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msvbd
2021-04-23 15:49:11 +02:00
parent 62f7e97316
commit 2e63d126e3
16 changed files with 72 additions and 80 deletions
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0
examples/USER/dpdext/README → examples/USER/misc/dpd_ext/README
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0
examples/USER/dpdext/dpdext/dpdext.data → examples/USER/misc/dpd_ext/dpdext/dpdext.data
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2
examples/USER/dpdext/dpdext/in.dpdext → examples/USER/misc/dpd_ext/dpdext/in.dpdext
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@ -23,7 +23,7 @@ mass 1 1.0
mass 2 2.0
###
pair_style dpdext ${T} ${rc} 3854262
pair_style dpd/ext ${T} ${rc} 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}

28
examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 → examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1
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@ -1,4 +1,4 @@
LAMMPS (10 Mar 2021)
LAMMPS (8 Apr 2021)
# DPD Fluid
variable T equal 1.0
@ -34,9 +34,9 @@ mass 1 1.0
mass 2 2.0
###
pair_style dpdext ${T} ${rc} 3854262
pair_style dpdext 1 ${rc} 3854262
pair_style dpdext 1 1 3854262
pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpd/ext 1 ${rc} 3854262
pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
@ -61,7 +61,7 @@ Neighbor list info ...
ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpdext, perpetual
(1) pair dpd/ext, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
@ -169,20 +169,20 @@ Step Time Temp Press
49000 490 1.0337198 7.5777833
49500 495 0.94052507 7.3661443
50000 500 0.98527818 7.1746325
Loop time of 10.2559 on 1 procs for 50000 steps with 200 atoms
Loop time of 9.88248 on 1 procs for 50000 steps with 200 atoms
Performance: 4212216.548 tau/day, 4875.251 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 4371371.882 tau/day, 5059.458 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 | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65
Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11
Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01
Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02
Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82
Other | | 0.03957 | | | 0.39
Pair | 8.7028 | 8.7028 | 8.7028 | 0.0 | 88.06
Neigh | 0.73687 | 0.73687 | 0.73687 | 0.0 | 7.46
Comm | 0.31881 | 0.31881 | 0.31881 | 0.0 | 3.23
Output | 0.0013947 | 0.0013947 | 0.0013947 | 0.0 | 0.01
Modify | 0.081394 | 0.081394 | 0.081394 | 0.0 | 0.82
Other | | 0.04118 | | | 0.42
Nlocal: 200.000 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0

30
examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 → examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4
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@ -1,4 +1,4 @@
LAMMPS (10 Mar 2021)
LAMMPS (8 Apr 2021)
# DPD Fluid
variable T equal 1.0
@ -34,9 +34,9 @@ mass 1 1.0
mass 2 2.0
###
pair_style dpdext ${T} ${rc} 3854262
pair_style dpdext 1 ${rc} 3854262
pair_style dpdext 1 1 3854262
pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpd/ext 1 ${rc} 3854262
pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD}
pair_coeff 1 2 25.1 4.51 4.54 0.51 0.54 1.21 #${rcD}
@ -61,7 +61,7 @@ Neighbor list info ...
ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpdext, perpetual
(1) pair dpd/ext, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
@ -169,20 +169,20 @@ Step Time Temp Press
49000 490 0.9759139 7.4839858
49500 495 0.91538068 7.1780491
50000 500 1.0310634 7.1522794
Loop time of 9.14414 on 4 procs for 50000 steps with 200 atoms
Loop time of 8.5908 on 4 procs for 50000 steps with 200 atoms
Performance: 4724338.550 tau/day, 5467.984 timesteps/s
96.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 5028633.375 tau/day, 5820.178 timesteps/s
95.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00
Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47
Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89
Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03
Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75
Other | | 0.07762 | | | 0.85
Pair | 4.9505 | 5.054 | 5.1885 | 4.1 | 58.83
Neigh | 0.47025 | 0.47603 | 0.47954 | 0.5 | 5.54
Comm | 2.7876 | 2.9237 | 3.0336 | 5.5 | 34.03
Output | 0.0024114 | 0.0029766 | 0.0046443 | 1.8 | 0.03
Modify | 0.062911 | 0.064188 | 0.065603 | 0.4 | 0.75
Other | | 0.06992 | | | 0.81
Nlocal: 50.0000 ave 53 max 46 min
Histogram: 1 0 0 0 1 0 0 0 1 1
@ -198,4 +198,4 @@ Dangerous builds = 5000
write_data final.data pair ij
System init for write_data ...
Total wall time: 0:00:09
Total wall time: 0:00:08

0
examples/USER/dpdext/dpdext_tstat/cg_spce.data → examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data
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0
examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot → examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot
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4
examples/USER/dpdext/dpdext_tstat/in.cg_spce → examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce
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@ -13,10 +13,10 @@ comm_modify vel yes
read_data cg_spce.data
pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD}
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
timestep 1.0
run_style verlet

