From adf4a23f58f19692ec351967e444d80c6524384e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 20 Mar 2022 15:28:31 -0400 Subject: [PATCH] refactor and apply clang-format - replace file reader code using TextFileReader and ValueTokenizer - replace traversing list of fixes with accessor functions - enable and apply clang-format - add examples for reading rigid bodies from file --- examples/rigid/connected-bodies.dat | 15 + examples/rigid/connected-bodies2.dat | 17 + examples/rigid/in.rigid.poems | 100 +-- examples/rigid/in.rigid.poems2 | 104 +-- examples/rigid/in.rigid.poems3 | 50 ++ examples/rigid/in.rigid.poems4 | 50 ++ examples/rigid/in.rigid.poems5 | 51 ++ examples/rigid/log.20Mar22.rigid.poems.g++.1 | 328 +++++++ examples/rigid/log.20Mar22.rigid.poems.g++.4 | 328 +++++++ examples/rigid/log.20Mar22.rigid.poems2.g++.1 | 330 +++++++ examples/rigid/log.20Mar22.rigid.poems2.g++.4 | 330 +++++++ examples/rigid/log.20Mar22.rigid.poems3.g++.1 | 329 +++++++ examples/rigid/log.20Mar22.rigid.poems3.g++.4 | 329 +++++++ examples/rigid/log.20Mar22.rigid.poems4.g++.1 | 328 +++++++ examples/rigid/log.20Mar22.rigid.poems4.g++.4 | 328 +++++++ examples/rigid/log.20Mar22.rigid.poems5.g++.1 | 329 +++++++ examples/rigid/log.20Mar22.rigid.poems5.g++.4 | 329 +++++++ examples/rigid/log.27Nov18.rigid.poems.g++.1 | 338 ------- examples/rigid/log.27Nov18.rigid.poems.g++.4 | 338 ------- examples/rigid/log.27Nov18.rigid.poems2.g++.1 | 342 -------- examples/rigid/log.27Nov18.rigid.poems2.g++.4 | 342 -------- examples/rigid/unconnected-bodies.dat | 14 + src/POEMS/fix_poems.cpp | 828 +++++++++--------- src/POEMS/fix_poems.h | 4 +- 24 files changed, 3950 insertions(+), 1931 deletions(-) create mode 100644 examples/rigid/connected-bodies.dat create mode 100644 examples/rigid/connected-bodies2.dat create mode 100644 examples/rigid/in.rigid.poems3 create mode 100644 examples/rigid/in.rigid.poems4 create mode 100644 examples/rigid/in.rigid.poems5 create mode 100644 examples/rigid/log.20Mar22.rigid.poems.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems2.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems2.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems3.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems3.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems4.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems4.g++.4 create mode 100644 examples/rigid/log.20Mar22.rigid.poems5.g++.1 create mode 100644 examples/rigid/log.20Mar22.rigid.poems5.g++.4 delete mode 100644 examples/rigid/log.27Nov18.rigid.poems.g++.1 delete mode 100644 examples/rigid/log.27Nov18.rigid.poems.g++.4 delete mode 100644 examples/rigid/log.27Nov18.rigid.poems2.g++.1 delete mode 100644 examples/rigid/log.27Nov18.rigid.poems2.g++.4 create mode 100644 examples/rigid/unconnected-bodies.dat diff --git a/examples/rigid/connected-bodies.dat b/examples/rigid/connected-bodies.dat new file mode 100644 index 0000000000..ec6fb7e693 --- /dev/null +++ b/examples/rigid/connected-bodies.dat @@ -0,0 +1,15 @@ +# Body definition file for POEMS fix +# 1 chain of 9 connected bodies + +# Format +# Body-ID Body-Type Atom-ID1 Atom-ID2 ... +1 1 1 2 3 4 5 6 7 8 9 +2 2 9 10 11 12 13 14 15 16 17 18 +3 1 18 19 20 21 22 23 24 25 26 27 +4 2 27 28 29 30 31 32 33 34 35 36 +5 3 36 37 38 39 40 41 42 43 44 45 +6 1 45 46 47 48 49 50 51 52 53 54 +7 2 54 55 56 57 58 59 60 61 62 63 +8 1 63 64 65 66 67 68 69 70 71 72 +9 2 72 73 74 75 76 77 78 79 80 81 + diff --git a/examples/rigid/connected-bodies2.dat b/examples/rigid/connected-bodies2.dat new file mode 100644 index 0000000000..468a716c3c --- /dev/null +++ b/examples/rigid/connected-bodies2.dat @@ -0,0 +1,17 @@ +# Body definition file for POEMS fix +# 2 chains of 4 and 5 connected rigid bodies, respectively + +# Format +# Body-ID Body-Type Atom-ID1 Atom-ID2 ... +# chain 1 +1 1 1 2 3 4 5 6 7 8 9 +2 2 9 10 11 12 13 14 15 16 17 18 +3 1 18 19 20 21 22 23 24 25 26 27 +4 2 27 28 29 30 31 32 33 34 35 36 +# chain 2 +5 3 37 38 39 40 41 42 43 44 45 +6 1 45 46 47 48 49 50 51 52 53 54 +7 2 54 55 56 57 58 59 60 61 62 63 +8 1 63 64 65 66 67 68 69 70 71 72 +9 2 72 73 74 75 76 77 78 79 80 81 + diff --git a/examples/rigid/in.rigid.poems b/examples/rigid/in.rigid.poems index aeb5e9e045..b6eb933846 100644 --- a/examples/rigid/in.rigid.poems +++ b/examples/rigid/in.rigid.poems @@ -1,81 +1,51 @@ # Simple rigid body system -units lj -atom_style atomic +units lj +atom_style atomic -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 -read_data data.rigid +read_data data.rigid -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & -# clump6 clump7 clump8 clump9 +velocity all create 100.0 4928459 # 1 chain of connected bodies -group clump1 id <> 1 9 -group clump2 id <> 9 18 -group clump3 id <> 18 27 -group clump4 id <> 27 36 -group clump5 id <> 36 45 -group clump6 id <> 45 54 -group clump7 id <> 54 63 -group clump8 id <> 63 72 -group clump9 id <> 72 81 +group clump1 id <> 1 9 +group clump2 id <> 9 18 +group clump3 id <> 18 27 +group clump4 id <> 27 36 +group clump5 id <> 36 45 +group clump6 id <> 45 54 +group clump7 id <> 54 63 +group clump8 id <> 63 72 +group clump9 id <> 72 81 fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & - clump6 clump7 clump8 clump9 + clump6 clump7 clump8 clump9 -# 2 chains of connected bodies +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 +thermo 100 -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +#dump 1 all atom 50 dump.rigid.poems -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 -thermo 100 +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.poems2 b/examples/rigid/in.rigid.poems2 index 3b7ab86d63..21adf6a1ee 100644 --- a/examples/rigid/in.rigid.poems2 +++ b/examples/rigid/in.rigid.poems2 @@ -1,81 +1,53 @@ # Simple rigid body system -units lj -atom_style atomic +units lj +atom_style atomic -pair_style lj/cut 2.5 +pair_style lj/cut 2.5 -read_data data.rigid +read_data data.rigid -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 & -# clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 & -# clump6 clump7 clump8 clump9 +velocity all create 100.0 4928459 # 2 chains of connected bodies -group clump1 id <> 1 9 -group clump2 id <> 9 18 -group clump3 id <> 18 27 -group clump4 id <> 27 36 -group clump5 id <> 37 45 -group clump6 id <> 45 54 -group clump7 id <> 54 63 -group clump8 id <> 63 72 -group clump9 id <> 72 81 +group clump1 id <> 1 9 +group clump2 id <> 9 18 +group clump3 id <> 18 27 +group clump4 id <> 27 36 +group clump5 id <> 37 45 +group clump6 id <> 45 54 +group clump7 id <> 54 63 +group clump8 id <> 63 72 +group clump9 id <> 72 81 -fix 1 all poems group clump1 clump2 clump3 clump4 -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 & + clump5 clump6 clump7 clump8 clump9 -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 -thermo 100 +thermo 100 -#dump 1 all atom 50 dump.rigid.poems2 +#dump 1 all atom 50 dump.rigid.poems2 -#dump 2 all image 100 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 -#dump 3 all movie 100 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 -timestep 0.0001 -thermo 50 -run 10000 +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.poems3 b/examples/rigid/in.rigid.poems3 new file mode 100644 index 0000000000..9c8c9f5be4 --- /dev/null +++ b/examples/rigid/in.rigid.poems3 @@ -0,0 +1,50 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +group clump2 id <> 10 18 +group clump3 id <> 19 27 +group clump4 id <> 28 36 +group clump5 id <> 37 45 +group clump6 id <> 46 54 +group clump7 id <> 55 63 +group clump8 id <> 64 72 +group clump9 id <> 73 81 + +fix 1 all poems file unconnected-bodies.dat + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.poems4 b/examples/rigid/in.rigid.poems4 new file mode 100644 index 0000000000..d782b90ea0 --- /dev/null +++ b/examples/rigid/in.rigid.poems4 @@ -0,0 +1,50 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +group clump2 id <> 9 18 +group clump3 id <> 18 27 +group clump4 id <> 27 36 +group clump5 id <> 36 45 +group clump6 id <> 45 54 +group clump7 id <> 54 63 +group clump8 id <> 63 72 +group clump9 id <> 72 81 + +fix 1 all poems file connected-bodies.dat + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/in.rigid.poems5 b/examples/rigid/in.rigid.poems5 new file mode 100644 index 0000000000..1085a4981e --- /dev/null +++ b/examples/rigid/in.rigid.poems5 @@ -0,0 +1,51 @@ +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +group clump2 id <> 9 18 +group clump3 id <> 18 27 +group clump4 id <> 27 36 +group clump5 id <> 37 45 +group clump6 id <> 45 54 +group clump7 id <> 54 63 +group clump8 id <> 63 72 +group clump9 id <> 72 81 + +fix 1 all poems file connected-bodies2.dat + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.1 b/examples/rigid/log.20Mar22.rigid.poems.g++.1 new file mode 100644 index 0000000000..32edd0fd0c --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.438428 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699118 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538604 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.029 99.812844 0 3680.6511 -16.185479 + 1450 21771.107 52.159653 0 3680.6775 -2.4756655 + 1500 21520.949 93.503876 0 3680.3286 2.1023573 + 1550 21351.419 121.6813 0 3680.2511 5.5159876 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21873 0 3679.8247 -1.1045277 + 1700 18501.33 596.4807 0 3680.0357 -15.6798 + 1750 18563.64 587.34824 0 3681.2882 33.532308 + 1800 19110.175 494.82517 0 3679.8543 18.024074 + 1850 21364.178 119.23765 0 3679.9339 2.5290144 + 1900 20146.588 322.15509 0 3679.9197 5.7317299 + 1950 20692.676 231.25264 0 3680.0319 4.297803 + 2000 20943.902 189.11251 0 3679.7629 -22.643824 + 2050 19667.823 401.86882 0 3679.8394 3.6241915 + 2100 20280.125 299.81485 0 3679.8357 7.4804047 + 2150 19181.201 483.6306 0 3680.4975 22.63342 + 2200 21301.144 130.54014 0 3680.7308 4.7074288 + 2250 20484.876 266.98315 0 3681.1291 -8.6578278 + 2300 18648.161 573.07329 0 3681.1001 -5.2550954 + 2350 21515.748 95.243054 0 3681.201 -9.386512 + 2400 21462.551 104.18267 0 3681.2745 -29.46442 + 2450 20107.732 330.99437 0 3682.2831 35.38497 + 2500 20771.509 220.47713 0 3682.3953 -12.324858 + 2550 20499.887 265.58494 0 3682.2327 -22.713874 + 2600 21462.182 105.24427 0 3682.2747 -10.175788 + 2650 21004.949 181.51383 0 3682.3387 4.949195 + 2700 18673.552 570.45017 0 3682.7089 21.201437 + 2750 21257.562 139.198 0 3682.1249 -7.5793039 + 2800 21559.645 88.844759 0 3682.119 -6.2360467 + 2850 20865.227 204.46262 0 3682.0004 0.39575069 + 2900 19428.614 443.93293 0 3682.0352 12.796676 + 2950 19630.1 410.18487 0 3681.8681 -0.50572623 + 3000 19663.218 404.06316 0 3681.2661 6.0827093 + 3050 19087.572 500.8452 0 3682.1073 -6.3526476 + 3100 18229.94 643.77681 0 3682.1001 11.453637 + 3150 18927.492 527.51919 0 3682.1011 -1.662863 + 3200 18320.514 628.55895 0 3681.978 21.176126 + 3250 18204.677 647.96462 0 3682.0775 11.331521 + 3300 19231.978 477.02117 0 3682.3509 3.8381593 + 3350 18153.44 656.70376 0 3682.2772 15.135615 + 3400 17476.768 770.0598 0 3682.8545 -3.394312 + 3450 21097.531 166.17241 0 3682.4276 3.74301 + 3500 17605.784 747.54808 0 3681.8454 3.3420627 + 3550 19238.34 476.00608 0 3682.3961 1.1413836 + 3600 18155.288 656.57434 0 3682.4557 3.4360446 + 3650 18735.622 559.2377 0 3681.8413 28.760363 + 3700 15310.261 1134.4215 0 3686.1317 44.207018 + 3750 15377.116 1123.4786 0 3686.3313 7.6773215 + 3800 18798.895 549.05928 0 3682.2084 -12.905825 + 3850 18322.563 628.87744 0 3682.6379 -16.067793 + 3900 19963.049 355.65441 0 3682.8292 3.4694064 + 3950 19925.48 361.2507 0 3682.1641 5.0058567 + 4000 19141.423 492.41081 0 3682.648 -12.782769 + 4050 20022.241 345.61655 0 3682.6568 -3.0149905 + 4100 21348.635 124.95646 0 3683.0624 -4.85779 + 4150 21011.812 181.1132 0 3683.0819 -3.9526196 + 4200 20222.276 312.63945 0 3683.0187 -23.63437 + 4250 20957.757 189.77152 0 3682.731 -1.3712469 + 4300 20070.215 337.5751 0 3682.611 -6.8816517 + 4350 21322.437 129.09228 0 3682.8318 -6.9442178 + 4400 19440.445 442.77531 0 3682.8495 -0.11606236 + 4450 20964.516 188.67174 0 3682.7577 4.8533525 + 4500 13530.08 1428.5497 0 3683.563 12.333187 + 4550 20461.637 272.58882 0 3682.8616 4.5111943 + 4600 17072.994 836.58228 0 3682.0812 5.7611617 + 4650 18860.748 539.82027 0 3683.2782 -2.5558958 + 4700 18373.927 621.04093 0 3683.3621 5.4020702 + 4750 20321.437 296.63662 0 3683.5428 8.9571617 + 4800 21083.122 169.84086 0 3683.6946 10.566368 + 4850 20499.669 267.7012 0 3684.3128 4.2924237 + 4900 20308.781 300.38168 0 3685.1785 -12.396923 + 4950 21043.303 178.56295 0 3685.7801 3.8923762 + 5000 20718.383 232.52208 0 3685.5859 -12.43234 + 5050 21005.749 184.4363 0 3685.3945 -7.6463487 + 5100 20714.133 233.27745 0 3685.6329 -1.6944135 + 5150 19577.452 422.73035 0 3685.639 -21.831219 + 5200 14044.647 1343.9545 0 3684.729 -6.8407194 + 5250 19089.805 504.0893 0 3685.7235 4.05641 + 5300 21094.745 169.94699 0 3685.7378 -0.66593212 + 5350 19907.559 366.77598 0 3684.7024 1.5248525 + 5400 20382.81 289.13263 0 3686.2676 -11.919321 + 5450 19593.693 420.70548 0 3686.3209 -1.1568628 + 5500 20906.08 202.09801 0 3686.4447 -2.4284971 + 5550 16315.465 965.56973 0 3684.8138 -33.178221 + 5600 19714.57 400.39687 0 3686.1586 19.950231 + 5650 20561.724 259.54797 0 3686.502 8.2074524 + 5700 19349.502 460.7789 0 3685.6959 16.252649 + 5750 21006.818 185.56805 0 3686.7044 -11.96089 + 5800 20268.2 307.97547 0 3686.0089 17.322311 + 5850 21018.322 184.16179 0 3687.2154 -14.379909 + 5900 19695.647 404.57094 0 3687.1787 -20.718904 + 5950 21021.687 183.66311 0 3687.2776 -15.206081 + 6000 18947.535 529.30554 0 3687.2281 17.863927 + 6050 15272.373 1141.012 0 3686.4075 -0.43375666 + 6100 17766.197 721.75792 0 3682.7908 11.378913 + 6150 18612.573 584.06688 0 3686.1623 17.543241 + 6200 19005.155 518.97146 0 3686.4973 -16.223107 + 6250 20997.507 187.55499 0 3687.1394 -11.613546 + 6300 19639.901 413.58048 0 3686.8974 14.407136 + 6350 19580.399 423.02818 0 3686.428 -5.5801796 + 6400 14134.119 1332.0662 0 3687.7527 84.864425 + 6450 21598.824 87.419966 0 3687.224 -5.8358352 + 6500 18208.216 649.29108 0 3683.9938 -8.1510884 + 6550 19364.586 459.59813 0 3687.0291 -12.053563 + 6600 20710.927 235.11914 0 3686.9403 -1.0470193 + 6650 21132.334 165.08091 0 3687.1366 1.0785471 + 6700 20217.285 317.589 0 3687.1365 0.055447462 + 6750 21232.279 148.57412 0 3687.2873 -2.4551657 + 6800 20292.683 304.76539 0 3686.8793 -0.42311295 + 6850 19056.291 510.49927 0 3686.5478 6.9533826 + 6900 20429.82 282.23764 0 3687.2076 -4.2360112 + 6950 21281.278 140.27361 0 3687.1533 -0.07475261 + 7000 17173.388 824.54446 0 3686.7758 10.753828 + 7050 18079.7 674.56274 0 3687.846 12.975804 + 7100 16433.233 950.73904 0 3689.6112 -10.5102 + 7150 19033.335 515.59672 0 3687.8193 0.29109447 + 7200 17286.428 809.02352 0 3690.0948 2.3015698 + 7250 