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Merge pull request #4273 from jtclemm/small-patches

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Few small patches to BPM, RHEO, and GRANULAR packages
This commit is contained in:
Axel Kohlmeyer
2024-08-21 16:33:28 -04:00
committed by GitHub
parent e142e4fe23 d1fb321eae
commit 92abea3372
12 changed files with 518 additions and 504 deletions
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2
doc/src/Howto_bpm.rst
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@ -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) <howto-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.
----------

3
doc/src/Howto_rheo.rst
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@ -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) <howto_rheo_clemmer>`.
:ref:`(Clemmer) <howto_rheo_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
<PKG-SPH>` package is likely better suited for your application. It has fewer advanced

2
doc/src/Packages_details.rst
View File

@ -350,6 +350,7 @@ models for mesoscale simulations of solids and fracture. See the
* :doc:`compute nbond/atom <compute_nbond_atom>`
* :doc:`fix nve/bpm/sphere <fix_nve_bpm_sphere>`
* :doc:`pair_style bpm/spring <pair_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 <fix_rheo_viscosity>`
* :doc:`pair_style rheo <pair_rheo>`
* :doc:`pair_style rheo/solid <pair_rheo_solid>`
* https://www.lammps.org/movies.html#rheopackage
* ``examples/rheo``
----------

17
doc/src/fix_add_heat.rst
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@ -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 <Build_package>` page for more info.
This fix requires that atoms store temperature and heat flow
as defined by the :doc:`fix property/atom <fix_property_atom>` command.
as defined by the :doc:`fix property/atom <fix_property_atom>` command or
included in certain atom styles, such as atom_style rheo/thermal.
Related commands
""""""""""""""""

2
examples/rheo/oxidation/in.rheo.oxidation
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@ -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

488
examples/rheo/oxidation/log.17Apr2024.oxidation.g++.4
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@ -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

486
examples/rheo/oxidation/log.27Jun2024.oxidation.g++.4 Normal file
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@ -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

2
src/BPM/bond_bpm_rotational.cpp
View File

@ -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]);

8
src/BPM/fix_update_special_bonds.cpp
View File

@ -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)

1
src/BPM/fix_update_special_bonds.h
View File

@ -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;

8
src/GRANULAR/fix_add_heat.cpp
View File

@ -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));
}
}
}

3
src/fix_neigh_history.h
View File

@ -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