38
examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 → examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1
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@ -1,4 +1,4 @@
LAMMPS (10 Mar 2021)
LAMMPS (8 Apr 2021)
# Coarse-Grained SPC/E Water
variable T equal 300.0
@ -18,19 +18,19 @@ Reading data file ...
1 by 1 by 1 MPI processor grid
reading atoms ...
2180 atoms
read_data CPU = 0.037 seconds
read_data CPU = 0.020 seconds
pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:461)
pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD}
pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
timestep 1.0
run_style verlet
@ -56,7 +56,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair dpdext/tstat, perpetual, copy from (1)
(2) pair dpd/ext/tstat, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
@ -264,20 +264,20 @@ Step Time Temp Press
1980 1980 299.14574 5166.3501
1990 1990 300.07254 10019.769
2000 2000 301.78176 8789.7968
Loop time of 79.8698 on 1 procs for 2000 steps with 2180 atoms
Loop time of 91.2059 on 1 procs for 2000 steps with 2180 atoms
Performance: 2.164 ns/day, 11.093 hours/ns, 25.041 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38
Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28
Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22
Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01
Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06
Other | | 0.03671 | | | 0.05
Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41
Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25
Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23
Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01
Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06
Other | | 0.03904 | | | 0.04
Nlocal: 2180.00 ave 2180 max 2180 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -290,4 +290,4 @@ Total # of neighbors = 261496
Ave neighs/atom = 119.95229
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:01:20
Total wall time: 0:01:31

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examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 → examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4
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@ -1,4 +1,4 @@
LAMMPS (10 Mar 2021)
LAMMPS (8 Apr 2021)
# Coarse-Grained SPC/E Water
variable T equal 300.0
@ -18,19 +18,19 @@ Reading data file ...
1 by 2 by 2 MPI processor grid
reading atoms ...
2180 atoms
read_data CPU = 0.012 seconds
read_data CPU = 0.005 seconds
pair_style hybrid/overlay table linear 1000 dpdext/tstat ${T} ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpdext/tstat 300 300 9 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat ${T} ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 ${T} ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 ${rc} 385262
pair_style hybrid/overlay table linear 1000 dpd/ext/tstat 300 300 9 385262
pair_coeff 1 1 table cg_spce_table.pot VOTCA ${rc}
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9
WARNING: 16 of 351 force values in table VOTCA are inconsistent with -dE/dr.
Should only be flagged at inflection points (../pair_table.cpp:461)
pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 ${rcD}
pair_coeff 1 1 dpdext/tstat 20.0 10.0 0.5 0.5 10
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 ${rcD}
pair_coeff 1 1 dpd/ext/tstat 20.0 10.0 0.5 0.5 10
timestep 1.0
run_style verlet
@ -56,7 +56,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
(2) pair dpdext/tstat, perpetual, copy from (1)
(2) pair dpd/ext/tstat, perpetual, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
@ -264,20 +264,20 @@ Step Time Temp Press
1980 1980 297.94119 5615.6403
1990 1990 298.37687 9727.308
2000 2000 296.08394 6400.2746
Loop time of 40.5503 on 4 procs for 2000 steps with 2180 atoms
Loop time of 41.5171 on 4 procs for 2000 steps with 2180 atoms
Performance: 4.261 ns/day, 5.632 hours/ns, 49.321 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77
Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27
Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76
Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02
Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06
Other | | 0.05032 | | | 0.12
Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83
Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27
Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70
Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02
Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06
Other | | 0.05335 | | | 0.13
Nlocal: 545.000 ave 559 max 531 min
Histogram: 1 0 0 0 1 1 0 0 0 1
@ -290,4 +290,4 @@ Total # of neighbors = 261662
Ave neighs/atom = 120.02844
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:40
Total wall time: 0:00:41

10
src/USER-DPDEXT/README
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@ -1,10 +0,0 @@
Martin Svoboda (ICPF, UJEP) - svobod.martin@gmail.com
Karel Sindelka (ICPF) - sindelka@icpf.cas.cz
Martin Lisal (ICPF, UJEP) - lisal@icpf.cas.cz
This package implements a generalised force field for dissipative
particle dynamics (DPD). The extension divides contributions
of dissipative and random forces to parrallel and perpendicular parts.
See the doc pages for "pair_style dpdext" and "pair_style dpdext/tstat".
There are example scripts for using this package in examples/USER/dpdext.

2
src/USER-MISC/README
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@ -90,6 +90,8 @@ pair_style coul/slater/long, Evangelos Voyiatzis, evoyiatzis at gmail.com, 26 Fe
pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
pair_style e3b, Steven Strong (U Chicago), stevene.strong at gmail dot com, 16 Apr 19
pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19
pair_style dpd/ext, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP, svobod.martin at gmail dot com, 23 Apr 21
pair_style dpd/ext/tstat, Martin Svoboda, Karel Sindelka, Martin Lisal, ICPF and UJEP , svobod.martin at gmail dot com, 23 Apr 21
pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11

0
src/USER-DPDEXT/pair_dpd_ext.cpp → src/USER-MISC/pair_dpd_ext.cpp
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src/USER-DPDEXT/pair_dpd_ext.h → src/USER-MISC/pair_dpd_ext.h
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0
src/USER-DPDEXT/pair_dpd_ext_tstat.cpp → src/USER-MISC/pair_dpd_ext_tstat.cpp
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src/USER-DPDEXT/pair_dpd_ext_tstat.h → src/USER-MISC/pair_dpd_ext_tstat.h
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