16811.962 886.6645 0 3688.6582 -7.4787512 + 7300 15992.461 1023.4849 0 3688.895 -5.2354222 + 7350 19211.451 487.63129 0 3689.5398 8.4351737 + 7400 19065.682 511.95629 0 3689.57 -12.47448 + 7450 21369.265 128.10098 0 3689.6451 2.2930546 + 7500 16807.109 888.64602 0 3689.8308 14.761969 + 7550 18063.046 679.21873 0 3689.7264 3.8950434 + 7600 17794.987 724.55404 0 3690.3851 14.379016 + 7650 17904.751 706.14354 0 3690.2688 23.813776 + 7700 19670.09 411.3021 0 3689.6504 14.099245 + 7750 18082.562 675.23975 0 3689.0001 15.788521 + 7800 17776.135 726.91445 0 3689.6037 6.9780735 + 7850 17062.575 846.33412 0 3690.0966 -8.9289256 + 7900 19059.2 513.07737 0 3689.6107 16.992843 + 7950 16269.685 978.48914 0 3690.1033 11.180179 + 8000 20115.278 336.91405 0 3689.4604 -6.4882518 + 8050 21173.72 161.15229 0 3690.1056 -2.2164491 + 8100 19238.235 484.42784 0 3690.8004 23.412709 + 8150 18438.4 617.58743 0 3690.6542 0.89156316 + 8200 21438.764 117.12721 0 3690.2546 -1.7193227 + 8250 21195.806 157.66607 0 3690.3003 3.820447 + 8300 21177.549 161.13702 0 3690.7286 0.94938203 + 8350 21060.267 181.06887 0 3691.1135 2.8179025 + 8400 20087.113 343.46206 0 3691.3142 8.1484473 + 8450 19298.478 474.87133 0 3691.2843 -16.239664 + 8500 21654.353 82.083485 0 3691.1423 -8.1464138 + 8550 19920.544 371.34795 0 3691.4386 20.765144 + 8600 21692.293 75.655154 0 3691.0373 -13.316763 + 8650 21231.322 151.8989 0 3690.4526 -11.388238 + 8700 19530.647 434.89585 0 3690.0037 2.7433786 + 8750 19720.63 403.07773 0 3689.8493 -6.416414 + 8800 21321.378 136.04091 0 3689.604 1.3661635 + 8850 19811.906 387.80489 0 3689.7893 3.704143 + 8900 19734.167 400.92444 0 3689.9523 2.5685155 + 8950 21076.459 177.18119 0 3689.9244 -11.939513 + 9000 20967.246 195.42966 0 3689.9707 2.0092705 + 9050 21122.023 169.62103 0 3689.9582 2.3791301 + 9100 20169.346 328.27229 0 3689.8299 -3.5017988 + 9150 21418.641 119.84513 0 3689.6187 2.486073 + 9200 20876.042 210.26452 0 3689.6048 -5.3839897 + 9250 21572.38 93.74407 0 3689.1407 -8.3676952 + 9300 20944.78 197.98577 0 3688.7824 1.3278314 + 9350 20706.52 237.48767 0 3688.5744 4.6944204 + 9400 16412.314 953.47251 0 3688.8581 26.134976 + 9450 20461.68 277.76243 0 3688.0424 17.647445 + 9500 20893.994 205.64261 0 3687.9749 -10.642418 + 9550 20503.447 270.63504 0 3687.8761 -17.769897 + 9600 19677.799 408.05887 0 3687.692 -2.7938604 + 9650 17480.971 774.1855 0 3687.6806 0.59827043 + 9700 17799.126 721.50817 0 3688.0292 44.387928 + 9750 20443.384 280.16837 0 3687.399 3.0619324 + 9800 20545.255 263.40108 0 3687.6102 3.6229381 + 9850 20722.819 233.57142 0 3687.3745 0.86462694 + 9900 21128.462 165.09767 0 3686.508 -6.9636843 + 9950 21343.307 130.46714 0 3687.685 -9.7382705 + 10000 20623.887 250.37866 0 3687.6932 2.7529835 +Loop time of 2.27157 on 1 procs for 10000 steps with 81 atoms + +Performance: 38035.351 tau/day, 4402.240 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.092926 | 0.092926 | 0.092926 | 0.0 | 4.09 +Neigh | 0.076362 | 0.076362 | 0.076362 | 0.0 | 3.36 +Comm | 0.0069691 | 0.0069691 | 0.0069691 | 0.0 | 0.31 +Output | 0.0037444 | 0.0037444 | 0.0037444 | 0.0 | 0.16 +Modify | 2.0832 | 2.0832 | 2.0832 | 0.0 | 91.71 +Other | | 0.00841 | | | 0.37 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 62 ave 62 max 62 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 905 ave 905 max 905 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 905 +Ave neighs/atom = 11.17284 +Neighbor list builds = 991 +Dangerous builds = 927 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems.g++.4 b/examples/rigid/log.20Mar22.rigid.poems.g++.4 new file mode 100644 index 0000000000..7e651a7aaf --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.001 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.4384281 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699115 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538606 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.03 99.812843 0 3680.6511 -16.185479 + 1450 21771.107 52.159652 0 3680.6775 -2.4756656 + 1500 21520.949 93.503872 0 3680.3286 2.1023574 + 1550 21351.419 121.68131 0 3680.2511 5.5159875 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21877 0 3679.8247 -1.104524 + 1700 18501.329 596.48084 0 3680.0357 -15.679806 + 1750 18563.639 587.34841 0 3681.2882 33.532316 + 1800 19110.174 494.82524 0 3679.8543 18.024079 + 1850 21364.178 119.23767 0 3679.9339 2.5290075 + 1900 20146.588 322.15506 0 3679.9197 5.7317368 + 1950 20692.674 231.25288 0 3680.0319 4.2977982 + 2000 20943.904 189.11229 0 3679.7629 -22.643749 + 2050 19667.815 401.87016 0 3679.8394 3.6240972 + 2100 20280.109 299.81759 0 3679.8357 7.4803647 + 2150 19181.146 483.63975 0 3680.4974 22.634167 + 2200 21301.194 130.53171 0 3680.7308 4.7072523 + 2250 20484.79 266.99736 0 3681.1291 -8.6583002 + 2300 18648.002 573.09962 0 3681.1 -5.2548835 + 2350 21515.851 95.225745 0 3681.2009 -9.3875216 + 2400 21462.37 104.21272 0 3681.2744 -29.459857 + 2450 20108.034 330.94394 0 3682.2829 35.37058 + 2500 20771.818 220.42545 0 3682.3951 -12.318936 + 2550 20502.815 265.09577 0 3682.2316 -22.726822 + 2600 21462.006 105.2733 0 3682.2744 -10.180394 + 2650 21009.656 180.72738 0 3682.3367 4.9580828 + 2700 18680.012 569.37179 0 3682.7071 21.114114 + 2750 21256.19 139.42201 0 3682.1203 -7.4744399 + 2800 21552.267 90.071446 0 3682.1159 -6.2906304 + 2850 20879.958 202.00905 0 3682.0021 0.57990903 + 2900 19018.645 512.35214 0 3682.1262 13.883084 + 2950 19819.365 378.55747 0 3681.785 -0.7348943 + 3000 20269.229 303.35149 0 3681.5563 6.3088075 + 3050 19236.727 475.99457 0 3682.1158 -10.703575 + 3100 18391.55 616.96976 0 3682.2281 9.850079 + 3150 20258.563 305.82076 0 3682.248 7.1951283 + 3200 20716.384 229.15502 0 3681.8856 2.9042294 + 3250 18662.237 572.0784 0 3682.4512 9.2108597 + 3300 19162.278 488.60646 0 3682.3195 3.3306562 + 3350 21235.679 142.98279 0 3682.2626 0.29397483 + 3400 17677.053 736.09247 0 3682.2679 32.75269 + 3450 20852.392 206.65618 0 3682.0548 -4.8319056 + 3500 21182.918 151.46754 0 3681.9539 -5.6330382 + 3550 20589.85 250.40724 0 3682.049 12.582133 + 3600 20973.659 186.28043 0 3681.8903 10.935266 + 3650 17838.632 707.92145 0 3681.0268 -17.200926 + 3700 21538.002 92.744409 0 3682.4114 -0.72124229 + 3750 21390.294 117.90865 0 3682.9576 -7.8431786 + 3800 17921.046 696.50311 0 3683.344 -9.4641531 + 3850 20356.471 290.22624 0 3682.9715 2.4593463 + 3900 20374.077 287.10249 0 3682.782 -1.9519082 + 3950 20563.915 255.29993 0 3682.619 -6.124649 + 4000 20991.467 184.76183 0 3683.3397 1.8954961 + 4050 17805.623 716.24698 0 3683.8509 -20.454944 + 4100 19916.389 363.86301 0 3683.2611 -0.27912557 + 4150 19221.623 480.01232 0 3683.6161 -11.562492 + 4200 20526.82 261.78571 0 3682.9224 -3.9522917 + 4250 20922.813 196.1799 0 3683.3154 0.11947446 + 4300 19956.66 357.78133 0 3683.8914 19.156093 + 4350 19735.73 394.45981 0 3683.7482 14.865775 + 4400 21702.656 67.099805 0 3684.2092 -13.502538 + 4450 18163.055 656.97231 0 3684.1482 -0.6243111 + 4500 17477.718 771.25976 0 3684.2127 -0.4664004 + 4550 20676.507 238.19814 0 3684.2827 -19.444969 + 4600 17322.922 796.77058 0 3683.9242 27.003966 + 4650 11905.158 1704.9151 0 3689.1082 15.574169 + 4700 18689.079 569.80982 0 3684.6563 -14.67311 + 4750 19821.745 381.01914 0 3684.6433 5.0436795 + 4800 20621.335 247.96269 0 3684.8518 -16.407263 + 4850 21923.814 30.965964 0 3684.935 -13.418244 + 4900 18840.555 544.41538 0 3684.5079 