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add support for a region keyword to fix edpd/source and fix tdpd/source

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This commit is contained in:
Axel Kohlmeyer
2023-04-21 17:58:28 -04:00
parent e6e7121445
commit 7c723b4852
31 changed files with 1869 additions and 726 deletions
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46
doc/src/fix_dpd_source.rst
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@ -18,18 +18,21 @@ Syntax
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* edpd/source or tdpd/source = style name of this fix command * edpd/source or tdpd/source = style name of this fix command
* index (only specified for tdpd/source) = index of chemical species (1 to Nspecies) * index (only specified for tdpd/source) = index of chemical species (1 to Nspecies)
* keyword = *sphere* or *cuboid* * keyword = *sphere* or *cuboid* or *region*
.. parsed-literal:: .. parsed-literal::
*sphere* values = cx,cy,cz,radius,source *sphere* args = cx cy cz radius source
cx,cy,cz = x,y,z center of spherical domain (distance units) cx,cy,cz = x,y,z center of spherical domain (distance units)
radius = radius of a spherical domain (distance units) radius = radius of a spherical domain (distance units)
source = heat source or concentration source (flux units, see below) source = heat source or concentration source (flux units, see below)
*cuboid* values = cx,cy,cz,dLx,dLy,dLz,source *cuboid* values = cx cy cz dLx dLy dLz source
cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units) cx,cy,cz = x,y,z center of a cuboid domain (distance units)
dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units) dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
source = heat source or concentration source (flux units, see below) source = heat source or concentration source (flux units, see below)
*region* values = region-ID source
region = ID of region for heat or concentration source
source = heat source or concentration source (flux units, see below)
Examples Examples
"""""""" """"""""
@ -40,6 +43,7 @@ Examples
fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01 fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01 fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01 fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01
fix 1 all tdpd/source 1 region lower -0.01
Description Description
""""""""""" """""""""""
@ -57,37 +61,45 @@ heat conduction with a source term (see Fig.12 in :ref:`(Li2014) <Li2014b>`)
or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as
an analog of a periodic Poiseuille flow problem. an analog of a periodic Poiseuille flow problem.
If the *sphere* keyword is used, the *cx,cy,cz,radius* defines a If the *sphere* keyword is used, the *cx, cy, cz, radius* values define
spherical domain to apply the source flux to. a spherical domain to apply the source flux to.
If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a If the *cuboid* keyword is used, the *cx, cy, cz, dLx, dLy, dLz* define
cuboid domain to apply the source flux to. a cuboid domain to apply the source flux to.
If the *region* keyword is used, the *region-ID* selects which
:doc:`region <region>` to apply the source flux to.
---------- ----------
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options No information of these fixes is written to :doc:`binary restart files
are relevant to this fix. No global or per-atom quantities are stored <restart>`. None of the :doc:`fix_modify <fix_modify>` options are
by this fix for access by various :doc:`output commands <Howto_output>`. relevant to these fixes. No global or per-atom quantities are stored by
No parameter of this fix can be used with the *start/stop* keywords of these fixes for access by various :doc:`output commands <Howto_output>`.
the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. No parameter of these fixes can be used with the *start/stop* keywords
of the :doc:`run <run>` command. These fixes are not invoked during
:doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""
This fix is part of the DPD-MESO package. It is only enabled if These fixes are part of the DPD-MESO package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Fix *edpd/source* must be used with the :doc:`pair_style edpd <pair_mesodpd>` command. Fix *tdpd/source* must be used with the Fix *edpd/source* must be used with the :doc:`pair_style edpd
<pair_mesodpd>` command. Fix *tdpd/source* must be used with the
:doc:`pair_style tdpd <pair_mesodpd>` command. :doc:`pair_style tdpd <pair_mesodpd>` command.
Related commands Related commands
"""""""""""""""" """"""""""""""""
:doc:`pair_style edpd <pair_mesodpd>`, :doc:`pair_style tdpd <pair_mesodpd>`, :doc:`pair_style edpd <pair_mesodpd>`, :doc:`pair_style tdpd <pair_mesodpd>`,
:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`, :doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>` :doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`,
:doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
Default Default
""""""" """""""

11
examples/PACKAGES/dpd-meso/edpd/in.edpd
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@ -11,13 +11,14 @@
### temperature-dependent properties". J. Comput. Phys., ### ### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### ### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
######################################################################## ########################################################################
units lj units lj
dimension 3 dimension 3
boundary p p p boundary p p p
neighbor 0.2 bin neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes neigh_modify every 1 delay 0 check yes
atom_style edpd atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd create_box 1 edpd

58
examples/PACKAGES/dpd-meso/edpd/in.edpd-region Normal file
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@ -0,0 +1,58 @@
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * edpd/temp 1.0
set atom * edpd/cv 1.0E5
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 &
power 10.54 -3.66 3.44 -4.10 &
kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/edpd 0.5
fix upper all edpd/source region upper 0.011
fix lower all edpd/source region lower -0.011
timestep 0.01
run 500
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500

142
examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1
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@ -1,142 +0,0 @@
LAMMPS (11 Aug 2017)
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * edpd/temp 1.0
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.64 | 11.64 | 11.64 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 201.73366
100 1.0069712 43.754293 0 45.264656 199.5369
200 0.98667561 43.716052 0 45.195973 196.72854
300 1.0036944 43.706299 0 45.211746 195.35714
400 1.0024228 43.697014 0 45.200554 197.0062
500 0.99968161 43.687445 0 45.186873 193.80596
Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms
Performance: 5346.567 tau/day, 6.188 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 75.106 | 75.106 | 75.106 | 0.0 | 92.95
Neigh | 4.9836 | 4.9836 | 4.9836 | 0.0 | 6.17
Comm | 0.31199 | 0.31199 | 0.31199 | 0.0 | 0.39
Output | 0.00048232 | 0.00048232 | 0.00048232 | 0.0 | 0.00
Modify | 0.29985 | 0.29985 | 0.29985 | 0.0 | 0.37
Other | | 0.09751 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749111 ave 749111 max 749111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749111
Ave neighs/atom = 46.8194
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Per MPI rank memory allocation (min/avg/max) = 12.14 | 12.14 | 12.14 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99968161 43.687397 0 45.186825 196.38426
100 1.0041443 43.668196 0 45.174318 195.38066
200 0.99628392 43.666173 0 45.160505 197.84675
300 1.0029116 43.66224 0 45.166513 199.67414
400 0.99922193 43.64406 0 45.142799 196.94404
500 0.99355431 43.623266 0 45.113505 195.94136
Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms
Performance: 5348.242 tau/day, 6.190 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 75.073 | 75.073 | 75.073 | 0.0 | 92.94
Neigh | 4.8786 | 4.8786 | 4.8786 | 0.0 | 6.04
Comm | 0.31086 | 0.31086 | 0.31086 | 0.0 | 0.38
Output | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.00
Modify | 0.4139 | 0.4139 | 0.4139 | 0.0 | 0.51
Other | | 0.09731 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749667 ave 749667 max 749667 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749667
Ave neighs/atom = 46.8542
Neighbor list builds = 178
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:02:41

