593854 -Neighbor list builds = 39932 -Dangerous builds = 0 - -Total wall time: 0:03:12 diff --git a/examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4 b/examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4 new file mode 100644 index 0000000000..b6b8fab6dc --- /dev/null +++ b/examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4 @@ -0,0 +1,486 @@ +LAMMPS (27 Jun 2024) +# ------ 2D oxidizing bar ------ # + +dimension 2 +units lj +atom_style hybrid rheo/thermal bond +boundary m m p +comm_modify vel yes +newton off + +region box block -60 60 0 80 -0.01 0.01 units box +create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50 +Created orthogonal box = (-60 0 -0.01) to (60 80 0.01) + 2 by 2 by 1 MPI processor grid + +region lbar block -15 0 3 80 EDGE EDGE units box +region rbar block 0 15 3 80 EDGE EDGE units box +region bar union 2 lbar rbar +region floor block EDGE EDGE EDGE 3.0 EDGE EDGE units box + +lattice hex 1.0 +Lattice spacing in x,y,z = 1.0745699 1.8612097 1.0745699 +create_atoms 1 region bar +Created 2255 atoms + using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01) + create_atoms CPU = 0.004 seconds +create_atoms 3 region floor +Created 446 atoms + using lattice units in orthogonal box = (-60 0 -0.01) to (60 80 0.01) + create_atoms CPU = 0.000 seconds + +set region rbar type 2 +Setting atom values ... + 1148 settings made for type +group bar type 1 2 +2255 atoms in group bar +group rbar type 2 +1148 atoms in group rbar +group floor type 3 +446 atoms in group floor + +set group all sph/e 0.0 +Setting atom values ... + 2701 settings made for sph/e +set group all rheo/status 1 +Setting atom values ... + 2701 settings made for rheo/status + +# ------ Model parameters ------# + +variable cut equal 3.0 +variable n equal 1.0 +variable rho0 equal 1.0 +variable cs equal 1.0 +variable mp equal ${rho0}/${n} +variable mp equal 1/${n} +variable mp equal 1/1 +variable zeta equal 0.05 +variable kappa equal 0.1*${rho0}/${mp} +variable kappa equal 0.1*1/${mp} +variable kappa equal 0.1*1/1 +variable dt_max equal 0.1*${cut}/${cs}/3 +variable dt_max equal 0.1*3/${cs}/3 +variable dt_max equal 0.1*3/1/3 +variable eta equal 0.05 +variable Cv equal 1.0 +variable L equal 0.1 +variable Tf equal 1.0 + +mass * ${mp} +mass * 1 +timestep 0.1 + +pair_style hybrid/overlay rheo ${cut} artificial/visc ${zeta} rheo/solid +pair_style hybrid/overlay rheo 3 artificial/visc ${zeta} rheo/solid +pair_style hybrid/overlay rheo 3 artificial/visc 0.05 rheo/solid +pair_coeff * * rheo +pair_coeff * * rheo/solid 1.0 1.0 1.0 + +special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 0 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.000 seconds +create_bonds many bar bar 1 0 1.5 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 73 49 1 + 3 neighbor lists, perpetual/occasional/extra = 2 1 0 + (1) command create_bonds, occasional + attributes: full, newton off + pair build: full/bin + stencil: full/bin/2d + bin: standard + (2) pair rheo, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: full/bin/2d + bin: standard + (3) pair rheo/solid, perpetual, trim from (2) + attributes: half, newton off, cut 1.3 + pair build: trim + stencil: none + bin: none +Added 6547 bonds, new total = 6547 +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 6 = max # of 1-2 neighbors + 101 = max # of special neighbors + special bonds CPU = 0.000 seconds +special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0 + +bond_style hybrid bpm/spring rheo/shell t/form 100 +bond_coeff 1 bpm/spring 1.0 1.0 1.0 +bond_coeff 2 rheo/shell 0.2 0.2 0.1 + +# ------ Apply dynamics ------# + +# Note: surface detection is not performed on solid bodies, so cannot use surface property +compute coord all rheo/property/atom coordination +variable surf atom c_coord<22 +group surf dynamic all var surf every 10 +dynamic group surf defined + +fix 1 all rheo ${cut} quintic 0 thermal shift surface/detection coordination 22 8 +fix 1 all rheo 3 quintic 0 thermal shift surface/detection coordination 22 8 +fix 2 all rheo/viscosity * constant ${eta} +fix 2 all rheo/viscosity * constant 0.05 +fix 3 all rheo/pressure * linear +fix 4 all rheo/thermal conductivity * constant ${kappa} specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 +fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant ${Cv} Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 +fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant ${Tf} latent/heat * constant ${L} react 1.5 1 +fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant ${L} react 1.5 1 +fix 4 all rheo/thermal conductivity * constant 0.1 specific/heat * constant 1 Tfreeze * constant 1 latent/heat * constant 0.1 react 1.5 1 + +fix 5 rbar rheo/oxidation 1.5 2 1.0 +fix 6 all wall/harmonic ylo EDGE 2.0 1.0 1.0 +fix 7 all gravity 5e-5 vector 0 -1 0 +fix 8 floor setforce 0.0 0.0 0.0 +fix 9 surf add/heat linear 1.1 0.5 +fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor +fix 11 all enforce2d + +compute surf all rheo/property/atom surface +compute rho all rheo/property/atom rho +compute phase all rheo/property/atom phase +compute temp all rheo/property/atom temperature +compute eng all rheo/property/atom energy +compute nbond_shell all rheo/property/atom nbond/shell +compute nbond_solid all nbond/atom bond/type 1 + +# ------ Output & Run ------ # + +thermo 200 +thermo_style custom step time ke press atoms + +#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_phase c_temp c_eng c_nbond_solid c_nbond_shell c_rho c_surf + +run 40000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- BPM bond style: doi:10.1039/D3SM01373A + +@Article{Clemmer2024, + author = {Clemmer, Joel T. and Monti, Joseph M. and Lechman, Jeremy B.}, + title = {A soft departure from jamming: the compaction of deformable + granular matter under high pressures}, + journal = {Soft Matter}, + year = 2024, + volume = 20, + number = 8, + pages = {1702--1718} +} + +- @article{PalermoInPrep, + journal = {in prep}, + title = {RHEO: A Hybrid Mesh-Free Model Framework for Dynamic Multi-Phase Flows}, + year = {2024}, + author = {Eric T. Palermo and Ki T. Wolf and Joel T. Clemmer and Thomas C. O'Connor}, +} + +- @article{ApplMathModel.130.310, + title = {A hybrid smoothed-particle hydrodynamics model of oxide skins on molten aluminum}, + journal = {Applied Mathematical Modelling}, + volume = {130}, + pages = {310-326}, + year = {2024}, + issn = {0307-904X}, + doi = {https://doi.org/10.1016/j.apm.2024.02.027}, + author = {Joel T. Clemmer and Flint Pierce and Thomas C. O'Connor and Thomas D. Nevins and Elizabeth M.C. Jones and Jeremy B. Lechman and John Tencer}, +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.3 + ghost atom cutoff = 3.3 + binsize = 1.65, bins = 73 49 1 + 8 neighbor lists, perpetual/occasional/extra = 7 1 0 + (1) pair rheo, perpetual, half/full from (3) + attributes: half, newton off + pair build: halffull/newtoff + stencil: none + bin: none + (2) pair rheo/solid, perpetual, trim from (4) + attributes: half, newton off, cut 1.3 + pair