11.005357 + 4950 15366.601 1124.2481 0 3685.3482 17.412375 + 5000 18274.314 639.01311 0 3684.732 5.3261109 + 5050 21173.687 155.83673 0 3684.7845 5.4056809 + 5100 21738.219 61.75201 0 3684.7885 -2.631945 + 5150 16597.949 918.84841 0 3685.1732 -10.124101 + 5200 20752.758 225.95919 0 3684.7522 -5.2441372 + 5250 17652.088 741.2645 0 3683.2793 2.0080739 + 5300 19907.523 366.53115 0 3684.4516 8.4266792 + 5350 20104.189 334.14522 0 3684.8433 17.21925 + 5400 21499.848 101.71631 0 3685.0243 -6.1103541 + 5450 21203.533 151.14574 0 3685.068 -5.9468503 + 5500 21076.513 172.45652 0 3685.2088 5.1418181 + 5550 20158.398 325.56609 0 3685.2992 -1.6486034 + 5600 20787.836 221.19563 0 3685.835 -10.66805 + 5650 19687.154 404.77204 0 3685.9644 -23.49128 + 5700 20419.311 282.58328 0 3685.8017 -0.52808211 + 5750 19738.522 395.95893 0 3685.7126 1.3889817 + 5800 18300.025 635.66905 0 3685.6732 23.490447 + 5850 20585.004 255.02032 0 3685.8543 -0.20699939 + 5900 20373.839 290.15881 0 3685.7987 -7.9712187 + 5950 18163.832 659.91192 0 3687.2173 5.4494586 + 6000 21049.247 177.43029 0 3685.6382 2.9138342 + 6050 21239.803 145.77613 0 3685.7433 -1.4927769 + 6100 20686.361 237.86454 0 3685.5913 -0.95516297 + 6150 20461.754 275.31546 0 3685.6079 -3.4166412 + 6200 19264.208 474.73017 0 3685.4316 11.750757 + 6250 21180.813 155.31746 0 3685.4529 2.8188219 + 6300 21047.543 177.4394 0 3685.3632 1.8641486 + 6350 20232.576 313.17716 0 3685.2731 2.8150209 + 6400 20185.616 321.33454 0 3685.6038 -3.8697311 + 6450 18969.632 523.95865 0 3685.5639 0.6725512 + 6500 17592.574 753.49959 0 3685.5952 -1.2557393 + 6550 21279.049 138.42524 0 3684.9335 -1.208945 + 6600 21408.457 116.4143 0 3684.4904 -1.5332953 + 6650 19758.218 391.17316 0 3684.2096 1.8511312 + 6700 20766.943 223.44631 0 3684.6036 -2.3672623 + 6750 20399.631 284.09914 0 3684.0377 -5.4089876 + 6800 21296.628 135.14662 0 3684.5847 -3.8442549 + 6850 20641.481 244.4451 0 3684.692 1.4020639 + 6900 20852.81 209.23009 0 3684.6984 1.8512104 + 6950 20940.555 194.66882 0 3684.7614 -6.554676 + 7000 19496.988 435.28199 0 3684.78 -15.120269 + 7050 19796.829 385.04227 0 3684.5138 -4.1068804 + 7100 19945.264 360.42431 0 3684.635 -4.0629042 + 7150 19431.123 446.12911 0 3684.6497 -6.8321751 + 7200 16864.851 873.80043 0 3684.6089 14.309069 + 7250 20438.75 277.85982 0 3684.3181 -11.41223 + 7300 17688.684 734.01576 0 3682.1298 35.938373 + 7350 21573.419 88.63421 0 3684.204 -3.9032749 + 7400 21198.486 150.72249 0 3683.8034 -7.1477117 + 7450 20586.708 252.93928 0 3684.0572 -7.6634645 + 7500 21815.377 48.180377 0 3684.0765 0.97457507 + 7550 17791.352 718.87564 0 3684.101 28.248235 + 7600 21828.874 45.928597 0 3684.0742 -0.25814944 + 7650 20827.961 212.35674 0 3683.6835 -3.4083384 + 7700 21319.176 130.43547 0 3683.6315 -12.434856 + 7750 20127.904 328.69643 0 3683.3471 -16.975711 + 7800 21741.772 59.679206 0 3683.3078 3.6261863 + 7850 19612.334 414.37418 0 3683.0964 1.3763274 + 7900 20071.318 337.74624 0 3682.9658 -0.40982763 + 7950 17925.664 695.29582 0 3682.9065 17.104439 + 8000 19125.978 492.76383 0 3680.4268 10.807662 + 8050 20233.848 310.42681 0 3682.7347 13.386237 + 8100 20551.619 257.86699 0 3683.1368 -13.97515 + 8150 21578.323 86.88362 0 3683.2708 -9.6811587 + 8200 21154.833 157.72897 0 3683.5344 0.62312375 + 8250 21321.143 129.83967 0 3683.3636 1.9536438 + 8300 21041.696 176.04177 0 3682.9911 4.7475567 + 8350 19883.39 369.32649 0 3683.2247 -7.0959328 + 8400 21626.067 79.062992 0 3683.4075 -14.919059 + 8450 21375.201 120.86836 0 3683.4019 -5.3461514 + 8500 20281.059 303.10304 0 3683.2796 3.7975093 + 8550 21170.533 154.48432 0 3682.9065 -1.1568561 + 8600 17754.931 724.00158 0 3683.1568 14.15254 + 8650 20685.478 235.65879 0 3683.2385 -5.2694179 + 8700 21489.165 101.90509 0 3683.4326 -4.2510612 + 8750 21106.682 165.41638 0 3683.1968 -3.9186708 + 8800 19149.516 491.5843 0 3683.1702 -11.419849 + 8850 21451.865 108.1814 0 3683.4923 -7.8256219 + 8900 19567.4 421.81206 0 3683.0454 -0.71997056 + 8950 20934.097 194.48033 0 3683.4965 -7.0106879 + 9000 18531.559 595.25957 0 3683.8528 3.7449399 + 9050 18868.821 537.22549 0 3682.029 9.9926092 + 9100 19972.527 354.73119 0 3683.4858 -0.30871263 + 9150 19641.651 409.18618 0 3682.7947 -1.3036238 + 9200 20019.08 346.19657 0 3682.7099 6.7425386 + 9250 19259.286 473.04973 0 3682.9308 -24.120659 + 9300 21597.757 82.971857 0 3682.598 -13.748483 + 9350 19348.379 457.23576 0 3681.9656 3.1571402 + 9400 19129.588 493.35235 0 3681.617 8.6293783 + 9450 20337.025 291.20959 0 3680.7138 6.8590795 + 9500 20581.788 249.65891 0 3679.9569 -18.892836 + 9550 19482.069 433.0077 0 3680.0192 23.029778 + 9600 19182.794 482.96871 0 3680.101 -11.081731 + 9650 20086.771 332.5311 0 3680.3263 -18.939681 + 9700 20274.046 300.98818 0 3679.9959 6.7538762 + 9750 18743.595 555.08045 0 3679.0129 8.2757138 + 9800 19464.311 435.66288 0 3679.7148 7.0528759 + 9850 21249.848 138.27382 0 3679.9152 -10.847402 + 9900 21156.214 153.84621 0 3679.8819 -7.8359674 + 9950 21643.134 72.547515 0 3679.7365 -10.507744 + 10000 19587.948 414.64942 0 3679.3075 6.1173553 +Loop time of 2.36879 on 4 procs for 10000 steps with 81 atoms + +Performance: 36474.344 tau/day, 4221.568 timesteps/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 | 0.005348 | 0.024925 | 0.056071 | 12.2 | 1.05 +Neigh | 0.0075012 | 0.022046 | 0.043933 | 9.3 | 0.93 +Comm | 0.13135 | 0.16461 | 0.1917 | 5.9 | 6.95 +Output | 0.0036298 | 0.004271 | 0.0056384 | 1.2 | 0.18 +Modify | 2.1147 | 2.1322 | 2.1418 | 0.7 | 90.01 +Other | | 0.02072 | | | 0.87 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 41 ave 78 max 11 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 193.5 ave 774 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 774 +Ave neighs/atom = 9.5555556 +Neighbor list builds = 989 +Dangerous builds = 915 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.1 b/examples/rigid/log.20Mar22.rigid.poems2.g++.1 new file mode 100644 index 0000000000..57f2040a67 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems2.g++.1 @@ -0,0 +1,330 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086359 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977442 0 3904.4178 9.0928158 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47231 0 3902.9213 0.6921524 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05177 0 3902.1317 4.6838621 + 850 19932.48 210.71175 0 3901.9118 3.4716043 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.874422 + 1200 20767.681 56.717094 0 3902.5839 -34.817444 + 1250 20625.583 82.586399 0 3902.1388 11.697329 + 1300 20690.013 71.006478 0 3902.4903 -29.292777 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.559 244.81785 0 3902.8844 6.7138514 + 1450 15690.149 998.342 0 3903.9252 48.124557 + 1500 20234.455 155.92516 0 3903.0465 13.17221 + 1550 20779.631 55.063009 0 3903.1428 -2.639045 + 1600 20642.753 80.233905 0 3902.9659 -2.4688467 + 1650 18785.696 423.90402 0 3902.7365 -5.6466663 + 1700 20965.076 20.760444 0 3903.182 -0.45364296 + 1750 18935.406 396.96067 0 3903.5173 25.913302 + 1800 20581.559 91.756972 0 3903.1567 3.8217234 + 1850 20616.946 85.184849 0 3903.1378 4.1907972 + 1900 16602.053 828.40949 0 3902.8637 -0.49505122 + 1950 20175.526 166.53362 0 3902.7421 5.603825 + 2000 20261.924 150.39322 0 3902.6014 -1.196958 + 2050 20170.339 167.40504 0 3902.6531 -0.80849882 + 2100 19820.132 231.26755 0 3901.6624 3.1476607 + 2150 20666.19 75.838461 