142
examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4
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@ -1,142 +0,0 @@
LAMMPS (11 Aug 2017)
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * edpd/temp 1.0
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.979 | 4.985 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 199.51547
100 1.0106415 43.744371 0 45.260239 196.39598
200 1.0053215 43.714413 0 45.222301 195.35298
300 0.99886399 43.713356 0 45.211559 196.74821
400 1.0035264 43.699086 0 45.204282 195.47446
500 1.0025285 43.698051 0 45.20175 197.27042
Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms
Performance: 20411.046 tau/day, 23.624 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.713 | 19.101 | 19.41 | 6.0 | 90.25
Neigh | 1.2687 | 1.2925 | 1.3177 | 1.5 | 6.11
Comm | 0.33013 | 0.66337 | 1.0747 | 34.3 | 3.13
Output | 0.00023484 | 0.00028092 | 0.00036526 | 0.0 | 0.00
Modify | 0.073931 | 0.075277 | 0.076306 | 0.3 | 0.36
Other | | 0.03227 | | | 0.15
Nlocal: 4000 ave 4067 max 3930 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 5997.5 ave 6052 max 5943 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 187388 ave 193157 max 181221 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 749552
Ave neighs/atom = 46.847
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Per MPI rank memory allocation (min/avg/max) = 5.221 | 5.23 | 5.236 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0025285 43.69801 0 45.201708 194.00452
100 0.9885969 43.679927 0 45.16273 196.28442
200 1.0028463 43.663067 0 45.167242 198.25592
300 1.0027516 43.648817 0 45.152851 198.82226
400 0.99695312 43.641469 0 45.136805 197.97499
500 0.98202292 43.627163 0 45.100105 199.16319
Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms
Performance: 20022.203 tau/day, 23.174 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 18.438 | 19.121 | 19.812 | 14.1 | 88.62
Neigh | 1.2568 | 1.2885 | 1.325 | 2.5 | 5.97
Comm | 0.29482 | 1.0219 | 1.7352 | 63.9 | 4.74
Output | 0.00027728 | 0.00029719 | 0.0003531 | 0.0 | 0.00
Modify | 0.11153 | 0.11265 | 0.1135 | 0.2 | 0.52
Other | | 0.03194 | | | 0.15
Nlocal: 4000 ave 4092 max 3899 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5974 ave 6019 max 5915 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 187414 ave 196149 max 178418 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 749658
Ave neighs/atom = 46.8536
Neighbor list builds = 181
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:42

178
examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.1 Normal file
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@ -0,0 +1,178 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * edpd/temp 1.0
Setting atom values ...
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values ...
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/edpd 0.5
fix upper all edpd/source region upper 0.01
fix lower all edpd/source region lower -0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair edpd command: doi:10.1016/j.jcp.2014.02.003
@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113--127}
}
@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038--11040}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 201.43068
100 0.99644296 43.749732 0 45.244303 200.44316
200 0.98985852 43.699081 0 45.183776 197.29314
300 1.0062075 43.708406 0 45.217622 194.61595
400 0.99858259 43.69758 0 45.19536 196.87253
500 0.99991379 43.677571 0 45.177348 194.59785
Loop time of 50.3705 on 1 procs for 500 steps with 16000 atoms
Performance: 8576.445 tau/day, 9.926 timesteps/s, 158.823 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 44.879 | 44.879 | 44.879 | 0.0 | 89.10
Neigh | 4.8096 | 4.8096 | 4.8096 | 0.0 | 9.55
Comm | 0.31711 | 0.31711 | 0.31711 | 0.0 | 0.63
Output | 0.0005095 | 0.0005095 | 0.0005095 | 0.0 | 0.00
Modify | 0.29611 | 0.29611 | 0.29611 | 0.0 | 0.59
Other | | 0.06781 | | | 0.13
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14106 ave 14106 max 14106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749963 ave 749963 max 749963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749963
Ave neighs/atom = 46.872687
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.6 | 12.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99991379 43.67752 0 45.177297 195.4932
100 1.0053402 43.685038 0 45.192954 196.73683
200 1.0052797 43.665955 0 45.173781 198.60396
300 0.98694632 43.650877 0 45.131204 199.11464
400 1.003189 43.639966 0 45.144655 196.20663
500 1.008172 43.625425 0 45.137589 196.69792
Loop time of 48.7446 on 1 procs for 500 steps with 16000 atoms
Performance: 8862.512 tau/day, 10.258 timesteps/s, 164.121 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 43.362 | 43.362 | 43.362 | 0.0 | 88.96
Neigh | 4.6255 | 4.6255 | 4.6255 | 0.0 | 9.49
Comm | 0.30073 | 0.30073 | 0.30073 | 0.0 | 0.62
Output | 0.00039502 | 0.00039502 | 0.00039502 | 0.0 | 0.00
Modify | 0.39271 | 0.39271 | 0.39271 | 0.0 | 0.81
Other | | 0.06321 | | | 0.13
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14131 ave 14131 max 14131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749932 ave 749932 max 749932 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749932
Ave neighs/atom = 46.87075
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:01:39

178
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@ -0,0 +1,178 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.001 seconds
mass 1 1.0
set atom * edpd/temp 1.0
Setting atom values ...
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values ...
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/edpd 0.5
fix upper all edpd/source region upper 0.01
fix lower all edpd/source region lower -0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair edpd command: doi:10.1016/j.jcp.2014.02.003
@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113--127}
}
@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038--11040}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.117 | 5.131 | 5.14 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 199.82261
100 1.0027045 43.752877 0 45.256839 196.18262
200 1.0019856 43.711184 0 45.214068 195.21873
300 1.0010549 43.708051 0 45.209539 196.54529
400 1.0072936 43.694617 0 45.205463 196.01853
500 0.99454965 43.693217 0 45.184948 194.56851
Loop time of 12.7478 on 4 procs for 500 steps with 16000 atoms
Performance: 33888.226 tau/day, 39.222 timesteps/s, 627.560 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.639 | 10.877 | 11.121 | 5.7 | 85.32
Neigh | 1.1777 | 1.1975 | 1.2184 | 1.6 | 9.39
Comm | 0.28879 | 0.554 | 0.81076 | 27.4 | 4.35
Output | 0.00025981 | 0.00035629 | 0.00051976 | 0.0 | 0.00
Modify | 0.077592 | 0.078284 | 0.078852 | 0.2 | 0.61
Other | | 0.04102 | | | 0.32
Nlocal: 4000 ave 4063 max 3941 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5986.75 ave 6036 max 5939 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 187308 ave 192682 max 181708 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 749234
Ave neighs/atom = 46.827125
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.382 | 5.391 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99454965 43.693155 0 45.184886 196.69629
100 0.98097933 43.671568 0 45.142946 196.18819
200 1.0040512 43.659697 0 45.165679 199.5338
300 0.99371064 43.648099 0 45.138571 199.01479
400 1.0089291 43.642011 0 45.15531 196.26533
500 0.99778837 43.62308 0 45.119669 195.60931
Loop time of 12.8197 on 4 procs for 500 steps with 16000 atoms
Performance: 33698.231 tau/day, 39.003 timesteps/s, 624.041 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.325 | 10.755 | 11.152 | 11.5 | 83.89
Neigh | 1.1476 | 1.1782 | 1.2083 | 2.7 | 9.19
Comm | 0.30192 | 0.72837 | 1.1882 | 47.4 | 5.68
Output | 0.00023835 | 0.00025987 | 0.00032262 | 0.0 | 0.00
Modify | 0.11909 | 0.11927 | 0.11961 | 0.1 | 0.93
Other | | 0.03872 | | | 0.30
Nlocal: 4000 ave 4123 max 3896 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 5978.75 ave 6017 max 5939 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 187413 ave 197959 max 177994 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 749653
Ave neighs/atom = 46.853313
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:00:25

175
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@ -0,0 +1,175 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * edpd/temp 1.0
Setting atom values ...
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values ...
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair edpd command: doi:10.1016/j.jcp.2014.02.003
@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113--127}
}
@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038--11040}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.1 | 12.1 | 12.1 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 201.43068
100 0.99644296 43.749732 0 45.244303 200.44316
200 0.98985852 43.699081 0 45.183776 197.29314
300 1.0062075 43.708406 0 45.217622 194.61595
400 0.99858259 43.69758 0 45.19536 196.87253
500 0.99991379 43.677571 0 45.177348 194.59785
Loop time of 48.2916 on 1 procs for 500 steps with 16000 atoms
Performance: 8945.662 tau/day, 10.354 timesteps/s, 165.660 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 43.121 | 43.121 | 43.121 | 0.0 | 89.29
Neigh | 4.5712 | 4.5712 | 4.5712 | 0.0 | 9.47
Comm | 0.28793 | 0.28793 | 0.28793 | 0.0 | 0.60
Output | 0.00040031 | 0.00040031 | 0.00040031 | 0.0 | 0.00
Modify | 0.24651 | 0.24651 | 0.24651 | 0.0 | 0.51
Other | | 0.06435 | | | 0.13
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14106 ave 14106 max 14106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749963 ave 749963 max 749963 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749963
Ave neighs/atom = 46.872687
Neighbor list builds = 181
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.6 | 12.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99991379 43.67752 0 45.177297 195.4932
100 1.0053402 43.685038 0 45.192954 196.73683
200 1.0052797 43.665955 0 45.173781 198.60396
300 0.98694632 43.650877 0 45.131204 199.11464
400 1.003189 43.639966 0 45.144655 196.20663
500 1.008172 43.625425 0 45.137589 196.69792
Loop time of 47.2499 on 1 procs for 500 steps with 16000 atoms
Performance: 9142.877 tau/day, 10.582 timesteps/s, 169.313 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 42.09 | 42.09 | 42.09 | 0.0 | 89.08
Neigh | 4.4695 | 4.4695 | 4.4695 | 0.0 | 9.46
Comm | 0.28364 | 0.28364 | 0.28364 | 0.0 | 0.60
Output | 0.00041768 | 0.00041768 | 0.00041768 | 0.0 | 0.00
Modify | 0.34551 | 0.34551 | 0.34551 | 0.0 | 0.73
Other | | 0.06079 | | | 0.13
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14131 ave 14131 max 14131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749932 ave 749932 max 749932 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749932
Ave neighs/atom = 46.87075
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:01:35