build: trim + stencil: none + bin: none + (3) compute RHEO/KERNEL, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/2d + bin: standard + (4) compute RHEO/GRAD, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) compute RHEO/VSHIFT, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) compute RHEO/SURFACE, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (7) fix rheo/thermal, occasional, trim from (4) + attributes: half, newton off, cut 3 + pair build: trim + stencil: none + bin: none + (8) fix rheo/oxidation, perpetual, trim from (3) + attributes: full, newton off, cut 1.8 + pair build: trim + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 25.96 | 25.96 | 25.96 Mbytes + Step Time KinEng Press Atoms + 0 0 0 0 2701 + 200 20 4.1737457e-07 1.298459e-07 2701 + 400 40 1.6692448e-06 4.9223021e-07 2701 + 600 60 3.7115752e-06 1.0476692e-05 2701 + 800 80 4.678922e-06 0.00015017477 2701 + 1000 100 4.7534549e-06 0.00027967322 2701 + 1200 120 3.4532974e-06 0.00045908503 2701 + 1400 140 1.4159611e-06 0.00055855688 2701 + 1600 160 4.5151976e-07 0.00058351591 2701 + 1800 180 5.1656107e-07 0.00055163637 2701 + 2000 200 1.882995e-06 0.00048349046 2701 + 2200 220 3.3481991e-06 0.00037790487 2701 + 2400 240 3.8173347e-06 0.00023972848 2701 + 2600 260 3.1832818e-06 9.5696995e-05 2701 + 2800 280 1.5994934e-06 -2.7484809e-05 2701 + 3000 300 3.573403e-07 -8.56391e-05 2701 + 3200 320 1.6485893e-07 -5.6974248e-05 2701 + 3400 340 8.5665044e-07 3.473389e-06 2701 + 3600 360 2.0801421e-06 5.7938582e-05 2701 + 3800 380 3.1934959e-06 0.00016746888 2701 + 4000 400 3.2540476e-06 0.00026471904 2701 + 4200 420 2.5603544e-06 0.00037699521 2701 + 4400 440 1.4309318e-06 0.00047456272 2701 + 4600 460 6.5231009e-07 0.00050551979 2701 + 4800 480 6.9010626e-07 0.00048100816 2701 + 5000 500 1.2663499e-06 0.00042166061 2701 + 5200 520 2.0653769e-06 0.00033547376 2701 + 5400 540 2.2709253e-06 0.00023015884 2701 + 5600 560 1.7864994e-06 0.00013378564 2701 + 5800 580 9.5638493e-07 4.4666688e-05 2701 + 6000 600 3.0331342e-07 -1.884252e-06 2701 + 6200 620 3.451498e-07 8.3090163e-07 2701 + 6400 640 9.5098597e-07 4.7759688e-05 2701 + 6600 660 1.8169765e-06 0.00011801205 2701 + 6800 680 2.3723951e-06 0.00019823562 2701 + 7000 700 2.3542553e-06 0.00028873701 2701 + 7200 720 1.9132157e-06 0.00036386547 2701 + 7400 740 1.4123115e-06 0.00040731263 2701 + 7600 760 1.2422941e-06 0.00041151319 2701 + 7800 780 1.4355275e-06 0.00038364583 2701 + 8000 800 1.7835754e-06 0.00032724239 2701 + 8200 820 1.961321e-06 0.00025932051 2701 + 8400 840 1.8005786e-06 0.00018763659 2701 + 8600 860 1.4274768e-06 0.00012392727 2701 + 8800 880 1.075959e-06 8.1241673e-05 2701 + 9000 900 1.014674e-06 7.0104531e-05 2701 + 9200 920 1.3155353e-06 8.7991534e-05 2701 + 9400 940 1.815649e-06 0.00012975516 2701 + 9600 960 2.2699387e-06 0.0001861001 2701 + 9800 980 2.4916284e-06 0.00024375475 2701 + 10000 1000 2.4741893e-06 0.00029466715 2701 + 10200 1020 2.3835838e-06 0.00032733587 2701 + 10400 1040 2.3816351e-06 0.00033659466 2701 + 10600 1060 2.5177605e-06 0.00032136429 2701 + 10800 1080 2.6973866e-06 0.00028678114 2701 + 11000 1100 2.8219278e-06 0.00023889501 2701 + 11200 1120 2.794743e-06 0.00019226876 2701 + 11400 1140 2.667182e-06 0.00015100316 2701 + 11600 1160 2.5918212e-06 0.00012484649 2701 + 11800 1180 2.6802845e-06 0.00011912201 2701 + 12000 1200 2.9620111e-06 0.00013336302 2701 + 12200 1220 3.3281225e-06 0.00016262605 2701 + 12400 1240 3.6587842e-06 0.00020175308 2701 + 12600 1260 3.8696418e-06 0.00023984351 2701 + 12800 1280 3.9774608e-06 0.00026981166 2701 + 13000 1300 4.0621923e-06 0.00028706126 2701 + 13200 1320 4.2118368e-06 0.00028639136 2701 + 13400 1340 4.4229032e-06 0.00026844105 2701 + 13600 1360 4.6415059e-06 0.00023789752 2701 + 13800 1380 4.8106868e-06 0.00020524655 2701 + 14000 1400 4.9343741e-06 0.00017392428 2701 + 14200 1420 5.0835921e-06 0.00015013775 2701 + 14400 1440 5.3365604e-06 0.0001413941 2701 + 14600 1460 5.7248817e-06 0.00014521418 2701 + 14800 1480 6.2145391e-06 0.00016109563 2701 + 15000 1500 6.7347576e-06 0.00018481456 2701 + 15200 1520 7.221694e-06 0.00020956545 2701 + 15400 1540 7.6762698e-06 0.0002293694 2701 + 15600 1560 8.1313425e-06 0.00024058679 2701 + 15800 1580 8.6053324e-06 0.00024015877 2701 + 16000 1600 9.1091988e-06 0.00022927412 2701 + 16200 1620 9.6165964e-06 0.00021035982 2701 + 16400 1640 1.0093906e-05 0.00018782673 2701 + 16600 1660 1.0561165e-05 0.00016863993 2701 + 16800 1680 1.1066274e-05 0.00015693261 2701 + 17000 1700 1.1661861e-05 0.00015221008 2701 + 17200 1720 1.236148e-05 0.00015781879 2701 + 17400 1740 1.3124872e-05 0.00017008789 2701 + 17600 1760 1.3924606e-05 0.00018628888 2701 + 17800 1780 1.4733479e-05 0.0002011741 2701 + 18000 1800 1.5558838e-05 0.00021115187 2701 + 18200 1820 1.6415631e-05 0.00021314897 2701 + 18400 1840 1.7287377e-05 0.00020793654 2701 + 18600 1860 1.8202577e-05 0.00019550685 2701 + 18800 1880 1.9126239e-05 0.00018102715 2701 + 19000 1900 2.0074716e-05 0.0001684831 2701 + 19200 1920 2.1090982e-05 0.00015956926 2701 + 19400 1940 2.2180303e-05 0.00015805759 2701 + 19600 1960 2.3330404e-05 0.00016157807 2701 + 19800 1980 2.4557652e-05 0.00017047221 2701 + 20000 2000 2.5841568e-05 0.00018216972 2701 + 20200 2020 2.7188233e-05 0.00018953358 2701 + 20400 2040 2.8576958e-05 0.00019304182 2701 + 20600 2060 2.999218e-05 0.00019239757 2701 + 20800 2080 3.1437794e-05 0.00018759619 2701 + 21000 2100 3.2938831e-05 0.00017863274 2701 + 21200 2120 3.4506515e-05 0.00016911647 2701 + 21400 2140 3.6126713e-05 0.00016161126 2701 + 21600 2160 3.7812343e-05 0.0001583968 2701 + 21800 2180 3.9564996e-05 0.00016178647 2701 + 22000 2200 4.1406387e-05 0.00016872633 2701 + 22200 2220 4.3340255e-05 0.00017435061 2701 + 22400 2240 4.5333317e-05 0.00017910049 2701 + 22600 2260 4.7311785e-05 0.0001800877 2701 + 22800 2280 4.9303605e-05 0.00017728464 2701 + 23000 2300 5.1334424e-05 0.00017486007 2701 + 23200 2320 5.3402091e-05 0.00016867905 2701 + 23400 2340 5.5505853e-05 0.00016402807 2701 + 23600 2360 5.7679415e-05 0.00016343865 2701 + 23800 2380 5.9920078e-05 0.00016623374 2701 + 24000 2400 6.2239328e-05 0.00017028032 2701 + 24200 2420 6.4624902e-05 0.00017371561 2701 + 24400 2440 6.7054046e-05 0.00017565916 2701 + 24600 2460 6.9522453e-05 0.00017545566 2701 + 24800 2480 7.2079202e-05 0.00017437049 2701 + 25000 2500 7.4716585e-05 0.00017043497 2701 + 25200 2520 7.7415627e-05 0.00016579093 2701 + 25400 2540 8.0169507e-05 0.00016268419 2701 + 25600 2560 8.3001779e-05 0.00016233687 2701 + 25800 2580 8.5921287e-05 0.00016275719 2701 + 26000 2600 8.8880908e-05 0.00016425339 2701 + 26200 2620 9.1881788e-05 0.00016478504 2701 + 26400 2640 9.4969348e-05 0.00016371806 2701 + 26600 2660 9.817611e-05 0.00016339555 2701 + 26800 2680 0.00010146396 0.00015937569 2701 + 27000 2700 0.00010485972 0.0001562082 2701 + 27200 2720 0.00010837565 0.00015181198 2701 + 27400 2740 0.00011187666 0.00015162336 2701 + 27600 2760 0.00011543324 0.0001606148 2701 + 27800 2780 0.00011905739 0.00016161123 2701 + 28000 2800 0.00012280117 0.00016267347 