0 3902.9106 0.53899287 + 2200 19873.51 222.53286 0 3902.8124 7.9310276 + 2250 18548.063 467.69698 0 3902.5235 16.905356 + 2300 20616.61 84.762399 0 3902.6531 -6.7872951 + 2350 18167.738 538.13635 0 3902.5322 -11.458285 + 2400 20120.227 177.01954 0 3902.9875 -1.2593018 + 2450 20436.599 118.32469 0 3902.8801 -6.5989174 + 2500 18919.923 400.26361 0 3903.9531 32.37476 + 2550 19675.809 259.77151 0 3903.4398 19.437327 + 2600 19739.842 247.86388 0 3903.3901 -7.519784 + 2650 20557.026 96.530313 0 3903.387 0.60211646 + 2700 20666.602 76.099892 0 3903.2484 0.16825503 + 2750 20924.585 28.453883 0 3903.3771 2.4227171 + 2800 20360.659 132.8596 0 3903.352 4.1440877 + 2850 20783.475 54.518625 0 3903.3102 -0.57312067 + 2900 20456.181 115.03745 0 3903.2191 -20.118887 + 2950 20779.493 55.321394 0 3903.3756 -0.26783079 + 3000 20011.867 197.30216 0 3903.2035 -1.4704201 + 3050 20741.875 62.208723 0 3903.2966 -7.5432815 + 3100 21001.754 14.148298 0 3903.362 2.9676438 + 3150 20244.086 154.44639 0 3903.3512 -1.9071213 + 3200 20639.615 81.136426 0 3903.2873 1.4826467 + 3250 20735.244 63.529571 0 3903.3895 2.1127055 + 3300 20142.891 173.22282 0 3903.3878 4.7739415 + 3350 19963.765 206.21899 0 3903.2126 5.5410771 + 3400 16628.667 824.13627 0 3903.519 36.087673 + 3450 19228.218 342.81569 0 3903.5968 3.1057274 + 3500 19759.293 244.57876 0 3903.707 2.2339557 + 3550 19853.21 227.06362 0 3903.584 -1.0882119 + 3600 19673.516 260.64854 0 3903.8923 -10.63775 + 3650 19619.238 270.5393 0 3903.7316 -6.3746003 + 3700 20756.865 59.790243 0 3903.6542 -8.3015766 + 3750 20265.025 150.47347 0 3903.2559 -5.7284695 + 3800 20944.683 24.669276 0 3903.3142 -0.070552298 + 3850 19344.831 320.59492 0 3902.971 13.040749 + 3900 19978.209 203.00247 0 3902.6708 0.15638133 + 3950 19864.118 224.19359 0 3902.734 0.453229 + 4000 17606.216 642.71493 0 3903.1252 -12.656002 + 4050 18017.895 566.54102 0 3903.1883 12.133906 + 4100 20092.963 182.17593 0 3903.095 7.7445947 + 4150 20555.337 96.395074 0 3902.939 -6.5429752 + 4200 20709.781 67.869199 0 3903.0138 -2.8653003 + 4250 18956.203 392.20748 0 3902.6155 -1.6249728 + 4300 17816.204 603.72704 0 3903.0241 23.089239 + 4350 18979.742 388.04678 0 3902.8138 3.2511108 + 4400 20272.085 148.82367 0 3902.9135 1.9518268 + 4450 18820.003 417.74789 0 3902.9337 6.3979299 + 4500 19991.936 200.50131 0 3902.7117 3.5118553 + 4550 20915.092 29.663898 0 3902.8291 -2.3174641 + 4600 20690.37 71.125087 0 3902.6752 -12.008575 + 4650 18893.76 404.50849 0 3903.3529 15.006184 + 4700 18611.123 456.1263 0 3902.6306 -5.3574892 + 4750 20497.821 106.5856 0 3902.4784 0.85039837 + 4800 20803.214 50.120522 0 3902.5675 3.8610873 + 4850 18849.598 411.72635 0 3902.3927 9.2029058 + 4900 18121.714 546.68042 0 3902.5533 9.4522272 + 4950 20377.499 128.99323 0 3902.6041 5.3825395 + 5000 20686.114 72.039749 0 3902.8016 -5.706271 + 5050 20180.449 165.51368 0 3902.634 -16.418461 + 5100 20274.947 148.36657 0 3902.9864 -5.6668309 + 5150 18042.324 560.74137 0 3901.9125 3.6791541 + 5200 20794.666 52.204446 0 3903.0685 -1.4517721 + 5250 19073.55 371.18834 0 3903.3272 -13.457439 + 5300 20821.412 47.364313 0 3903.1813 2.258098 + 5350 20583.073 91.271191 0 3902.9513 5.4323985 + 5400 20490.967 108.41184 0 3903.0353 4.122905 + 5450 18141.79 543.66874 0 3903.2594 -0.19951075 + 5500 20274.012 148.55528 0 3903.002 5.0489974 + 5550 17806.237 605.43454 0 3902.8858 43.80619 + 5600 20999.825 14.341937 0 3903.1983 1.0879933 + 5650 20930.929 27.025347 0 3903.1234 -7.0860209 + 5700 20677.725 73.853093 0 3903.0614 2.6864775 + 5750 20521.264 102.87509 0 3903.1092 2.6940548 + 5800 20792.571 52.596021 0 3903.0721 1.2910217 + 5850 20518.674 103.26595 0 3903.0204 -9.2547271 + 5900 18417.885 491.66696 0 3902.3865 -12.049357 + 5950 17243.837 709.37858 0 3902.6817 -6.2357188 + 6000 20262.525 149.56918 0 3901.8885 -0.28964823 + 6050 19883.554 219.14043 0 3901.2801 2.3071707 + 6100 16548.178 838.47869 0 3902.956 -11.715644 + 6150 19601.177 272.14674 0 3901.9944 -0.9008056 + 6200 20499.796 106.2363 0 3902.4949 0.79071424 + 6250 19601.106 272.50139 0 3902.3359 -1.9306693 + 6300 17210.685 712.70535 0 3899.8692 4.8890923 + 6350 19911.896 214.91041 0 3902.2985 12.691129 + 6400 18834.642 411.87123 0 3899.7678 -1.9447856 + 6450 20216.311 158.39781 0 3902.1591 2.6009109 + 6500 20452.025 114.97122 0 3902.3832 0.14644416 + 6550 19142.589 357.34097 0 3902.2649 2.8968485 + 6600 20412.915 122.08784 0 3902.2573 3.1343105 + 6650 17317.867 699.39994 0 3906.4123 42.25563 + 6700 20479.771 109.8036 0 3902.3537 1.3520625 + 6750 20306.902 142.12484 0 3902.6623 2.2032106 + 6800 20755.367 58.994834 0 3902.5814 -0.90518094 + 6850 20471.259 111.7197 0 3902.6936 1.5799331 + 6900 20702.025 69.15032 0 3902.8586 9.3910371 + 6950 20477.695 110.34414 0 3902.5099 1.8181164 + 7000 20560.727 95.057704 0 3902.5998 -15.686006 + 7050 20336.675 136.39386 0 3902.4448 1.3704327 + 7100 20757.399 58.950153 0 3902.913 -6.4250981 + 7150 20870.958 38.095649 0 3903.088 -4.1962169 + 7200 20706.869 68.489134 0 3903.0944 2.8322659 + 7250 20386.713 127.7432 0 3903.0604 6.0287391 + 7300 18391.773 497.21001 0 3903.0939 19.202343 + 7350 20178.898 166.4993 0 3903.3322 1.5682417 + 7400 16858.704 781.78682 0 3903.7691 21.317514 + 7450 17509.513 660.71963 0 3903.2221 -5.9456143 + 7500 19974.601 204.20412 0 3903.2043 -0.69202711 + 7550 20917.053 29.73415 0 3903.2626 -3.9962577 + 7600 20923.518 28.482703 0 3903.2083 -1.9016251 + 7650 20549.528 97.630612 0 3903.0987 3.5512257 + 7700 20861.441 39.903885 0 3903.1337 2.4426264 + 7750 18843.349 413.64461 0 3903.1537 2.677739 + 7800 20616.054 85.214364 0 3903.0021 3.9639004 + 7850 16478.851 851.93376 0 3903.5728 7.3763128 + 7900 20312.115 141.35103 0 3902.8539 4.6707271 + 7950 20389.623 127.16589 0 3903.0219 3.4414001 + 8000 20452.117 115.30715 0 3902.7362 -1.0162528 + 8050 20857.093 40.791886 0 3903.2164 -15.150068 + 8100 19817.543 233.4997 0 3903.415 0.89346046 + 8150 18649.521 449.9112 0 3903.5262 -0.40053588 + 8200 19619.276 270.37616 0 3903.5754 5.5161492 + 8250 20393.176 127.01336 0 3903.5275 2.122613 + 8300 19145.912 358.00424 0 3903.5435 3.863924 + 8350 19636.311 267.17226 0 3903.5262 -7.1496084 + 8400 19086.332 368.86693 0 3903.3729 7.0968952 + 8450 19494.416 292.89527 0 3902.9723 3.1750935 + 8500 20041.919 191.77756 0 3903.244 0.95215503 + 8550 20357.561 133.15478 0 3903.0736 -0.14020152 + 8600 16998.797 756.07003 0 3903.9954 -16.724408 + 8650 20853.26 41.386996 0 3903.1017 -3.2612965 + 8700 20767.768 57.360884 0 3903.2438 1.1157649 + 8750 20752.546 60.106518 0 3903.1705 0.39130547 + 8800 20574.407 92.99798 0 3903.0734 0.61728166 + 8850 20326.99 138.94203 0 3903.1995 -1.9434522 + 8900 17408.108 679.53222 0 3903.2559 21.935371 + 8950 20471.21 112.2721 0 3903.2368 1.8142747 + 9000 19129.591 360.35257 0 3902.8694 4.5786395 + 9050 20439.668 117.89541 0 3903.0191 2.5585685 + 9100 20780.375 54.788664 0 3903.0062 3.8312459 + 9150 19904.559 216.61504 0 3902.6445 12.150414 + 9200 20961.295 21.52065 0 3903.2419 -0.2120699 + 9250 19315.252 326.44175 0 3903.3402 -19.740867 + 9300 20653.002 78.77764 0 3903.4076 -7.8068233 + 9350 18961.572 391.20947 0 3902.6117 -12.660843 + 9400 16262.179 892.67633 0 3904.191 22.2435 + 9450 17064.394 743.33301 0 3903.406 36.139436 + 9500 18075.588 555.06436 0 3902.3954 24.598176 + 9550 20487.738 109.06287 0 3903.0884 2.6320759 + 9600 20358.609 133.36993 0 3903.4828 0.76449113 + 9650 19849.022 228.46312 