175
examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.4 Normal file
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@ -0,0 +1,175 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Heat conduction analog of periodic Poiseuille flow problem ###
### using energy-conserving DPD (eDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### mDPD system setup follows Fig.12 in the publication: ###
### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
### "Energy-conserving dissipative particle dynamics with ###
### temperature-dependent properties". J. Comput. Phys., ###
### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style edpd
comm_modify vel yes
region edpd block -10 10 -10 10 -5 5 units box
create_box 1 edpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.001 seconds
mass 1 1.0
set atom * edpd/temp 1.0
Setting atom values ...
16000 settings made for edpd/temp
set atom * edpd/cv 1.0E5
Setting atom values ...
16000 settings made for edpd/cv
pair_style edpd 1.58 9872598
#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
compute mythermo all temp
thermo 100
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/edpd 0.5
fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair edpd command: doi:10.1016/j.jcp.2014.02.003
@Article{ZLi2014_JCP,
author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.},
title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties},
journal = {Journal of Computational Physics},
year = {2014},
volume = {265},
pages = {113--127}
}
@Article{ZLi2015_CC,
author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.},
title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers},
journal = {Chemical Communications},
year = {2015},
volume = {51},
pages = {11038--11040}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.117 | 5.131 | 5.14 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 199.82261
100 1.0027045 43.752877 0 45.256839 196.18262
200 1.0019856 43.711184 0 45.214068 195.21873
300 1.0010549 43.708051 0 45.209539 196.54529
400 1.0072936 43.694617 0 45.205463 196.01853
500 0.99454965 43.693217 0 45.184948 194.56851
Loop time of 13.0053 on 4 procs for 500 steps with 16000 atoms
Performance: 33217.163 tau/day, 38.446 timesteps/s, 615.133 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.938 | 11.134 | 11.288 | 4.2 | 85.61
Neigh | 1.2077 | 1.2246 | 1.245 | 1.3 | 9.42
Comm | 0.35942 | 0.53326 | 0.73893 | 21.1 | 4.10
Output | 0.00020183 | 0.0002942 | 0.00046431 | 0.0 | 0.00
Modify | 0.071992 | 0.072633 | 0.073227 | 0.2 | 0.56
Other | | 0.04006 | | | 0.31
Nlocal: 4000 ave 4063 max 3941 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5986.75 ave 6036 max 5939 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 187308 ave 192682 max 181708 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 749234
Ave neighs/atom = 46.827125
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep 0
compute temp all edpd/temp/atom
compute ccT all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
run 500
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.369 | 5.382 | 5.391 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99454965 43.693155 0 45.184886 196.69629
100 0.98097933 43.671568 0 45.142946 196.18819
200 1.0040512 43.659697 0 45.165679 199.5338
300 0.99371064 43.648099 0 45.138571 199.01479
400 1.0089291 43.642011 0 45.15531 196.26533
500 0.99778837 43.62308 0 45.119669 195.60931
Loop time of 12.6544 on 4 procs for 500 steps with 16000 atoms
Performance: 34138.237 tau/day, 39.512 timesteps/s, 632.190 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.254 | 10.646 | 10.994 | 10.5 | 84.13
Neigh | 1.1417 | 1.1712 | 1.2006 | 2.5 | 9.26
Comm | 0.31692 | 0.68901 | 1.1043 | 44.5 | 5.44
Output | 0.00024359 | 0.00026159 | 0.00031441 | 0.0 | 0.00
Modify | 0.10931 | 0.10967 | 0.11008 | 0.1 | 0.87
Other | | 0.03831 | | | 0.30
Nlocal: 4000 ave 4123 max 3896 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 5978.75 ave 6017 max 5939 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 187413 ave 197959 max 177994 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 749653
Ave neighs/atom = 46.853313
Neighbor list builds = 182
Dangerous builds = 0
Total wall time: 0:00:25

24
examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.1 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 811.832 0.985962 4.05916
2 -8.5 807.15 0.965817 4.03575
3 -7.5 820.714 0.952312 4.10357
4 -6.5 820.906 0.944107 4.10453
5 -5.5 822.302 0.940236 4.11151
6 -4.5 819.292 0.940284 4.09646
7 -3.5 826.204 0.944248 4.13102
8 -2.5 813.71 0.952638 4.06855
9 -1.5 814.242 0.966266 4.07121
10 -0.5 802.846 0.986518 4.01423
11 0.5 795.896 1.01321 3.97948
12 1.5 788.566 1.03398 3.94283
13 2.5 781.844 1.04805 3.90922
14 3.5 786.72 1.05675 3.9336
15 4.5 772.912 1.06082 3.86456
16 5.5 777.098 1.0607 3.88549
17 6.5 777.032 1.05662 3.88516
18 7.5 783.43 1.04804 3.91715
19 8.5 788.66 1.03368 3.9433
20 9.5 788.644 1.01283 3.94322

24
examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.4 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 807.598 0.986162 4.03799
2 -8.5 814.152 0.965805 4.07076
3 -7.5 816.566 0.952189 4.08283
4 -6.5 821.804 0.944066 4.10902
5 -5.5 813.33 0.940228 4.06665
6 -4.5 824.512 0.940269 4.12256
7 -3.5 823.87 0.944219 4.11935
8 -2.5 818.798 0.952545 4.09399
9 -1.5 813.634 0.966087 4.06817
10 -0.5 799.048 0.986285 3.99524
11 0.5 795.018 1.01315 3.97509
12 1.5 794.164 1.03394 3.97082
13 2.5 782.116 1.04808 3.91058
14 3.5 778.19 1.05667 3.89095
15 4.5 779.816 1.06065 3.89908
16 5.5 772.218 1.06068 3.86109
17 6.5 780.734 1.05659 3.90367
18 7.5 784.08 1.04783 3.9204
19 8.5 786.276 1.03371 3.93138
20 9.5 794.076 1.01303 3.97038

24
examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.1 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 811.832 0.985962 4.05916
2 -8.5 807.15 0.965817 4.03575
3 -7.5 820.714 0.952312 4.10357
4 -6.5 820.906 0.944107 4.10453
5 -5.5 822.302 0.940236 4.11151
6 -4.5 819.292 0.940284 4.09646
7 -3.5 826.204 0.944248 4.13102
8 -2.5 813.71 0.952638 4.06855
9 -1.5 814.242 0.966266 4.07121
10 -0.5 802.846 0.986518 4.01423
11 0.5 795.896 1.01321 3.97948
12 1.5 788.566 1.03398 3.94283
13 2.5 781.844 1.04805 3.90922
14 3.5 786.72 1.05675 3.9336
15 4.5 772.912 1.06082 3.86456
16 5.5 777.098 1.0607 3.88549
17 6.5 777.032 1.05662 3.88516
18 7.5 783.43 1.04804 3.91715
19 8.5 788.66 1.03368 3.9433
20 9.5 788.644 1.01283 3.94322

