diff --git a/examples/USER/dpdext/README b/examples/USER/misc/dpd_ext/README similarity index 100% rename from examples/USER/dpdext/README rename to examples/USER/misc/dpd_ext/README diff --git a/examples/USER/dpdext/dpdext/dpdext.data b/examples/USER/misc/dpd_ext/dpdext/dpdext.data similarity index 100% rename from examples/USER/dpdext/dpdext/dpdext.data rename to examples/USER/misc/dpd_ext/dpdext/dpdext.data diff --git a/examples/USER/dpdext/dpdext/in.dpdext b/examples/USER/misc/dpd_ext/dpdext/in.dpdext similarity index 95% rename from examples/USER/dpdext/dpdext/in.dpdext rename to examples/USER/misc/dpd_ext/dpdext/in.dpdext index 3101be9a1c..726f3a7b39 100755 --- a/examples/USER/dpdext/dpdext/in.dpdext +++ b/examples/USER/misc/dpd_ext/dpdext/in.dpdext @@ -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} diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 index ef61ed11b8..862aea77af 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.1 @@ -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 diff --git a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 similarity index 90% rename from examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 index bbbf47a46c..12b35ecf53 100644 --- a/examples/USER/dpdext/dpdext/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext/log.10Mar21.dpdext.g++.4 @@ -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 diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce.data b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce.data rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce.data diff --git a/examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot b/examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot similarity index 100% rename from examples/USER/dpdext/dpdext_tstat/cg_spce_table.pot rename to examples/USER/misc/dpd_ext/dpdext_tstat/cg_spce_table.pot diff --git a/examples/USER/dpdext/dpdext_tstat/in.cg_spce b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce similarity index 76% rename from examples/USER/dpdext/dpdext_tstat/in.cg_spce rename to examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce index ea1a3dfcba..b93dc3eec5 100755 --- a/examples/USER/dpdext/dpdext_tstat/in.cg_spce +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/in.cg_spce @@ -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 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 index 6916a5dd6e..8f75dfa917 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.1 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.1 @@ -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 diff --git a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 similarity index 91% rename from examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 rename to examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 index 890414d580..278aba0687 100644 --- a/examples/USER/dpdext/dpdext_tstat/log.10Mar21.dpdext.g++.4 +++ b/examples/USER/misc/dpd_ext/dpdext_tstat/log.10Mar21.dpdext.g++.4 @@ -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 diff --git a/src/USER-DPDEXT/README b/src/USER-DPDEXT/README deleted file mode 100644 index 73f8d047f8..0000000000 --- a/src/USER-DPDEXT/README +++ /dev/null @@ -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. diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 314fe6146e..3e2c8ed000 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -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 diff --git a/src/USER-DPDEXT/pair_dpd_ext.cpp b/src/USER-MISC/pair_dpd_ext.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.cpp rename to src/USER-MISC/pair_dpd_ext.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext.h b/src/USER-MISC/pair_dpd_ext.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext.h rename to src/USER-MISC/pair_dpd_ext.h diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.cpp b/src/USER-MISC/pair_dpd_ext_tstat.cpp similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.cpp rename to src/USER-MISC/pair_dpd_ext_tstat.cpp diff --git a/src/USER-DPDEXT/pair_dpd_ext_tstat.h b/src/USER-MISC/pair_dpd_ext_tstat.h similarity index 100% rename from src/USER-DPDEXT/pair_dpd_ext_tstat.h rename to src/USER-MISC/pair_dpd_ext_tstat.h