0 3904.208 9.5547064 + 9700 20448.112 116.8757 0 3903.5632 -1.0845697 + 9750 20472.78 112.51661 0 3903.7722 -0.30676738 + 9800 19491.99 293.35361 0 3902.9814 -20.10857 + 9850 19895.603 218.42479 0 3902.7957 -0.18235641 + 9900 19704.336 254.55068 0 3903.5019 14.553184 + 9950 17689.462 627.9788 0 3903.805 4.9918088 + 10000 20184.205 165.29396 0 3903.1097 2.9472364 +Loop time of 2.2898 on 1 procs for 10000 steps with 81 atoms + +Performance: 37732.583 tau/day, 4367.197 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.053341 | 0.053341 | 0.053341 | 0.0 | 2.33 +Neigh | 0.056174 | 0.056174 | 0.056174 | 0.0 | 2.45 +Comm | 0.0087028 | 0.0087028 | 0.0087028 | 0.0 | 0.38 +Output | 0.0036774 | 0.0036774 | 0.0036774 | 0.0 | 0.16 +Modify | 2.1598 | 2.1598 | 2.1598 | 0.0 | 94.32 +Other | | 0.008128 | | | 0.35 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 113 ave 113 max 113 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 582 ave 582 max 582 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 582 +Ave neighs/atom = 7.1851852 +Neighbor list builds = 993 +Dangerous builds = 950 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems2.g++.4 b/examples/rigid/log.20Mar22.rigid.poems2.g++.4 new file mode 100644 index 0000000000..89585cd109 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems2.g++.4 @@ -0,0 +1,330 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086358 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977039 0 3904.4174 9.0928122 + 250 19552.211 283.50525 0 3904.285 15.670466 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717095 0 3902.5839 -34.817444 + 1250 20625.583 82.586198 0 3902.1386 11.697328 + 1300 20690.013 71.006478 0 3902.4903 -29.29278 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.56 244.81784 0 3902.8844 6.7138497 + 1450 15690.149 998.34213 0 3903.9252 48.124569 + 1500 20234.455 155.92516 0 3903.0465 13.172207 + 1550 20779.631 55.063019 0 3903.1428 -2.6390455 + 1600 20642.753 80.233821 0 3902.9659 -2.4688431 + 1650 18785.698 423.90364 0 3902.7365 -5.6466892 + 1700 20965.076 20.760451 0 3903.182 -0.45366172 + 1750 18935.412 396.95958 0 3903.5173 25.913174 + 1800 20581.554 91.757912 0 3903.1567 3.8218442 + 1850 20616.949 85.184789 0 3903.1382 4.1907933 + 1900 16601.896 828.43849 0 3902.8638 -0.49468175 + 1950 20175.564 166.52646 0 3902.7421 5.6035728 + 2000 20262.525 150.28224 0 3902.6017 -1.1967705 + 2050 20168.994 167.65314 0 3902.6521 -0.80723928 + 2100 19810.955 232.96524 0 3901.6605 3.1936531 + 2150 20667.232 75.645145 0 3902.9103 0.54812734 + 2200 19863.772 224.34646 0 3902.8228 7.9294465 + 2250 18808.943 419.2084 0 3902.3461 14.344526 + 2300 20573.665 92.761842 0 3902.6999 -6.7671703 + 2350 19075.104 369.95414 0 3902.3809 -9.5353568 + 2400 20273.873 148.53775 0 3902.9586 -1.93796 + 2450 20087.769 182.30216 0 3902.2593 2.131796 + 2500 20711.602 67.530554 0 3903.0124 2.6280244 + 2550 19971.224 204.75926 0 3903.134 3.1760522 + 2600 20620.084 85.027145 0 3903.5612 -0.92888063 + 2650 19737.546 248.65474 0 3903.7559 -3.3218688 + 2700 20650.724 79.522243 0 3903.7303 -7.5918025 + 2750 19863.245 225.2505 0 3903.6292 9.2140221 + 2800 18992.457 386.73547 0 3903.8572 2.6244537 + 2850 18703.899 440.48356 0 3904.1685 14.561348 + 2900 17939.805 581.74599 0 3903.932 -8.0863089 + 2950 20867.516 39.38186 0 3903.7367 3.0985423 + 3000 19767.994 242.8847 0 3903.6243 1.5943109 + 3050 20397.448 126.31591 0 3903.6212 -0.14982775 + 3100 20978.114 19.126395 0 3903.9623 -9.6797253 + 3150 18303.556 513.8514 0 3903.3989 4.5940322 + 3200 19156.505 356.46608 0 3903.9671 10.071308 + 3250 17484.205 666.52199 0 3904.3377 -4.1641768 + 3300 18069.94 557.75947 0 3904.0447 11.868707 + 3350 20855.645 41.964632 0 3904.1212 5.4186293 + 3400 18011.986 568.76255 0 3904.3155 25.262783 + 3450 18669.69 446.92755 0 3904.2776 -4.194499 + 3500 20248.799 154.22147 0 3903.9991 3.9211572 + 3550 20226.024 158.64726 0 3904.2072 1.5299114 + 3600 20267.02 151.25631 0 3904.4082 -8.9821729 + 3650 20522.946 103.65382 0 3904.1994 -14.433796 + 3700 20892.319 35.294614 0 3904.2426 -21.264596 + 3750 19942.202 211.02993 0 3904.0304 -1.6428817 + 3800 20421.678 122.08118 0 3903.8734 1.7137935 + 3850 17899.53 588.82593 0 3903.5536 -24.450276 + 3900 20721.119 66.486999 0 3903.7312 -7.1772088 + 3950 20946.484 24.799445 0 3903.778 -0.4028037 + 4000 20985.362 17.608355 0 3903.7865 4.7522266 + 4050 19969.779 205.46466 0 3903.5719 18.941639 + 4100 20479.578 110.56561 0 3903.08 2.3715952 + 4150 18110.701 549.53348 0 3903.367 1.133321 + 4200 19321.098 325.58216 0 3903.5634 -3.7574942 + 4250 20734.436 63.87616 0 3903.5865 0.48350623 + 4300 19446.823 302.1727 0 3903.4362 4.0462392 + 4350 20494.669 108.1918 0 3903.501 2.9789077 + 4400 20379.244 129.61413 0 3903.5482 4.0881089 + 4450 19710.564 253.4251 0 3903.5295 5.3334683 + 4500 20744.753 61.785082 0 3903.406 4.0015409 + 4550 19948.024 208.76984 0 3902.8484 2.705423 + 4600 18367.368 502.69569 0 3904.0602 21.476471 + 4650 20559.367 96.133242 0 3903.4234 2.2549454 + 4700 20940.135 25.547808 0 3903.3505 -8.9042666 + 4750 20128.703 175.82088 0 3903.3584 -8.1450176 + 4800 20632.27 82.543887 0 3903.3347 -0.55649542 + 4850 19864.539 224.63792 0 3903.2563 7.1553461 + 4900 19332.037 323.15561 0 3903.1625 17.020214 + 4950 19055.575 373.68069 0 3902.4908 10.149457 + 5000 20219.484 159.21383 0 3903.5627 3.1806346 + 5050 17557.761 652.32864 0 3903.7659 10.733736 + 5100 20615.337 85.795304 0 3903.4503 -3.6035636 + 5150 20759.853 59.155843 0 3903.573 2.0152286 + 5200 20082.007 184.39375 0 3903.2839 -5.3745109 + 5250 18689.521 442.59842 0 3903.6208 -9.8911164 + 5300 20038.496 192.34221 0 3903.1749 -2.1437039 + 5350 19897.455 218.70142 0 3903.4154 0.64582116 + 5400 18732.385 434.21543 0 3903.1755 12.98676 + 5450 19831.487 230.79099 0 3903.2886 11.439958 + 5500 20079.89 184.6953 0 3903.1935 4.0906279 + 5550 20453.497 115.47128 0 3903.1559 7.8844436 + 5600 16673.041 815.52661 0 3903.1267 -20.17797 + 5650 19691.378 256.6412 0 3903.1928 3.7103317 + 5700 20345.743 135.29997 0 3903.0302 5.6373816 + 5750 20769.613 56.906603 0 3903.1312 -17.564762 + 5800 20713.369 67.38314 0 3903.1922 -5.340631 + 5850 20799.947 51.348865 0 3903.1909 -2.7827653 + 5900 19581.933 273.51588 0 3899.7997 12.347375 + 5950 20444.438 116.909 0 3902.9161 -0.74896654 + 6000 18970.948 389.99664 0 3903.1352 26.642912 + 6050 19414.753 307.13217 0 3902.4568 25.86316 + 6100 20780.042 54.586474 0 3902.7424 1.5387425 + 6150 20885.872 35.091585 0 3902.8456 -8.251884 + 6200 19825.81 231.40943 0 3902.8558 6.7196589 + 6250 20578.278 92.255994 0 3903.0481 -5.9647091 + 6300 20093.43 181.8699 0 3902.8754 -9.9906069 + 6350 20605.294 87.180289 0 3902.9755 -3.5643876 + 6400 19737.257 247.84828 0 3902.8958 -4.2783347 + 6450 19884.717 220.81633 0 3903.1714 3.8758905 + 6500 18719.372 436.94802 0 3903.4984 1.7865904 + 6550 20096.883 181.63346 0 3903.2784 2.395512 + 6600 20888.673 35.003062 0 3903.2758 2.7728947 + 6650 20437.85 118.16373 0 3902.9507 8.1456757 + 6700 19241.051 339.73065 0 3902.8882 13.740454 + 6750 20407.542 123.94326 0 3903.1177 7.6285942 + 6800 20536.785 99.976706 0 3903.0851 8.3496632 + 6850 20625.328 83.579677 0 3903.0849 6.5074992 + 6900 20705.37 68.944625 0 3903.2724 3.1905177 + 6950 18872.424 408.67134 0 3903.5647 6.2638845 + 7000 20072.762 186.18051 0 3903.3586 -22.780407 + 7050 20461.879 114.07495 0 3903.3117 -11.495523 + 7100 19811.566 