24
examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.4 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_temp density/number
500 20 16000
1 -9.5 807.598 0.986162 4.03799
2 -8.5 814.152 0.965805 4.07076
3 -7.5 816.566 0.952189 4.08283
4 -6.5 821.804 0.944066 4.10902
5 -5.5 813.33 0.940228 4.06665
6 -4.5 824.512 0.940269 4.12256
7 -3.5 823.87 0.944219 4.11935
8 -2.5 818.798 0.952545 4.09399
9 -1.5 813.634 0.966087 4.06817
10 -0.5 799.048 0.986285 3.99524
11 0.5 795.018 1.01315 3.97509
12 1.5 794.164 1.03394 3.97082
13 2.5 782.116 1.04808 3.91058
14 3.5 778.19 1.05667 3.89095
15 4.5 779.816 1.06065 3.89908
16 5.5 772.218 1.06068 3.86109
17 6.5 780.734 1.05659 3.90367
18 7.5 784.08 1.04783 3.9204
19 8.5 786.276 1.03371 3.93138
20 9.5 794.076 1.01303 3.97038

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1
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@ -1,24 +0,0 @@
# Chunk-averaged data for fix stat and group c_cc2
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 797.17 0.986661 1.0077
2 -8.5 802.61 0.967974 1.02003
3 -7.5 795.46 0.957045 1.02873
4 -6.5 806.46 0.951271 1.03428
5 -5.5 802.34 0.94898 1.03692
6 -4.5 799.84 0.949378 1.03673
7 -3.5 798.4 0.952505 1.03374
8 -2.5 800.36 0.959322 1.02778
9 -1.5 797.65 0.971516 1.01867
10 -0.5 808.88 0.990644 1.00626
11 0.5 786.29 1.00924 0.993828
12 1.5 807.16 1.02831 0.981436
13 2.5 797.54 1.04071 0.972184
14 3.5 799.67 1.04749 0.966258
15 4.5 799.61 1.05063 0.963256
16 5.5 806.11 1.05105 0.963052
17 6.5 803.67 1.04877 0.965688
18 7.5 797.39 1.04305 0.971187
19 8.5 801.85 1.03208 0.97993
20 9.5 791.54 1.01351 0.992209

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4
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@ -1,24 +0,0 @@
# Chunk-averaged data for fix stat and group c_cc2
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 806.92 0.986675 1.00766
2 -8.5 798.01 0.96792 1.02003
3 -7.5 805.43 0.956909 1.02883
4 -6.5 800.54 0.951207 1.03432
5 -5.5 794.14 0.948967 1.03691
6 -4.5 799.75 0.949379 1.03672
7 -3.5 799.65 0.952492 1.03374
8 -2.5 799.94 0.959331 1.02778
9 -1.5 800.96 0.971664 1.01861
10 -0.5 803.97 0.99074 1.00622
11 0.5 800.66 1.00949 0.993673
12 1.5 779.22 1.02824 0.981461
13 2.5 809.13 1.04056 0.972274
14 3.5 805.23 1.04747 0.966272
15 4.5 795.95 1.05061 0.96327
16 5.5 796.4 1.05105 0.963035
17 6.5 806.1 1.04883 0.965621
18 7.5 806.41 1.04305 0.971224
19 8.5 792.2 1.03211 0.979955
20 9.5 799.39 1.01362 0.992156

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.1 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000.000000000004
1 -9.5 798.2 0.986606 1.00775
2 -8.5 801.34 0.967792 1.02028
3 -7.5 792.01 0.956909 1.02905
4 -6.5 798.48 0.951127 1.03467
5 -5.5 808.94 0.948624 1.03746
6 -4.5 802.1 0.948627 1.03746
7 -3.5 790.74 0.951056 1.03473
8 -2.5 809.14 0.956893 1.02906
9 -1.5 799.53 0.967894 1.0202
10 -0.5 798.82 0.986603 1.00777
11 0.5 798.16 1.01347 0.992221
12 1.5 801.96 1.03218 0.979759
13 2.5 798.11 1.04314 0.970901
14 3.5 800.84 1.04893 0.965282
15 4.5 794.76 1.05139 0.962527
16 5.5 794.45 1.05138 0.962529
17 6.5 806.49 1.04893 0.965277
18 7.5 798.97 1.04311 0.970928
19 8.5 804.17 1.03219 0.979718
20 9.5 802.79 1.01346 0.992165

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.4 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 799.42 0.986758 1.00767
2 -8.5 805.75 0.96799 1.02012
3 -7.5 792.98 0.956887 1.02906
4 -6.5 819.2 0.951051 1.03475
5 -5.5 787.47 0.9486 1.0375
6 -4.5 815.17 0.948622 1.03747
7 -3.5 790.12 0.951102 1.03469
8 -2.5 804.82 0.956976 1.02899
9 -1.5 794.72 0.968 1.02013
10 -0.5 793.38 0.986471 1.00785
11 0.5 794.01 1.01316 0.992392
12 1.5 811.96 1.032 0.979939
13 2.5 788.73 1.0431 0.970974
14 3.5 800.05 1.04891 0.965292
15 4.5 798.16 1.05138 0.962513
16 5.5 806.01 1.0514 0.962495
17 6.5 805.21 1.04895 0.965252
18 7.5 803.09 1.04305 0.970998
19 8.5 803.11 1.03195 0.979936
20 9.5 786.64 1.0134 0.992218

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.1 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000.000000000004
1 -9.5 798.2 0.986606 1.00775
2 -8.5 801.34 0.967792 1.02028
3 -7.5 792.01 0.956909 1.02905
4 -6.5 798.48 0.951127 1.03467
5 -5.5 808.94 0.948624 1.03746
6 -4.5 802.1 0.948627 1.03746
7 -3.5 790.74 0.951056 1.03473
8 -2.5 809.14 0.956893 1.02906
9 -1.5 799.53 0.967894 1.0202
10 -0.5 798.82 0.986603 1.00777
11 0.5 798.16 1.01347 0.992221
12 1.5 801.96 1.03218 0.979759
13 2.5 798.11 1.04314 0.970901
14 3.5 800.84 1.04893 0.965282
15 4.5 794.76 1.05139 0.962527
16 5.5 794.45 1.05138 0.962529
17 6.5 806.49 1.04893 0.965277
18 7.5 798.97 1.04311 0.970928
19 8.5 804.17 1.03219 0.979718
20 9.5 802.79 1.01346 0.992165

24
examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.4 Normal file
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@ -0,0 +1,24 @@
# Chunk-averaged data for fix stat and group all
# Timestep Number-of-chunks Total-count
# Chunk Coord1 Ncount c_cc1 c_cc2
100 20 16000
1 -9.5 799.42 0.986758 1.00767
2 -8.5 805.75 0.96799 1.02012
3 -7.5 792.98 0.956887 1.02906
4 -6.5 819.2 0.951051 1.03475
5 -5.5 787.47 0.9486 1.0375
6 -4.5 815.17 0.948622 1.03747
7 -3.5 790.12 0.951102 1.03469
8 -2.5 804.82 0.956976 1.02899
9 -1.5 794.72 0.968 1.02013
10 -0.5 793.38 0.986471 1.00785
11 0.5 794.01 1.01316 0.992392
12 1.5 811.96 1.032 0.979939
13 2.5 788.73 1.0431 0.970974
14 3.5 800.05 1.04891 0.965292
15 4.5 798.16 1.05138 0.962513
16 5.5 806.01 1.0514 0.962495
17 6.5 805.21 1.04895 0.965252
18 7.5 803.09 1.04305 0.970998
19 8.5 803.11 1.03195 0.979936
20 9.5 786.64 1.0134 0.992218

11
examples/PACKAGES/dpd-meso/tdpd/in.tdpd
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@ -11,13 +11,14 @@
### advection-diffusion-reaction problems. J. Chem. Phys., ### ### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### ### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
######################################################################## ########################################################################
units lj units lj
dimension 3 dimension 3
boundary p p p boundary p p p
neighbor 0.2 bin neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes neigh_modify every 1 delay 0 check yes
atom_style tdpd 2 atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd create_box 1 tdpd

