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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 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 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} 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 # DPD Fluid
variable T equal 1.0 variable T equal 1.0
@ -34,9 +34,9 @@ mass 1 1.0
mass 2 2.0 mass 2 2.0
### ###
pair_style dpdext ${T} ${rc} 3854262 pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpdext 1 ${rc} 3854262 pair_style dpd/ext 1 ${rc} 3854262
pair_style dpdext 1 1 3854262 pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 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} 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 ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8 binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpdext, perpetual (1) pair dpd/ext, perpetual
attributes: half, newton on attributes: half, newton on
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
@ -169,20 +169,20 @@ Step Time Temp Press
49000 490 1.0337198 7.5777833 49000 490 1.0337198 7.5777833
49500 495 0.94052507 7.3661443 49500 495 0.94052507 7.3661443
50000 500 0.98527818 7.1746325 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 Performance: 4371371.882 tau/day, 5059.458 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads 99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 8.9888 | 8.9888 | 8.9888 | 0.0 | 87.65 Pair | 8.7028 | 8.7028 | 8.7028 | 0.0 | 88.06
Neigh | 0.832 | 0.832 | 0.832 | 0.0 | 8.11 Neigh | 0.73687 | 0.73687 | 0.73687 | 0.0 | 7.46
Comm | 0.30913 | 0.30913 | 0.30913 | 0.0 | 3.01 Comm | 0.31881 | 0.31881 | 0.31881 | 0.0 | 3.23
Output | 0.0021966 | 0.0021966 | 0.0021966 | 0.0 | 0.02 Output | 0.0013947 | 0.0013947 | 0.0013947 | 0.0 | 0.01
Modify | 0.084161 | 0.084161 | 0.084161 | 0.0 | 0.82 Modify | 0.081394 | 0.081394 | 0.081394 | 0.0 | 0.82
Other | | 0.03957 | | | 0.39 Other | | 0.04118 | | | 0.42
Nlocal: 200.000 ave 200 max 200 min Nlocal: 200.000 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0 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 # DPD Fluid
variable T equal 1.0 variable T equal 1.0
@ -34,9 +34,9 @@ mass 1 1.0
mass 2 2.0 mass 2 2.0
### ###
pair_style dpdext ${T} ${rc} 3854262 pair_style dpd/ext ${T} ${rc} 3854262
pair_style dpdext 1 ${rc} 3854262 pair_style dpd/ext 1 ${rc} 3854262
pair_style dpdext 1 1 3854262 pair_style dpd/ext 1 1 3854262
pair_coeff 1 1 25.0 4.5 4.53 0.5 0.53 1.2 #${rcD} pair_coeff 1 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} 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 ghost atom cutoff = 1.52
binsize = 0.76, bins = 8 8 8 binsize = 0.76, bins = 8 8 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0 1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpdext, perpetual (1) pair dpd/ext, perpetual
attributes: half, newton on attributes: half, newton on
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
@ -169,20 +169,20 @@ Step Time Temp Press
49000 490 0.9759139 7.4839858 49000 490 0.9759139 7.4839858
49500 495 0.91538068 7.1780491 49500 495 0.91538068 7.1780491
50000 500 1.0310634 7.1522794 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 Performance: 5028633.375 tau/day, 5820.178 timesteps/s
96.6% CPU use with 4 MPI tasks x no OpenMP threads 95.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 5.0824 | 5.212 | 5.3376 | 5.1 | 57.00 Pair | 4.9505 | 5.054 | 5.1885 | 4.1 | 58.83
Neigh | 0.49498 | 0.50029 | 0.505 | 0.6 | 5.47 Neigh | 0.47025 | 0.47603 | 0.47954 | 0.5 | 5.54
Comm | 3.1637 | 3.2822 | 3.4143 | 6.3 | 35.89 Comm | 2.7876 | 2.9237 | 3.0336 | 5.5 | 34.03
Output | 0.0025831 | 0.003088 | 0.004569 | 1.5 | 0.03 Output | 0.0024114 | 0.0029766 | 0.0046443 | 1.8 | 0.03
Modify | 0.067261 | 0.068927 | 0.070535 | 0.5 | 0.75 Modify | 0.062911 | 0.064188 | 0.065603 | 0.4 | 0.75
Other | | 0.07762 | | | 0.85 Other | | 0.06992 | | | 0.81
Nlocal: 50.0000 ave 53 max 46 min Nlocal: 50.0000 ave 53 max 46 min
Histogram: 1 0 0 0 1 0 0 0 1 1 Histogram: 1 0 0 0 1 0 0 0 1 1
@ -198,4 +198,4 @@ Dangerous builds = 5000
write_data final.data pair ij write_data final.data pair ij
System init for write_data ... 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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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 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 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 timestep 1.0
run_style verlet 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 # Coarse-Grained SPC/E Water
variable T equal 300.0 variable T equal 300.0
@ -18,19 +18,19 @@ Reading data file ...
