diff --git a/doc/src/fix_dpd_source.rst b/doc/src/fix_dpd_source.rst index ef1a70c3d4..61c328eb42 100644 --- a/doc/src/fix_dpd_source.rst +++ b/doc/src/fix_dpd_source.rst @@ -18,18 +18,21 @@ Syntax * ID, group-ID are documented in :doc:`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) -* keyword = *sphere* or *cuboid* +* keyword = *sphere* or *cuboid* or *region* .. 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) radius = radius of a spherical domain (distance units) source = heat source or concentration source (flux units, see below) - *cuboid* values = cx,cy,cz,dLx,dLy,dLz,source - cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units) + *cuboid* values = cx cy cz dLx dLy dLz source + 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) 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 """""""" @@ -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 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 1 region lower -0.01 Description """"""""""" @@ -57,37 +61,45 @@ heat conduction with a source term (see Fig.12 in :ref:`(Li2014) `) or diffusion with a source term (see Fig.1 in :ref:`(Li2015) `), as an analog of a periodic Poiseuille flow problem. -If the *sphere* keyword is used, the *cx,cy,cz,radius* defines a -spherical domain to apply the source flux to. +If the *sphere* keyword is used, the *cx, cy, cz, radius* values define +a spherical domain to apply the source flux to. -If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a -cuboid domain to apply the source flux to. +If the *cuboid* keyword is used, the *cx, cy, cz, dLx, dLy, dLz* define +a cuboid domain to apply the source flux to. + +If the *region* keyword is used, the *region-ID* selects which +:doc:`region ` to apply the source flux to. ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various :doc:`output commands `. -No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +No information of these fixes is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to these fixes. No global or per-atom quantities are stored by +these fixes for access by various :doc:`output commands `. +No parameter of these fixes can be used with the *start/stop* keywords +of the :doc:`run ` command. These fixes are not invoked during +:doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +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 +` page for more info. -Fix *edpd/source* must be used with the :doc:`pair_style edpd ` command. Fix *tdpd/source* must be used with the +Fix *edpd/source* must be used with the :doc:`pair_style edpd +` command. Fix *tdpd/source* must be used with the :doc:`pair_style tdpd ` command. Related commands """""""""""""""" :doc:`pair_style edpd `, :doc:`pair_style tdpd `, -:doc:`compute edpd/temp/atom `, :doc:`compute tdpd/cc/atom ` +:doc:`compute edpd/temp/atom `, +:doc:`compute tdpd/cc/atom ` Default """"""" diff --git a/examples/PACKAGES/dpd-meso/edpd/in.edpd b/examples/PACKAGES/dpd-meso/edpd/in.edpd index af1a79d73d..bea1beac73 100644 --- a/examples/PACKAGES/dpd-meso/edpd/in.edpd +++ b/examples/PACKAGES/dpd-meso/edpd/in.edpd @@ -11,13 +11,14 @@ ### 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 +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin 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 create_box 1 edpd diff --git a/examples/PACKAGES/dpd-meso/edpd/in.edpd-region b/examples/PACKAGES/dpd-meso/edpd/in.edpd-region new file mode 100644 index 0000000000..f12487ca02 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/in.edpd-region @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1 b/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1 deleted file mode 100644 index af975f877c..0000000000 --- a/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.1 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4 b/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4 deleted file mode 100644 index 21206d38c6..0000000000 --- a/examples/PACKAGES/dpd-meso/edpd/log.16Aug17.edpd.g++.4 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.1 b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.1 new file mode 100644 index 0000000000..2bf88da208 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.4 b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.4 new file mode 100644 index 0000000000..41be7a7840 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd-region.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.1 b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.1 new file mode 100644 index 0000000000..0c6b9a6cd7 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.4 b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.4 new file mode 100644 index 0000000000..6897e5755f --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/log.21Apr23.edpd.