58
examples/PACKAGES/dpd-meso/tdpd/in.tdpd-region Normal file
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########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
create_atoms 1 random 16000 276438 NULL
mass 1 1.0
set atom * cc 1 1.0
set atom * cc 2 1.0
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 region upper 0.01
fix lower1 all tdpd/source 1 region lower -0.01
fix upper2 all tdpd/source 2 region upper -0.01
fix lower2 all tdpd/source 2 region lower 0.01
timestep 0.01
run 500
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100

146
examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1
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@ -1,146 +0,0 @@
LAMMPS (11 Aug 2017)
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * cc 1 1.0
16000 settings made for cc index 1
set atom * cc 2 1.0
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.3 | 11.3 | 11.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 202.19166
50 0.99837766 43.949877 0 45.447349 195.80936
100 0.99846831 43.756995 0 45.254604 198.22348
150 1.0026903 43.72408 0 45.228021 196.61676
200 1.0063144 43.722388 0 45.231765 194.17954
250 1.0032304 43.721864 0 45.226615 197.85829
300 0.9932656 43.703526 0 45.193331 196.57406
350 1.0002916 43.720498 0 45.220841 193.55346
400 0.99475486 43.722965 0 45.215004 196.81546
450 1.0011803 43.712447 0 45.214124 200.46118
500 1.0009006 43.708984 0 45.210241 197.38953
Loop time of 96.0326 on 1 procs for 500 steps with 16000 atoms
Performance: 4498.474 tau/day, 5.207 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 90.083 | 90.083 | 90.083 | 0.0 | 93.80
Neigh | 5.049 | 5.049 | 5.049 | 0.0 | 5.26
Comm | 0.34141 | 0.34141 | 0.34141 | 0.0 | 0.36
Output | 0.00092816 | 0.00092816 | 0.00092816 | 0.0 | 0.00
Modify | 0.45991 | 0.45991 | 0.45991 | 0.0 | 0.48
Other | | 0.09865 | | | 0.10
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14091 ave 14091 max 14091 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749379 ave 749379 max 749379 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749379
Ave neighs/atom = 46.8362
Neighbor list builds = 183
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Per MPI rank memory allocation (min/avg/max) = 11.8 | 11.8 | 11.8 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0009006 43.708984 0 45.210241 199.3205
50 1.0007276 43.704844 0 45.205842 197.77053
100 1.0039032 43.714201 0 45.219961 197.31118
Loop time of 19.0326 on 1 procs for 100 steps with 16000 atoms
Performance: 4539.577 tau/day, 5.254 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.842 | 17.842 | 17.842 | 0.0 | 93.74
Neigh | 0.98674 | 0.98674 | 0.98674 | 0.0 | 5.18
Comm | 0.066013 | 0.066013 | 0.066013 | 0.0 | 0.35
Output | 0.00016284 | 0.00016284 | 0.00016284 | 0.0 | 0.00
Modify | 0.11795 | 0.11795 | 0.11795 | 0.0 | 0.62
Other | | 0.02012 | | | 0.11
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14126 ave 14126 max 14126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 748927 ave 748927 max 748927 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 748927
Ave neighs/atom = 46.8079
Neighbor list builds = 37
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:55

146
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@ -1,146 +0,0 @@
LAMMPS (11 Aug 2017)
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
mass 1 1.0
set atom * cc 1 1.0
16000 settings made for cc index 1
set atom * cc 2 1.0
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.814 | 4.823 | 4.829 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.948932 0 50.448838 199.65978
50 1.0153476 43.948796 0 45.471722 198.3346
100 1.0064284 43.754875 0 45.264424 197.5308
150 0.99609985 43.726751 0 45.220807 197.50623
200 1.0016604 43.720283 0 45.22268 197.81129
250 1.0054979 43.718568 0 45.22672 195.79405
300 0.9997618 43.716617 0 45.216166 197.84788
350 0.99170101 43.72093 0 45.208389 196.07711
400 1.0043692 43.71648 0 45.22294 199.55247
450 1.0086263 43.709988 0 45.222833 198.20516
500 1.0029076 43.717879 0 45.222146 197.26281
Loop time of 24.5533 on 4 procs for 500 steps with 16000 atoms
Performance: 17594.412 tau/day, 20.364 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.236 | 22.418 | 22.736 | 4.0 | 91.30
Neigh | 1.2759 | 1.2883 | 1.3077 | 1.1 | 5.25
Comm | 0.35749 | 0.69526 | 0.88462 | 24.1 | 2.83
Output | 0.00043321 | 0.00050318 | 0.00070691 | 0.0 | 0.00
Modify | 0.11555 | 0.11648 | 0.11888 | 0.4 | 0.47
Other | | 0.03473 | | | 0.14
Nlocal: 4000 ave 4012 max 3982 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 5986.25 ave 6016 max 5956 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 187309 ave 188264 max 186087 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 749235
Ave neighs/atom = 46.8272
Neighbor list builds = 180
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.074 | 5.082 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0029076 43.717879 0 45.222146 198.45789
50 1.0077982 43.713264 0 45.224867 196.56183
100 1.0036823 43.708022 0 45.213451 196.00815
Loop time of 4.79577 on 4 procs for 100 steps with 16000 atoms
Performance: 18015.870 tau/day, 20.852 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.3481 | 4.39 | 4.4398 | 1.7 | 91.54
Neigh | 0.25477 | 0.25675 | 0.25963 | 0.4 | 5.35
Comm | 0.059327 | 0.11194 | 0.15608 | 11.0 | 2.33
Output | 0.00011206 | 0.00011748 | 0.00011992 | 0.0 | 0.00
Modify | 0.030417 | 0.030622 | 0.030739 | 0.1 | 0.64
Other | | 0.006301 | | | 0.13
Nlocal: 4000 ave 4010 max 3987 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 5985.25 ave 6025 max 5959 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 187304 ave 188092 max 186449 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Total # of neighbors = 749216
Ave neighs/atom = 46.826
Neighbor list builds = 38
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:29

174
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@ -0,0 +1,174 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * cc 1 1.0
Setting atom values ...
16000 settings made for cc index 1
set atom * cc 2 1.0
Setting atom values ...
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 region upper 0.01
fix lower1 all tdpd/source 1 region lower -0.01
fix upper2 all tdpd/source 2 region upper -0.01
fix lower2 all tdpd/source 2 region lower 0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair tdpd command: doi:10.1063/1.4923254
@Article{ZLi2015_JCP,
author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
journal = {The Journal of Chemical Physics},
year = {2015},
volume = {143},
number = {1},
pages = {014101}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.51 | 12.51 | 12.51 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 201.70031
50 1.011026 43.947278 0 45.463722 194.91628
100 1.0038328 43.75705 0 45.262706 197.34972
150 1.0024595 43.731513 0 45.235109 196.71302
200 0.99175816 43.70274 0 45.190285 194.60811
250 0.99533515 43.714618 0 45.207528 197.48663
300 0.99335422 43.711138 0 45.201076 196.84197
350 1.0012089 43.71311 0 45.214829 193.04504
400 1.0085738 43.717565 0 45.230331 197.2073
450 0.99147043 43.722807 0 45.209919 200.14351
500 1.0005014 43.717024 0 45.217682 197.81942
Loop time of 60.8937 on 1 procs for 500 steps with 16000 atoms
Performance: 7094.326 tau/day, 8.211 timesteps/s, 131.376 katom-step/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 54.659 | 54.659 | 54.659 | 0.0 | 89.76
Neigh | 5.4068 | 5.4068 | 5.4068 | 0.0 | 8.88
Comm | 0.3543 | 0.3543 | 0.3543 | 0.0 | 0.58
Output | 0.000998 | 0.000998 | 0.000998 | 0.0 | 0.00
Modify | 0.40125 | 0.40125 | 0.40125 | 0.0 | 0.66
Other | | 0.0716 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14049 ave 14049 max 14049 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749053 ave 749053 max 749053 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749053
Ave neighs/atom = 46.815812
Neighbor list builds = 184
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 13.01 | 13.01 | 13.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0005014 43.717024 0 45.217682 199.49297
50 0.99569204 43.716832 0 45.210276 197.52311
100 0.99430734 43.714806 0 45.206174 197.74323
Loop time of 13.6219 on 1 procs for 100 steps with 16000 atoms
Performance: 6342.747 tau/day, 7.341 timesteps/s, 117.458 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.231 | 12.231 | 12.231 | 0.0 | 89.79
Neigh | 1.1657 | 1.1657 | 1.1657 | 0.0 | 8.56
Comm | 0.08547 | 0.08547 | 0.08547 | 0.0 | 0.63
Output | 0.00018984 | 0.00018984 | 0.00018984 | 0.0 | 0.00
Modify | 0.12218 | 0.12218 | 0.12218 | 0.0 | 0.90
Other | | 0.01695 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14065 ave 14065 max 14065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749621 ave 749621 max 749621 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749621
Ave neighs/atom = 46.851312
Neighbor list builds = 36
Dangerous builds = 0
Total wall time: 0:01:14