2701 + 28200 2820 0.00012665753 0.00016393863 2701 + 28400 2840 0.00013061568 0.00016168097 2701 + 28600 2860 0.00013469542 0.00015439793 2701 + 28800 2880 0.00013889392 0.00014870639 2701 + 29000 2900 0.00014307887 0.00015020156 2701 + 29200 2920 0.00014714875 0.00015727801 2701 + 29400 2940 0.0001510796 0.00016230922 2701 + 29600 2960 0.0001551489 0.00016725059 2701 + 29800 2980 0.00015918695 0.0001556229 2701 + 30000 3000 0.00016145717 0.00015704562 2701 + 30200 3020 0.00016164704 0.00015902669 2701 + 30400 3040 0.00016250791 0.00017587854 2701 + 30600 3060 0.0001639094 0.00016958759 2701 + 30800 3080 0.00016479103 0.00016810892 2701 + 31000 3100 0.00016521873 0.00016027053 2701 + 31200 3120 0.00016540216 0.00015397865 2701 + 31400 3140 0.00016690063 0.00015955009 2701 + 31600 3160 0.00016832002 0.00015593907 2701 + 31800 3180 0.00016948949 0.00015690982 2701 + 32000 3200 0.0001700061 0.00016199222 2701 + 32200 3220 0.00017122936 0.00016220019 2701 + 32400 3240 0.00017198531 0.00015194229 2701 + 32600 3260 0.00017286097 0.00014880433 2701 + 32800 3280 0.00017395847 0.00014887179 2701 + 33000 3300 0.00017527125 0.00015338612 2701 + 33200 3320 0.00017667877 0.00014965389 2701 + 33400 3340 0.00017944144 0.00014195087 2701 + 33600 3360 0.0001807053 0.00014509998 2701 + 33800 3380 0.00018242869 0.00014683629 2701 + 34000 3400 0.00018415985 0.00014295872 2701 + 34200 3420 0.00018635902 0.00013823794 2701 + 34400 3440 0.00018885401 0.00013629126 2701 + 34600 3460 0.00019106836 0.000138816 2701 + 34800 3480 0.00019256787 0.00014358744 2701 + 35000 3500 0.00019410016 0.0001420669 2701 + 35200 3520 0.00019563657 0.0001340349 2701 + 35400 3540 0.00019734994 0.00012994197 2701 + 35600 3560 0.00019880477 0.00013331695 2701 + 35800 3580 0.00020014422 0.00013848097 2701 + 36000 3600 0.00020165626 0.00013796434 2701 + 36200 3620 0.00020297057 0.0001346407 2701 + 36400 3640 0.00020432584 0.00012838525 2701 + 36600 3660 0.00020530152 0.00012848442 2701 + 36800 3680 0.00020709012 0.0001296875 2701 + 37000 3700 0.00020939979 0.00017016832 2701 + 37200 3720 0.00021026158 0.00017388254 2701 + 37400 3740 0.00021203076 0.00012169741 2701 + 37600 3760 0.00021407912 0.00012467048 2701 + 37800 3780 0.00021652866 0.000129545 2701 + 38000 3800 0.00021927979 0.00013537464 2701 + 38200 3820 0.00022175274 0.00014124275 2701 + 38400 3840 0.00022431717 0.0001456533 2701 + 38600 3860 0.00022586947 0.00015646735 2701 + 38800 3880 0.00021974508 0.0001467496 2701 + 39000 3900 0.00021270891 0.0001291023 2701 + 39200 3920 0.00020709839 0.00014468038 2701 + 39400 3940 0.00020138943 0.000156103 2701 + 39600 3960 0.00019579027 0.00015207179 2701 + 39800 3980 0.00019219602 0.0001548601 2701 + 40000 4000 0.00018931715 0.00013543387 2701 +Loop time of 169.513 on 4 procs for 40000 steps with 2701 atoms + +Performance: 2038784.562 tau/day, 235.970 timesteps/s, 637.356 katom-step/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 16.279 | 22.828 | 28 | 98.9 | 13.47 +Bond | 0.88503 | 1.4645 | 2.0916 | 36.3 | 0.86 +Neigh | 29.832 | 29.954 | 30.069 | 1.5 | 17.67 +Comm | 1.2274 | 1.3406 | 1.4623 | 7.3 | 0.79 +Output | 0.0041506 | 0.0054325 | 0.0062685 | 1.1 | 0.00 +Modify | 107.8 | 113.27 | 120.23 | 47.8 | 66.82 +Other | | 0.6549 | | | 0.39 + +Nlocal: 675.25 ave 1362 max 1 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 94.75 ave 154 max 45 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 10485 ave 21200 max 18 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +FullNghs: 20408.5 ave 