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.1 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.1 new file mode 100644 index 0000000000..fb9f4996f6 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.4 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.4 new file mode 100644 index 0000000000..70178560f6 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd-region.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.1 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.1 new file mode 100644 index 0000000000..fb9f4996f6 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.4 b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.4 new file mode 100644 index 0000000000..70178560f6 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/edpd/temp.profile.21Apr23.edpd.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 deleted file mode 100644 index a872600504..0000000000 --- a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.1 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 deleted file mode 100644 index de34ef26c3..0000000000 --- a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.16Aug17.tdpd.g++.4 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.1 new file mode 100644 index 0000000000..ff47d3664b --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.4 new file mode 100644 index 0000000000..6f91e8d37e --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd-region.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.1 new file mode 100644 index 0000000000..ff47d3664b --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.4 new file mode 100644 index 0000000000..6f91e8d37e --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/cc.profile.21Apr23.tdpd.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/in.tdpd b/examples/PACKAGES/dpd-meso/tdpd/in.tdpd index 5107e7a454..6ebe366e12 100644 --- a/examples/PACKAGES/dpd-meso/tdpd/in.tdpd +++ b/examples/PACKAGES/dpd-meso/tdpd/in.tdpd @@ -11,13 +11,14 @@ ### 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 +units lj +dimension 3 +boundary p p p +neighbor 0.2 bin 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 create_box 1 tdpd diff --git a/examples/PACKAGES/dpd-meso/tdpd/in.tdpd-region b/examples/PACKAGES/dpd-meso/tdpd/in.tdpd-region new file mode 100644 index 0000000000..a735ae7fe9 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/in.tdpd-region @@ -0,0 +1,58 @@ +######################################################################## +### 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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1 deleted file mode 100644 index 21b618148c..0000000000 --- a/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.1 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.4 deleted file mode 100644 index 6cd99168f4..0000000000 --- a/examples/PACKAGES/dpd-meso/tdpd/log.16Aug17.tdpd.g++.4 +++ /dev/null @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.1 new file mode 100644 index 0000000000..bb5278b93b --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.4 new file mode 100644 index 0000000000..a0badc6442 --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd-region.g++.4 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.1 b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.1 new file mode 100644 index 0000000000..c9f919bdde --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.1 @@ -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 diff --git a/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.4 b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.4 new file mode 100644 index 0000000000..afa63967fb --- /dev/null +++ b/examples/PACKAGES/dpd-meso/tdpd/log.21Apr23.tdpd.g++.4 @@ -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 diff --git a/src/DPD-MESO/fix_edpd_source.cpp b/src/DPD-MESO/fix_edpd_source.cpp index cd54521ce2..2e3358bf48 100644 --- a/src/DPD-MESO/fix_edpd_source.cpp +++ b/src/DPD-MESO/fix_edpd_source.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,7 +14,9 @@ #include "fix_edpd_source.h" #include "atom.h" +#include "domain.h" #include "error.h" +#include "region.h" #include #include @@ -23,40 +24,53 @@ using namespace LAMMPS_NS; using namespace FixConst; +enum { SPHERE, CUBOID, REGION }; + /* ---------------------------------------------------------------------- */ 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) - error->all(FLERR,"Illegal fix edpd/source command"); + if (narg < 4) utils::missing_cmd_args(FLERR, "fix edpd/source", error); 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) { - if (narg != 9 ) error->all(FLERR,"Illegal fix edpd/source command (5 args for sphere)"); - 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 (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"); +FixEDPDSource::~FixEDPDSource() +{ + delete[] idregion; } /* ---------------------------------------------------------------------- */ @@ -72,6 +86,12 @@ int FixEDPDSource::setmask() 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; 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++) { if (mask[i] & groupbit) { - if (option == 0) { + if (option == SPHERE) { drx = x[i][0] - center[0]; dry = x[i][1] - center[1]; drz = x[i][2] - center[2]; - rsq = drx*drx + dry*dry + drz*drz; - if (rsq < radius_sq) - edpd_flux[i] += value*edpd_cv[i]; - } - else if (option == 1) { + rsq = drx * drx + dry * dry + drz * drz; + if (rsq < radius_sq) edpd_flux[i] += value * edpd_cv[i]; + } else if (option == CUBOID) { drx = x[i][0] - center[0]; dry = x[i][1] - center[1]; drz = x[i][2] - center[2]; - if (fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz) - edpd_flux[i] += value*edpd_cv[i]; + if (fabs(drx) <= 0.5 * dLx && fabs(dry) <= 0.5 * dLy && fabs(drz) <= 0.5 * dLz) + 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]; } } } diff --git a/src/DPD-MESO/fix_edpd_source.h b/src/DPD-MESO/fix_edpd_source.h index 6fd3566319..a7ae583951 100644 --- a/src/DPD-MESO/fix_edpd_source.h +++ b/src/DPD-MESO/fix_edpd_source.h @@ -27,12 +27,15 @@ namespace LAMMPS_NS { class FixEDPDSource : public Fix { public: FixEDPDSource(class LAMMPS *, int, char **); + ~FixEDPDSource() override; int setmask() override; void init() override; void post_force(int) override; protected: int option; + char *idregion; + class Region *region; double center[3], radius, dLx, dLy, dLz; double value; }; diff --git a/src/DPD-MESO/fix_tdpd_source.cpp b/src/DPD-MESO/fix_tdpd_source.cpp index 053d96568b..c5856b5b8c 100644 --- a/src/DPD-MESO/fix_tdpd_source.cpp +++ b/src/DPD-MESO/fix_tdpd_source.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -15,7 +14,9 @@ #include "fix_tdpd_source.h" #include "atom.h" +#include "domain.h" #include "error.h" +#include "region.h" #include #include @@ -23,41 +24,55 @@ using namespace LAMMPS_NS; using namespace FixConst; +enum { SPHERE, CUBOID, REGION }; + /* ---------------------------------------------------------------------- */ 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) - error->all(FLERR,"Illegal fix tdpd/source command"); + if (narg < 4) utils::missing_cmd_args(FLERR, "fix tdpd/source", error); 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; - else if (strcmp(arg[iarg],"cuboid") == 0) option = 1; - else error->all(FLERR,"Illegal fix tdpd/source command"); - iarg++; + if (strcmp(arg[iarg], "sphere") == 0) { + option = SPHERE; + if (narg != 10) error->all(FLERR, "Illegal fix tdpd/source command (5 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 != 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); - 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 != 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"); +/* ---------------------------------------------------------------------- */ + +FixTDPDSource::~FixTDPDSource() +{ + delete[] idregion; } /* ---------------------------------------------------------------------- */ @@ -73,6 +88,12 @@ int FixTDPDSource::setmask() 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; 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++) { if (mask[i] & groupbit) { - if (option == 0) { + if (option == SPHERE) { drx = x[i][0] - center[0]; dry = x[i][1] - center[1]; drz = x[i][2] - center[2]; - rsq = drx*drx + dry*dry + drz*drz; - if (rsq < radius_sq) - cc_flux[i][cc_index-1] += value; - } - else if (option == 1) { + rsq = drx * drx + dry * dry + drz * drz; + if (rsq < radius_sq) cc_flux[i][cc_index - 1] += value; + } else if (option == CUBOID) { drx = x[i][0] - center[0]; dry = x[i][1] - center[1]; drz = x[i][2] - center[2]; - if (fabs(drx) <= 0.5*dLx && fabs(dry) <= 0.5*dLy && fabs(drz) <= 0.5*dLz) - cc_flux[i][cc_index-1] += value; + if (fabs(drx) <= 0.5 * dLx && fabs(dry) <= 0.5 * dLy && fabs(drz) <= 0.5 * dLz) + 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; } } } diff --git a/src/DPD-MESO/fix_tdpd_source.h b/src/DPD-MESO/fix_tdpd_source.h index d19c5bb2fc..ada8acad59 100644 --- a/src/DPD-MESO/fix_tdpd_source.h +++ b/src/DPD-MESO/fix_tdpd_source.h @@ -27,6 +27,7 @@ namespace LAMMPS_NS { class FixTDPDSource : public Fix { public: FixTDPDSource(class LAMMPS *, int, char **); + ~FixTDPDSource() override; int setmask() override; void init() override; void post_force(int) override; @@ -34,11 +35,11 @@ class FixTDPDSource : public Fix { protected: int option; int cc_index; + char *idregion; + class Region *region; double center[3], radius, dLx, dLy, dLz; double value; }; - } // namespace LAMMPS_NS - #endif #endif