174
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@ -0,0 +1,174 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * cc 1 1.0
Setting atom values ...
16000 settings made for cc index 1
set atom * cc 2 1.0
Setting atom values ...
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
region upper block -10.0 10.0 0.0 10.0 -5.0 5.0
region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 region upper 0.01
fix lower1 all tdpd/source 1 region lower -0.01
fix upper2 all tdpd/source 2 region upper -0.01
fix lower2 all tdpd/source 2 region lower 0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair tdpd command: doi:10.1063/1.4923254
@Article{ZLi2015_JCP,
author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
journal = {The Journal of Chemical Physics},
year = {2015},
volume = {143},
number = {1},
pages = {014101}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.337 | 5.351 | 5.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 199.59508
50 1.0164166 43.95706 0 45.48159 198.02944
100 0.99583217 43.760777 0 45.254431 198.26943
150 1.0025022 43.730114 0 45.233774 198.402
200 0.99563635 43.72379 0 45.217151 197.6948
250 1.0117752 43.724349 0 45.241917 195.70427
300 0.98950567 43.72333 0 45.207496 197.582
350 0.99351667 43.719413 0 45.209595 194.69504
400 1.0050663 43.715857 0 45.223362 198.50199
450 1.003148 43.712337 0 45.216965 196.26462
500 0.99888463 43.712357 0 45.21059 195.78645
Loop time of 22.3891 on 4 procs for 500 steps with 16000 atoms
Performance: 19295.099 tau/day, 22.332 timesteps/s, 357.317 katom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 17.856 | 18.173 | 18.45 | 5.1 | 81.17
Neigh | 1.6551 | 1.6692 | 1.6857 | 0.8 | 7.46
Comm | 2.0487 | 2.343 | 2.6753 | 14.8 | 10.46
Output | 0.00071266 | 0.0011251 | 0.0019874 | 1.5 | 0.01
Modify | 0.13934 | 0.14111 | 0.14281 | 0.3 | 0.63
Other | | 0.06188 | | | 0.28
Nlocal: 4000 ave 4013 max 3992 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 5990 ave 6012 max 5980 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 187350 ave 188412 max 186633 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 749401
Ave neighs/atom = 46.837562
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.588 | 5.602 | 5.61 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99888463 43.712357 0 45.21059 197.42728
50 1.0015386 43.71567 0 45.217884 198.28372
100 1.0053363 43.718221 0 45.226131 195.45072
Loop time of 3.97512 on 4 procs for 100 steps with 16000 atoms
Performance: 21735.219 tau/day, 25.157 timesteps/s, 402.504 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0699 | 3.1608 | 3.2663 | 4.0 | 79.51
Neigh | 0.28562 | 0.29 | 0.29411 | 0.6 | 7.30
Comm | 0.36815 | 0.47529 | 0.56754 | 10.4 | 11.96
Output | 0.00012585 | 0.0001705 | 0.00018551 | 0.0 | 0.00
Modify | 0.039921 | 0.040036 | 0.04031 | 0.1 | 1.01
Other | | 0.008843 | | | 0.22
Nlocal: 4000 ave 4024 max 3988 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 5977 ave 6004 max 5941 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 187313 ave 188798 max 186723 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 749253
Ave neighs/atom = 46.828313
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:26

171
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@ -0,0 +1,171 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * cc 1 1.0
Setting atom values ...
16000 settings made for cc index 1
set atom * cc 2 1.0
Setting atom values ...
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair tdpd command: doi:10.1063/1.4923254
@Article{ZLi2015_JCP,
author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
journal = {The Journal of Chemical Physics},
year = {2015},
volume = {143},
number = {1},
pages = {014101}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.51 | 12.51 | 12.51 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 201.70031
50 1.011026 43.947278 0 45.463722 194.91628
100 1.0038328 43.75705 0 45.262706 197.34972
150 1.0024595 43.731513 0 45.235109 196.71302
200 0.99175816 43.70274 0 45.190285 194.60811
250 0.99533515 43.714618 0 45.207528 197.48663
300 0.99335422 43.711138 0 45.201076 196.84197
350 1.0012089 43.71311 0 45.214829 193.04504
400 1.0085738 43.717565 0 45.230331 197.2073
450 0.99147043 43.722807 0 45.209919 200.14351
500 1.0005014 43.717024 0 45.217682 197.81942
Loop time of 59.9704 on 1 procs for 500 steps with 16000 atoms
Performance: 7203.552 tau/day, 8.337 timesteps/s, 133.399 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 53.892 | 53.892 | 53.892 | 0.0 | 89.86
Neigh | 5.3558 | 5.3558 | 5.3558 | 0.0 | 8.93
Comm | 0.34774 | 0.34774 | 0.34774 | 0.0 | 0.58
Output | 0.00089543 | 0.00089543 | 0.00089543 | 0.0 | 0.00
Modify | 0.30481 | 0.30481 | 0.30481 | 0.0 | 0.51
Other | | 0.06955 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14049 ave 14049 max 14049 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749053 ave 749053 max 749053 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749053
Ave neighs/atom = 46.815812
Neighbor list builds = 184
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 13.01 | 13.01 | 13.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.0005014 43.717024 0 45.217682 199.49297
50 0.99569204 43.716832 0 45.210276 197.52311
100 0.99430734 43.714806 0 45.206174 197.74323
Loop time of 12.1636 on 1 procs for 100 steps with 16000 atoms
Performance: 7103.169 tau/day, 8.221 timesteps/s, 131.540 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.931 | 10.931 | 10.931 | 0.0 | 89.87
Neigh | 1.0581 | 1.0581 | 1.0581 | 0.0 | 8.70
Comm | 0.071199 | 0.071199 | 0.071199 | 0.0 | 0.59
Output | 0.00016157 | 0.00016157 | 0.00016157 | 0.0 | 0.00
Modify | 0.088319 | 0.088319 | 0.088319 | 0.0 | 0.73
Other | | 0.01448 | | | 0.12
Nlocal: 16000 ave 16000 max 16000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14065 ave 14065 max 14065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 749621 ave 749621 max 749621 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 749621
Ave neighs/atom = 46.851312
Neighbor list builds = 36
Dangerous builds = 0
Total wall time: 0:01:12

171
examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.4 Normal file
View File