1 by 1 by 1 MPI processor grid 1 by 1 by 1 MPI processor grid
reading atoms ... reading atoms ...
2180 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 dpd/ext/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 dpd/ext/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 dpd/ext/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 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 ${rc}
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 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. 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) 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 dpd/ext/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 10
timestep 1.0 timestep 1.0
run_style verlet run_style verlet
@ -56,7 +56,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
(2) pair dpdext/tstat, perpetual, copy from (1) (2) pair dpd/ext/tstat, perpetual, copy from (1)
attributes: half, newton on attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
@ -264,20 +264,20 @@ Step Time Temp Press
1980 1980 299.14574 5166.3501 1980 1980 299.14574 5166.3501
1990 1990 300.07254 10019.769 1990 1990 300.07254 10019.769
2000 2000 301.78176 8789.7968 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 Performance: 1.895 ns/day, 12.667 hours/ns, 21.928 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads 99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 79.378 | 79.378 | 79.378 | 0.0 | 99.38 Pair | 90.668 | 90.668 | 90.668 | 0.0 | 99.41
Neigh | 0.22454 | 0.22454 | 0.22454 | 0.0 | 0.28 Neigh | 0.23231 | 0.23231 | 0.23231 | 0.0 | 0.25
Comm | 0.17969 | 0.17969 | 0.17969 | 0.0 | 0.22 Comm | 0.20819 | 0.20819 | 0.20819 | 0.0 | 0.23
Output | 0.0063846 | 0.0063846 | 0.0063846 | 0.0 | 0.01 Output | 0.0049558 | 0.0049558 | 0.0049558 | 0.0 | 0.01
Modify | 0.044496 | 0.044496 | 0.044496 | 0.0 | 0.06 Modify | 0.052906 | 0.052906 | 0.052906 | 0.0 | 0.06
Other | | 0.03671 | | | 0.05 Other | | 0.03904 | | | 0.04
Nlocal: 2180.00 ave 2180 max 2180 min Nlocal: 2180.00 ave 2180 max 2180 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -290,4 +290,4 @@ Total # of neighbors = 261496
Ave neighs/atom = 119.95229 Ave neighs/atom = 119.95229
Neighbor list builds = 25 Neighbor list builds = 25
Dangerous builds = 0 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 # Coarse-Grained SPC/E Water
variable T equal 300.0 variable T equal 300.0
@ -18,19 +18,19 @@ Reading data file ...
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
reading atoms ... reading atoms ...
2180 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 dpd/ext/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 dpd/ext/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 dpd/ext/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 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 ${rc}
pair_coeff 1 1 table cg_spce_table.pot VOTCA 9 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. 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) 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 dpd/ext/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 10
timestep 1.0 timestep 1.0
run_style verlet run_style verlet
@ -56,7 +56,7 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton stencil: half/bin/3d/newton
bin: standard bin: standard
(2) pair dpdext/tstat, perpetual, copy from (1) (2) pair dpd/ext/tstat, perpetual, copy from (1)
attributes: half, newton on attributes: half, newton on
pair build: copy pair build: copy
stencil: none stencil: none
@ -264,20 +264,20 @@ Step Time Temp Press
1980 1980 297.94119 5615.6403 1980 1980 297.94119 5615.6403
1990 1990 298.37687 9727.308 1990 1990 298.37687 9727.308
2000 2000 296.08394 6400.2746 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 Performance: 4.162 ns/day, 5.766 hours/ns, 48.173 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads 99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 37.953 | 38.022 | 38.132 | 1.1 | 93.77 Pair | 38.667 | 38.954 | 39.453 | 4.8 | 93.83
Neigh | 0.10585 | 0.10835 | 0.10994 | 0.5 | 0.27 Neigh | 0.10947 | 0.11039 | 0.11153 | 0.3 | 0.27
Comm | 2.2287 | 2.3368 | 2.405 | 4.6 | 5.76 Comm | 1.8661 | 2.3644 | 2.652 | 19.6 | 5.70
Output | 0.0072037 | 0.0081832 | 0.011022 | 1.8 | 0.02 Output | 0.0082644 | 0.0094232 | 0.01281 | 2.0 | 0.02
Modify | 0.023132 | 0.024188 | 0.025948 | 0.7 | 0.06 Modify | 0.024678 | 0.025206 | 0.025888 | 0.3 | 0.06
Other | | 0.05032 | | | 0.12 Other | | 0.05335 | | | 0.13
Nlocal: 545.000 ave 559 max 531 min Nlocal: 545.000 ave 559 max 531 min
Histogram: 1 0 0 0 1 1 0 0 0 1 Histogram: 1 0 0 0 1 1 0 0 0 1
@ -290,4 +290,4 @@ Total # of neighbors = 261662
Ave neighs/atom = 120.02844 Ave neighs/atom = 120.02844
Neighbor list builds = 26 Neighbor list builds = 26
Dangerous builds = 0 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 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 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 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 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 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 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11

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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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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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