41306 max 18 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 81634 +Ave neighs/atom = 30.223621 +Ave special neighs/atom = 1.7304702 +Neighbor list builds = 39994 +Dangerous builds = 0 +Total wall time: 0:02:50 diff --git a/src/BPM/bond_bpm_rotational.cpp b/src/BPM/bond_bpm_rotational.cpp index 00e6f61e74..630f6ac906 100644 --- a/src/BPM/bond_bpm_rotational.cpp +++ b/src/BPM/bond_bpm_rotational.cpp @@ -294,7 +294,7 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag, c = q21[0] * q21[0] - q21[1] * q21[1] - q21[2] * q21[2] + q21[3] * q21[3]; theta = acos_limit(c); - // Separately calculte magnitude of quaternion in x-y and out of x-y planes + // Separately calculate magnitude of quaternion in x-y and out of x-y planes // to avoid dividing by zero mag_out_plane = (q21[0] * q21[0] + q21[3] * q21[3]); mag_in_plane = (q21[1] * q21[1] + q21[2] * q21[2]); diff --git a/src/BPM/fix_update_special_bonds.cpp b/src/BPM/fix_update_special_bonds.cpp index c71f6973d0..d9a11c7819 100644 --- a/src/BPM/fix_update_special_bonds.cpp +++ b/src/BPM/fix_update_special_bonds.cpp @@ -251,6 +251,14 @@ void FixUpdateSpecialBonds::pre_force(int /*vflag*/) new_created_pairs.clear(); } + +/* ---------------------------------------------------------------------- */ + +void FixUpdateSpecialBonds::post_run() +{ + pre_exchange(); +} + /* ---------------------------------------------------------------------- */ void FixUpdateSpecialBonds::add_broken_bond(int i, int j) diff --git a/src/BPM/fix_update_special_bonds.h b/src/BPM/fix_update_special_bonds.h index 30d0faeb4b..b244c21a15 100644 --- a/src/BPM/fix_update_special_bonds.h +++ b/src/BPM/fix_update_special_bonds.h @@ -33,6 +33,7 @@ class FixUpdateSpecialBonds : public Fix { void setup(int) override; void pre_exchange() override; void pre_force(int) override; + void post_run() override; void add_broken_bond(int, int); void add_created_bond(int, int); void write_restart(FILE *) override; diff --git a/src/GRANULAR/fix_add_heat.cpp b/src/GRANULAR/fix_add_heat.cpp index 642ea806e8..73bf8a9a26 100644 --- a/src/GRANULAR/fix_add_heat.cpp +++ b/src/GRANULAR/fix_add_heat.cpp @@ -21,7 +21,6 @@ #include "error.h" #include "input.h" #include "memory.h" -#include "update.h" #include "variable.h" using namespace LAMMPS_NS; @@ -125,7 +124,6 @@ void FixAddHeat::post_force(int /*vflag*/) int *mask = atom->mask; double *heatflow = atom->heatflow; double *temperature = atom->temperature; - double dtinv = 1.0 / update->dt; if (vstyle == ATOM) { if (atom->nmax > maxatom) { @@ -150,11 +148,11 @@ void FixAddHeat::post_force(int /*vflag*/) if (vstyle == ATOM) vtmp = vatom[i]; if (style == ADD) { - heatflow[i] += dtinv * vtmp; + heatflow[i] += vtmp; } else if (style == LINEAR) { - heatflow[i] += dtinv * prefactor * (vtmp - temperature[i]); + heatflow[i] += prefactor * (vtmp - temperature[i]); } else if (style == QUARTIC) { - heatflow[i] += dtinv * prefactor * (pow(vtmp, 4.0) - pow(temperature[i], 4.0)); + heatflow[i] += prefactor * (pow(vtmp, 4.0) - pow(temperature[i], 4.0)); } } } diff --git a/src/fix_neigh_history.h b/src/fix_neigh_history.h index 628539e0e6..0d5f127de0 100644 --- a/src/fix_neigh_history.h +++ b/src/fix_neigh_history.h @@ -60,6 +60,9 @@ class FixNeighHistory : public Fix { int size_restart(int) override; int maxsize_restart() override; + int get_dnum() const { return dnum; } + int get_maxpartner() const { return maxpartner; } + protected: int newton_pair; // same as force setting int dnum, dnumbytes; // dnum = # of values per neighbor