@ -0,0 +1,171 @@
LAMMPS (28 Mar 2023 - Development)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
########################################################################
### Pure diffusion with a reaction source term analog of a periodic ###
### Poiseuille flow problem using transport DPD (tDPD) simulation ###
### ###
### Created : Zhen Li (zhen_li@brown.edu) ###
### Division of Applied Mathematics, Brown University. ###
### ###
### tDPD system setup follows Fig.1 in the publication: ###
### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
### "Transport dissipative particle dynamics model for mesoscopic ###
### advection-diffusion-reaction problems. J. Chem. Phys., ###
### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
########################################################################
units lj
dimension 3
boundary p p p
neighbor 0.2 bin
neigh_modify every 1 delay 0 check yes
atom_style tdpd 2
comm_modify vel yes
region tdpd block -10 10 -10 10 -5 5 units box
create_box 1 tdpd
Created orthogonal box = (-10 -10 -5) to (10 10 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 random 16000 276438 NULL
Created 16000 atoms
using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5)
create_atoms CPU = 0.002 seconds
mass 1 1.0
set atom * cc 1 1.0
Setting atom values ...
16000 settings made for cc index 1
set atom * cc 2 1.0
Setting atom values ...
16000 settings made for cc index 2
pair_style tdpd 1.0 1.58 9872598
pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
compute mythermo all temp
thermo 50
thermo_modify temp mythermo
thermo_modify flush yes
velocity all create 1.0 432982 loop local dist gaussian
fix mvv all mvv/tdpd 0.5
fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
timestep 0.01
run 500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair tdpd command: doi:10.1063/1.4923254
@Article{ZLi2015_JCP,
author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.},
title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems},
journal = {The Journal of Chemical Physics},
year = {2015},
volume = {143},
number = {1},
pages = {014101}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 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 = 1.78
ghost atom cutoff = 1.78
binsize = 0.89, bins = 23 23 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tdpd, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.337 | 5.351 | 5.36 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1 48.942039 0 50.441946 199.59508
50 1.0164166 43.95706 0 45.48159 198.02944
100 0.99583217 43.760777 0 45.254431 198.26943
150 1.0025022 43.730114 0 45.233774 198.402
200 0.99563635 43.72379 0 45.217151 197.6948
250 1.0117752 43.724349 0 45.241917 195.70427
300 0.98950567 43.72333 0 45.207496 197.582
350 0.99351667 43.719413 0 45.209595 194.69504
400 1.0050663 43.715857 0 45.223362 198.50199
450 1.003148 43.712337 0 45.216965 196.26462
500 0.99888463 43.712357 0 45.21059 195.78645
Loop time of 16.464 on 4 procs for 500 steps with 16000 atoms
Performance: 26239.140 tau/day, 30.369 timesteps/s, 485.910 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.166 | 14.302 | 14.373 | 2.1 | 86.87
Neigh | 1.406 | 1.4132 | 1.4179 | 0.4 | 8.58
Comm | 0.53805 | 0.61257 | 0.75493 | 10.7 | 3.72
Output | 0.00041375 | 0.00062178 | 0.00091415 | 0.0 | 0.00
Modify | 0.088249 | 0.089209 | 0.090198 | 0.2 | 0.54
Other | | 0.04683 | | | 0.28
Nlocal: 4000 ave 4013 max 3992 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 5990 ave 6012 max 5980 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 187350 ave 188412 max 186633 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 749401
Ave neighs/atom = 46.837562
Neighbor list builds = 182
Dangerous builds = 0
reset_timestep 0
compute cc1 all tdpd/cc/atom 1
compute cc2 all tdpd/cc/atom 2
compute bin all chunk/atom bin/1d y 0.0 1.0
fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.588 | 5.602 | 5.61 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.99888463 43.712357 0 45.21059 197.42728
50 1.0015386 43.71567 0 45.217884 198.28372
100 1.0053363 43.718221 0 45.226131 195.45072
Loop time of 3.09095 on 4 procs for 100 steps with 16000 atoms
Performance: 27952.588 tau/day, 32.353 timesteps/s, 517.641 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6867 | 2.6999 | 2.7131 | 0.8 | 87.35
Neigh | 0.2523 | 0.25332 | 0.25501 | 0.2 | 8.20
Comm | 0.087738 | 0.10048 | 0.11401 | 4.0 | 3.25
Output | 0.00014184 | 0.00015461 | 0.00015946 | 0.0 | 0.01
Modify | 0.028066 | 0.028154 | 0.02831 | 0.1 | 0.91
Other | | 0.008906 | | | 0.29
Nlocal: 4000 ave 4024 max 3988 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 5977 ave 6004 max 5941 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 187313 ave 188798 max 186723 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 749253
Ave neighs/atom = 46.828313
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:19

94
src/DPD-MESO/fix_edpd_source.cpp
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@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -15,7 +14,9 @@
#include "fix_edpd_source.h" #include "fix_edpd_source.h"
#include "atom.h" #include "atom.h"
#include "domain.h"
#include "error.h" #include "error.h"
#include "region.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -23,40 +24,53 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
enum { SPHERE, CUBOID, REGION };
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixEDPDSource::FixEDPDSource(LAMMPS *lmp, int narg, char **arg) : FixEDPDSource::FixEDPDSource(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) Fix(lmp, narg, arg), idregion(nullptr), region(nullptr)
{ {
if (strcmp(style,"edpd/source") != 0 && narg < 4) if (narg < 4) utils::missing_cmd_args(FLERR, "fix edpd/source", error);
error->all(FLERR,"Illegal fix edpd/source command");
int iarg = 3; int iarg = 3;
if (strcmp(arg[iarg], "sphere") == 0) {
option = SPHERE;
if (narg != 9) error->all(FLERR, "Illegal fix edpd/source command (4 args for sphere)");
++iarg;
center[0] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[1] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[2] = utils::numeric(FLERR, arg[iarg++], false, lmp);
radius = utils::numeric(FLERR, arg[iarg++], false, lmp);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else if (strcmp(arg[iarg], "cuboid") == 0) {
option = CUBOID;
if (narg != 11) error->all(FLERR, "Illegal fix edpd/source command (6 args for cuboid)");
++iarg;
center[0] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[1] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[2] = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLx = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLy = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLz = utils::numeric(FLERR, arg[iarg++], false, lmp);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else if (strcmp(arg[iarg], "region") == 0) {
option = REGION;
if (narg != 6) error->all(FLERR, "Illegal fix edpd/source command (2 args for region)");
++iarg;
if (!domain->get_region_by_id(arg[iarg]))
error->all(FLERR, "Region {} for fix edpd/source does not exist", arg[iarg]);
idregion = utils::strdup(arg[iarg++]);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else
error->all(FLERR, "Illegal fix edpd/source command option {}", arg[iarg]);
}
if (strcmp(arg[iarg],"sphere") == 0) option = 0; /* ---------------------------------------------------------------------- */
else if (strcmp(arg[iarg],"cuboid") == 0) option = 1;
else error->all(FLERR,"Illegal fix edpd/source command");
iarg++;
if (option == 0) { FixEDPDSource::~FixEDPDSource()
if (narg != 9 ) error->all(FLERR,"Illegal fix edpd/source command (5 args for sphere)"); {
center[0] = utils::numeric(FLERR,arg[iarg++],false,lmp); delete[] idregion;
center[1] = utils::numeric(FLERR,arg[iarg++],false,lmp);
center[2] = utils::numeric(FLERR,arg[iarg++],false,lmp);
radius = utils::numeric(FLERR,arg[iarg++],false,lmp);
value = utils::numeric(FLERR,arg[iarg++],false,lmp);
}
else if (option == 1) {
if (narg != 11 ) error->all(FLERR,"Illegal fix edpd/edpd command (7 args for cuboid)");
center[0] = utils::numeric(FLERR,arg[iarg++],false,lmp);
center[1] = utils::numeric(FLERR,arg[iarg++],false,lmp);
center[2] = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLx = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLy = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLz = utils::numeric(FLERR,arg[iarg++],false,lmp);
value = utils::numeric(FLERR,arg[iarg++],false,lmp);
}
else error->all(FLERR,"Illegal fix edpd/source command");
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -72,6 +86,12 @@ int FixEDPDSource::setmask()
void FixEDPDSource::init() void FixEDPDSource::init()
{ {
// set index and check validity of region
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix edpd/source does not exist", idregion);
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -85,24 +105,26 @@ void FixEDPDSource::post_force(int /*vflag*/)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double drx, dry, drz, rsq; double drx, dry, drz, rsq;
double radius_sq = radius*radius*radius; double radius_sq = radius * radius * radius;
if (region) region->prematch();
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (option == 0) { if (option == SPHERE) {
drx = x[i][0] - center[0]; drx = x[i][0] - center[0];
dry = x[i][1] - center[1]; dry = x[i][1] - center[1];
drz = x[i][2] - center[2]; drz = x[i][2] - center[2];
rsq = drx*drx + dry*dry + drz*drz; rsq = drx * drx + dry * dry + drz * drz;
if (rsq < radius_sq) if (rsq < radius_sq) edpd_flux[i] += value * edpd_cv[i];
edpd_flux[i] += value*edpd_cv[i]; } else if (option == CUBOID) {
}
else if (option == 1) {
drx = x[i][0] - center[0]; drx = x[i][0] - center[0];
dry = x[i][1] - center[1]; dry = x[i][1] - center[1];
drz = x[i][2] - center[2]; drz = x[i][2] - center[2];
if (fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz) if (fabs(drx) <= 0.5 * dLx && fabs(dry) <= 0.5 * dLy && fabs(drz) <= 0.5 * dLz)
edpd_flux[i] += value*edpd_cv[i]; edpd_flux[i] += value * edpd_cv[i];
} else if (option == REGION) {
if (region->match(x[i][0], x[i][1], x[i][2])) edpd_flux[i] += value * edpd_cv[i];
} }
} }
} }

3
src/DPD-MESO/fix_edpd_source.h
View File

@ -27,12 +27,15 @@ namespace LAMMPS_NS {
class FixEDPDSource : public Fix { class FixEDPDSource : public Fix {
public: public:
FixEDPDSource(class LAMMPS *, int, char **); FixEDPDSource(class LAMMPS *, int, char **);
~FixEDPDSource() override;
int setmask() override; int setmask() override;
void init() override; void init() override;
void post_force(int) override; void post_force(int) override;
protected: protected:
int option; int option;
char *idregion;
class Region *region;
double center[3], radius, dLx, dLy, dLz; double center[3], radius, dLx, dLy, dLz;
double value; double value;
}; };

97
src/DPD-MESO/fix_tdpd_source.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories https://www.lammps.org/, Sandia National Laboratories
@ -15,7 +14,9 @@
#include "fix_tdpd_source.h" #include "fix_tdpd_source.h"
#include "atom.h" #include "atom.h"
#include "domain.h"
#include "error.h" #include "error.h"
#include "region.h"
#include <cmath> #include <cmath>
#include <cstring> #include <cstring>
@ -23,41 +24,55 @@
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
using namespace FixConst; using namespace FixConst;
enum { SPHERE, CUBOID, REGION };
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
FixTDPDSource::FixTDPDSource(LAMMPS *lmp, int narg, char **arg) : FixTDPDSource::FixTDPDSource(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) Fix(lmp, narg, arg), idregion(nullptr), region(nullptr)
{ {
if (strcmp(style,"tdpd/source") != 0 && narg < 4) if (narg < 4) utils::missing_cmd_args(FLERR, "fix tdpd/source", error);
error->all(FLERR,"Illegal fix tdpd/source command");
int iarg = 3; int iarg = 3;
cc_index = utils::inumeric(FLERR,arg[iarg++],false,lmp); cc_index = utils::inumeric(FLERR, arg[iarg++], false, lmp);
if (strcmp(arg[iarg],"sphere") == 0) option = 0; if (strcmp(arg[iarg], "sphere") == 0) {
else if (strcmp(arg[iarg],"cuboid") == 0) option = 1; option = SPHERE;
else error->all(FLERR,"Illegal fix tdpd/source command"); if (narg != 10) error->all(FLERR, "Illegal fix tdpd/source command (5 args for sphere)");
iarg++; ++iarg;
center[0] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[1] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[2] = utils::numeric(FLERR, arg[iarg++], false, lmp);
radius = utils::numeric(FLERR, arg[iarg++], false, lmp);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else if (strcmp(arg[iarg], "cuboid") == 0) {
option = CUBOID;
if (narg != 12) error->all(FLERR, "Illegal fix tdpd/source command (7 args for cuboid)");
++iarg;
center[0] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[1] = utils::numeric(FLERR, arg[iarg++], false, lmp);
center[2] = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLx = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLy = utils::numeric(FLERR, arg[iarg++], false, lmp);
dLz = utils::numeric(FLERR, arg[iarg++], false, lmp);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else if (strcmp(arg[iarg], "region") == 0) {
option = REGION;
if (narg != 7) error->all(FLERR, "Illegal fix tdpd/source command (2 args for region)");
++iarg;
if (!domain->get_region_by_id(arg[iarg]))
error->all(FLERR, "Region {} for fix tdpd/source does not exist", arg[iarg]);
idregion = utils::strdup(arg[iarg++]);
value = utils::numeric(FLERR, arg[iarg++], false, lmp);
} else
error->all(FLERR, "Illegal fix tdpd/source command option {}", arg[iarg]);
}
if (option == 0) { /* ---------------------------------------------------------------------- */
if (narg != 10 ) error->all(FLERR,"Illegal fix tdpd/source command (5 args for sphere)");
center[0] = utils::numeric(FLERR,arg[iarg++],false,lmp); FixTDPDSource::~FixTDPDSource()
center[1] = utils::numeric(FLERR,arg[iarg++],false,lmp); {
center[2] = utils::numeric(FLERR,arg[iarg++],false,lmp); delete[] idregion;
radius = utils::numeric(FLERR,arg[iarg++],false,lmp);
value = utils::numeric(FLERR,arg[iarg++],false,lmp);
}
else if (option == 1) {
if (narg != 12 ) error->all(FLERR,"Illegal fix tdpd/edpd command (7 args for cuboid)");
center[0] = utils::numeric(FLERR,arg[iarg++],false,lmp);
center[1] = utils::numeric(FLERR,arg[iarg++],false,lmp);
center[2] = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLx = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLy = utils::numeric(FLERR,arg[iarg++],false,lmp);
dLz = utils::numeric(FLERR,arg[iarg++],false,lmp);
value = utils::numeric(FLERR,arg[iarg++],false,lmp);
}
else error->all(FLERR,"Illegal fix tdpd/source command");
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -73,6 +88,12 @@ int FixTDPDSource::setmask()
void FixTDPDSource::init() void FixTDPDSource::init()
{ {
// set index and check validity of region
if (idregion) {
region = domain->get_region_by_id(idregion);
if (!region) error->all(FLERR, "Region {} for fix tdpd/source does not exist", idregion);
}
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -85,24 +106,26 @@ void FixTDPDSource::post_force(int /*vflag*/)
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
double drx, dry, drz, rsq; double drx, dry, drz, rsq;
double radius_sq = radius*radius*radius; double radius_sq = radius * radius * radius;
if (region) region->prematch();
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (option == 0) { if (option == SPHERE) {
drx = x[i][0] - center[0]; drx = x[i][0] - center[0];
dry = x[i][1] - center[1]; dry = x[i][1] - center[1];
drz = x[i][2] - center[2]; drz = x[i][2] - center[2];
rsq = drx*drx + dry*dry + drz*drz; rsq = drx * drx + dry * dry + drz * drz;
if (rsq < radius_sq) if (rsq < radius_sq) cc_flux[i][cc_index - 1] += value;
cc_flux[i][cc_index-1] += value; } else if (option == CUBOID) {
}
else if (option == 1) {
drx = x[i][0] - center[0]; drx = x[i][0] - center[0];
dry = x[i][1] - center[1]; dry = x[i][1] - center[1];
drz = x[i][2] - center[2]; drz = x[i][2] - center[2];
if (fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz) if (fabs(drx) <= 0.5 * dLx && fabs(dry) <= 0.5 * dLy && fabs(drz) <= 0.5 * dLz)
cc_flux[i][cc_index-1] += value; cc_flux[i][cc_index - 1] += value;
} else if (option == REGION) {
if (region->match(x[i][0], x[i][1], x[i][2])) cc_flux[i][cc_index - 1] += value;
} }
} }
} }

5
src/DPD-MESO/fix_tdpd_source.h
View File

@ -27,6 +27,7 @@ namespace LAMMPS_NS {
class FixTDPDSource : public Fix { class FixTDPDSource : public Fix {
public: public:
FixTDPDSource(class LAMMPS *, int, char **); FixTDPDSource(class LAMMPS *, int, char **);
~FixTDPDSource() override;
int setmask() override; int setmask() override;
void init() override; void init() override;
void post_force(int) override; void post_force(int) override;
@ -34,11 +35,11 @@ class FixTDPDSource : public Fix {
protected: protected:
int option; int option;
int cc_index; int cc_index;
char *idregion;
class Region *region;
double center[3], radius, dLx, dLy, dLz; double center[3], radius, dLx, dLy, dLz;
double value; double value;
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS
#endif #endif
#endif #endif