234.50237 0 3903.3108 1.1212695 + 7150 20742.918 61.884088 0 3903.1651 -3.7907508 + 7200 20911.192 30.599903 0 3903.0429 -7.0262304 + 7250 20879.755 36.30274 0 3902.9241 -5.8018787 + 7300 20682.32 72.703261 0 3902.7626 -3.3446789 + 7350 19401.046 309.70672 0 3902.493 3.4836528 + 7400 20220.542 157.83897 0 3902.3838 2.3400031 + 7450 17691.193 625.47764 0 3901.6244 25.239568 + 7500 19745.294 245.02566 0 3901.5615 5.3622843 + 7550 19685.719 256.70983 0 3902.2133 3.4560563 + 7600 18830.192 415.10021 0 3902.1727 -0.10282681 + 7650 19613.136 270.18979 0 3902.2521 8.2241536 + 7700 20989.015 15.636879 0 3902.4915 1.2955204 + 7750 20301.583 142.90625 0 3902.4586 0.12548373 + 7800 18360.147 502.50342 0 3902.5307 17.117272 + 7850 20796.478 51.032537 0 3902.2321 -3.0993883 + 7900 20284.267 145.64296 0 3901.9887 -1.2682383 + 7950 20280.983 146.13471 0 3901.8723 3.5999841 + 8000 20915.869 28.730821 0 3902.0399 2.4987291 + 8050 20745.162 60.19981 0 3901.8964 4.0643481 + 8100 20509.039 103.70462 0 3901.6748 1.0771863 + 8150 20212.97 158.64893 0 3901.7916 3.0000215 + 8200 20323.463 138.25912 0 3901.8634 -1.2802945 + 8250 19997.284 198.37183 0 3901.5727 -2.6431964 + 8300 20138.402 171.75824 0 3901.092 1.7669897 + 8350 20367.568 130.22531 0 3901.9972 -1.2153731 + 8400 19945.534 208.35675 0 3901.9741 1.6021151 + 8450 20112.534 177.18642 0 3901.7298 2.2413008 + 8500 20686.7 71.116816 0 3901.9873 2.2888545 + 8550 18081.94 553.83586 0 3902.3432 7.8257937 + 8600 18320.081 505.67086 0 3898.2784 16.554878 + 8650 20235.305 154.43021 0 3901.709 3.1740823 + 8700 20355.413 132.22512 0 3901.746 4.3436482 + 8750 20087.188 182.11349 0 3901.9631 10.422134 + 8800 20400.795 124.09819 0 3902.0232 2.1179177 + 8850 20678.731 72.825797 0 3902.2204 -3.4491441 + 8900 20372.643 129.5072 0 3902.2189 -8.2166415 + 8950 20851.731 40.899364 0 3902.331 -5.8382839 + 9000 20318.076 139.61775 0 3902.2243 -4.1960802 + 9050 16879.415 776.53739 0 3902.3549 -14.429475 + 9100 19135.149 358.68223 0 3902.2284 -15.50479 + 9150 20689.556 70.939656 0 3902.339 -2.9876179 + 9200 19949.801 207.54882 0 3901.9564 6.4259245 + 9250 20207.027 160.2813 0 3902.3233 1.7402195 + 9300 20030.005 192.99466 0 3902.2548 5.300728 + 9350 19795.291 236.24003 0 3902.0347 5.8677745 + 9400 18232.093 526.18752 0 3902.501 19.344893 + 9450 18789.641 422.30568 0 3901.8687 -7.5185247 + 9500 16332.599 874.10423 0 3898.6597 16.241378 + 9550 18572.572 462.19972 0 3901.5649 -10.777359 + 9600 19859.645 223.32209 0 3901.0341 0.89631957 + 9650 19092.741 365.35768 0 3901.0504 6.7830005 + 9700 18391.154 495.72792 0 3901.4972 6.0683847 + 9750 17790.092 608.60997 0 3903.0714 8.2090184 + 9800 17681.783 628.99951 0 3903.4038 14.231747 + 9850 17804.412 605.54067 0 3902.654 22.308453 + 9900 19134.472 359.37911 0 3902.7999 8.5633158 + 9950 20099.055 180.28604 0 3902.3332 4.7905855 + 10000 20035.447 192.30744 0 3902.5754 1.8299201 +Loop time of 2.31994 on 4 procs for 10000 steps with 81 atoms + +Performance: 37242.315 tau/day, 4310.453 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0052789 | 0.014781 | 0.038634 | 11.4 | 0.64 +Neigh | 0.0081228 | 0.016514 | 0.033404 | 7.7 | 0.71 +Comm | 0.12269 | 0.13668 | 0.14951 | 3.1 | 5.89 +Output | 0.0034489 | 0.0039413 | 0.0050811 | 1.1 | 0.17 +Modify | 2.1036 | 2.1312 | 2.1509 | 1.2 | 91.86 +Other | | 0.01685 | | | 0.73 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 35.25 ave 47 max 24 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 137.5 ave 252 max 0 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 550 +Ave neighs/atom = 6.7901235 +Neighbor list builds = 994 +Dangerous builds = 956 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.1 b/examples/rigid/log.20Mar22.rigid.poems3.g++.1 new file mode 100644 index 0000000000..b565d9f79d --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems3.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 5267.6607 16.443791 + 150 16682.639 17.488068 0 5269.43 14.900278 + 200 16733.955 1.3724268 0 5269.4692 14.569123 + 250 16738.877 -0.15250573 0 5269.4939 14.496287 + 300 16738.611 -0.05516662 0 5269.5077 14.495909 + 350 16738.515 -0.01744351 0 5269.5152 14.496329 + 400 16738.488 -0.0060096677 0 5269.5178 14.496497 + 450 16738.479 -0.0012712918 0 5269.5199 14.496575 + 500 16738.479 -0.00081070354 0 5269.5203 14.49658 + 550 16738.479 -0.00083205205 0 5269.5203 14.496577 + 600 16738.479 -0.0005835658 0 5269.5206 14.49658 + 650 16738.479 -0.00047227225 0 5269.5206 14.496583 + 700 16738.479 0 0 5269.521 14.496593 + 750 16738.479 0 0 5269.5211 14.496595 + 800 16738.479 0 0 5269.5211 14.496596 + 850 16738.479 0 0 5269.5211 14.496595 + 900 16738.479 0 0 5269.5212 14.496593 + 950 16738.485 -0.003532391 0 5269.5196 14.496546 + 1000 16738.609 -0.051135033 0 5269.5109 14.496098 + 1050 16737.381 0.32991002 0 5269.5055 14.525627 + 1100 16737.915 0.16210932 0 5269.5058 14.531848 + 1150 16738.726 -0.089235332 0 5269.5098 14.509768 + 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 + 1250 16738.48 0 0 5269.5214 14.510585 + 1300 16738.48 0 0 5269.5214 14.510587 + 1350 16738.48 0 0 5269.5215 14.510588 + 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 + 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 + 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 + 1550 16738.48 0 0 5269.5216 14.510582 + 1600 16738.48 0 0 5269.5216 14.510581 + 1650 16738.481 0 0 5269.5216 14.510581 + 1700 16738.481 0 0 5269.5217 14.510582 + 1750 16738.481 0 0 5269.5217 14.510583 + 1800 16738.481 0 0 5269.5217 14.510585 + 1850 16738.481 0 0 5269.5218 14.510585 + 1900 16738.481 0 0 5269.5218 14.510585 + 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 + 2000 16738.514 -0.013238802 0 5269.5188 14.510401 + 2050 16738.578 -0.03654435 0 5269.5158 14.510155 + 2100 16738.656 -0.063182323 0 5269.5137 14.510082 + 2150 16738.63 -0.056004395 0 5269.5127 14.510096 + 2200 16738.579 -0.038415873 0 5269.5143 14.510273 + 2250 16738.538 -0.023709094 0 5269.516 14.510414 + 2300 16738.512 -0.013252539 0 5269.5182 14.510501 + 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 + 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 + 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 + 2500 16738.491 -0.005189304 0 5269.5197 14.510606 + 2550 16738.604 -0.044988104 0 5269.5155 14.510185 + 2600 16738.446 0.00096754005 0 5269.5117 14.510521 + 2650 16732.887 1.753125 0 5269.5138 14.598792 + 2700 16738.784 -0.10629556 0 5269.5107 14.499176 + 2750 16734.136 1.359459 0 5269.5135 14.594678 + 2800 16738.608 -0.047184149 0 5269.5147 14.510254 + 2850 16738.509 -0.012527238 0 5269.5181 14.509344 + 2900 16738.487 -0.0026065529 0 5269.521 14.509512 + 2950 16738.498 -0.0082248532 0 5269.519 14.509457 + 3000 16738.683 -0.071294028 0 5269.514 14.509005 + 3050 16717.444 6.5874862 0 5269.4864 14.834144 + 3100 16657.654 25.431253 0 5269.5074 14.467824 + 3150 16739.322 -0.28964062 0 5269.497 13.658821 + 3200 16733.615 1.4969789 0 5269.487 11.998304 + 3250 16737.289 0.35071214 0 5269.4974 11.918931 + 3300 16732.493 1.8663821 0 5269.503 12.109003 + 3350 16738.717 -0.087719164 0 5269.5085 11.979747 + 3400 16738.586 -0.045267897 0 5269.5095 11.97972 + 3450 16738.662 -0.071274216 0 5269.5076 11.979564 + 3500 16738.853 -0.13644992 0 5269.5026 11.979658 + 3550 16729.612 2.7475277 0 5269.4774 12.195939 + 3600 16728.659 3.0596069 0 5269.4893 12.241248 + 3650 16738.923 -0.15949792 0 5269.5014 11.991857 + 3700 16738.76 -0.10695054 0 5269.5028 11.992932 + 3750 16738.751 -0.10105954 0 5269.5057 11.993137 + 3800 16738.597 -0.048627545 0 5269.5097 11.993456 + 3850 16738.507 -0.016053927 0 5269.5138 11.992973 + 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 + 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 + 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 + 4050 16738.472 -0.00023792127 0 5269.5187 11.993172 + 4100 16738.472 0 0 5269.5189 11.993188 + 4150 16738.472 0 0 5269.5189 11.993188 + 4200 16738.472 0 0 5269.519 11.993178 + 4250 16738.472 0 0 5269.519 11.993164 + 4300 16738.472 0 0 5269.5191 11.993152 + 4350 16738.473 0 0 5269.5191 11.993147 + 4400 16738.473 0 0 5269.5192 11.993149 + 4450 16738.473 0 0 5269.5192 11.993158 + 4500 16738.473 0 0 5269.5193 11.99317 + 4550 16738.473 0 0 5269.5193 11.993176 + 4600 16738.473 0 0 5269.5194 11.993174 + 4650 16738.473 0 0 5269.5194 11.993167 + 4700 16738.474 0 0 5269.5195 11.993162 + 4750 16738.474 0 0 5269.5195 11.99316 + 4800 16738.474 0 0 5269.5196 11.99316 + 4850 16738.474 0 0 5269.5196 11.993163 + 4900 16738.474 0 0 5269.5197 11.99317 + 4950 16738.474 0 0 5269.5197 11.993176 + 5000 16738.475 0 0 5269.5198 11.993174 + 5050 16738.475 0 0 5269.5198 11.993165 + 5100 16738.475 0 0 5269.5199 11.993155 + 5150 16738.475 0 0 5269.5199 11.99315 + 5200 16738.475 0 0 5269.52 11.993153 + 5250 16738.475 0 0 5269.52 11.993161 + 5300 16738.476 0 0 5269.5201 11.993173 + 5350 16738.476 0 0 5269.5201 11.993185 + 5400 16738.476 0 0 5269.5202 11.993189 + 5450 16738.476 0 0 5269.5202 11.993181 + 5500 16738.476 0 0 5269.5203 11.993165 + 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 + 5600 16738.534 -0.020777802 0 5269.5177 11.992799 + 5650 16738.649 -0.059321662 0 5269.5153 11.993266 + 5700 16409.08 103.75288 0 5269.5745 23.626238 + 5750 16738.578 -0.036776519 0 5269.5155 11.910545 + 5800 16738.484 -0.0047306177 0 5269.518 11.911008 + 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 + 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 + 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 + 6000 16738.477 0 0 5269.5206 11.911044 + 6050 16738.477 0 0 5269.5207 11.911034 + 6100 16738.478 0 0 5269.5207 11.911032 + 6150 16738.478 0 0 5269.5208 11.911037 + 6200 16738.478 0 0 5269.5208 11.911049 + 6250 16738.478 0 0 5269.5209 11.911062 + 6300 16738.478 0 0 5269.5209 11.911068 + 6350 16738.478 0 0 5269.521 11.911065 + 6400 16738.478 0 0 5269.521 11.911058 + 6450 16738.479 0 0 5269.5211 11.911052 + 6500 16738.479 0 0 5269.5211 11.911047 + 6550 16738.479 0 0 5269.5212 11.911046 + 6600 16738.479 0 0 5269.5212 11.911049 + 6650 16738.479 0 0 5269.5213 11.911056 + 6700 16738.479 0 0 5269.5213 11.911062 + 6750 16738.48 0 0 5269.5214 11.91106 + 6800 16738.48 0 0 5269.5214 11.911051 + 6850 16738.48 0 0 5269.5215 11.911044 + 6900 16738.48 0 0 5269.5215 11.911041 + 6950 16738.48 0 0 5269.5216 11.911045 + 7000 16738.48 0 0 5269.5216 11.911053 + 7050 16738.481 0 0 5269.5217 11.911063 + 7100 16738.481 0 0 5269.5217 11.911071 + 7150 16738.481 0 0 5269.5218 11.911072 + 7200 16738.481 0 0 5269.5218 11.911063 + 7250 16738.481 0 0 5269.5219 11.911048 + 7300 16738.481 0 0 5269.5219 11.911036 + 7350 16738.482 0 0 5269.522 11.911031 + 7400 16738.482 0 0 5269.522 11.911035 + 7450 16738.482 0 0 5269.5221 11.911046 + 7500 16738.482 0 0 5269.5221 11.911062 + 7550 16738.482 0 0 5269.5222 11.911077 + 7600 16738.482 0 0 5269.5222 11.911081 + 7650 16738.483 0 0 5269.5223 11.911071 + 7700 16738.483 0 0 5269.5223 11.911054 + 7750 16738.483 0 0 5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974054 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.000227631 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306436 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567429 0 5269.522 11.911005 + 9500 16738.495 -0.0036645351 0 5269.5224 11.910982 + 9550 16738.49 -0.0010673912 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.00058544643 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244931 0 5269.5242 11.911015 +Loop time of 2.30195 on 1 procs for 10000 steps with 81 atoms + +Performance: 37533.440 tau/day, 4344.148 timesteps/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 | 0.0076839 | 0.0076839 | 0.0076839 | 0.0 | 0.33 +Neigh | 0.029562 | 0.029562 | 0.029562 | 0.0 | 1.28 +Comm | 0.0084877 | 0.0084877 | 0.0084877 | 0.0 | 0.37 +Output | 0.0037958 | 0.0037958 | 0.0037958 | 0.0 | 0.16 +Modify | 2.2446 | 2.2446 | 2.2446 | 0.0 | 97.51 +Other | | 0.00785 | | | 0.34 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 69 ave 69 max 69 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems3.g++.4 b/examples/rigid/log.20Mar22.rigid.poems3.g++.4 new file mode 100644 index 0000000000..39fd6245e0 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems3.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# unconnected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 10 18 +9 atoms in group clump2 +group clump3 id <> 19 27 +9 atoms in group clump3 +group clump4 id <> 28 36 +9 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 46 54 +9 atoms in group clump6 +group clump7 id <> 55 63 +9 atoms in group clump7 +group clump8 id <> 64 72 +9 atoms in group clump8 +group clump9 id <> 73 81 +9 atoms in group clump9 + +fix 1 all poems file unconnected-bodies.dat +WARNING: No joints between rigid bodies, use fix rigid instead (src/POEMS/fix_poems.cpp:1035) +9 clusters, 9 bodies, 0 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 115.29439 5235.9179 0 5272.2142 -2.7403788 + 50 14910.686 571.71596 0 5265.8207 32.006226 + 100 16298.5 136.65142 0 5267.6607 16.443791 + 150 16682.639 17.488068 0 5269.43 14.900278 + 200 16733.955 1.3724268 0 5269.4692 14.569123 + 250 16738.877 -0.15250573 0 5269.4939 14.496287 + 300 16738.611 -0.05516662 0 5269.5077 14.495909 + 350 16738.515 -0.01744351 0 5269.5152 14.496329 + 400 16738.488 -0.0060096677 0 5269.5178 14.496497 + 450 16738.479 -0.0012712918 0 5269.5199 14.496575 + 500 16738.479 -0.00081070354 0 5269.5203 14.49658 + 550 16738.479 -0.00083205205 0 5269.5203 14.496577 + 600 16738.479 -0.0005835658 0 5269.5206 14.49658 + 650 16738.479 -0.00047227225 0 5269.5206 14.496583 + 700 16738.479 0 0 5269.521 14.496593 + 750 16738.479 0 0 5269.5211 14.496595 + 800 16738.479 0 0 5269.5211 14.496596 + 850 16738.479 0 0 5269.5211 14.496595 + 900 16738.479 0 0 5269.5212 14.496593 + 950 16738.485 -0.003532391 0 5269.5196 14.496546 + 1000 16738.609 -0.051135033 0 5269.5109 14.496098 + 1050 16737.381 0.32991002 0 5269.5055 14.525627 + 1100 16737.915 0.16210932 0 5269.5058 14.531848 + 1150 16738.726 -0.089235332 0 5269.5098 14.509768 + 1200 16738.49 -0.0075446298 0 5269.5169 14.510489 + 1250 16738.48 0 0 5269.5214 14.510585 + 1300 16738.48 0 0 5269.5214 14.510587 + 1350 16738.48 0 0 5269.5215 14.510588 + 1400 16738.48 -0.00044742303 0 5269.5211 14.510581 + 1450 16738.481 -0.0010975104 0 5269.5207 14.51057 + 1500 16738.481 -0.00057925965 0 5269.5211 14.510575 + 1550 16738.48 0 0 5269.5216 14.510582 + 1600 16738.48 0 0 5269.5216 14.510581 + 1650 16738.481 0 0 5269.5216 14.510581 + 1700 16738.481 0 0 5269.5217 14.510582 + 1750 16738.481 0 0 5269.5217 14.510583 + 1800 16738.481 0 0 5269.5217 14.510585 + 1850 16738.481 0 0 5269.5218 14.510585 + 1900 16738.481 0 0 5269.5218 14.510585 + 1950 16738.487 -0.0031700155 0 5269.5206 14.510534 + 2000 16738.514 -0.013238802 0 5269.5188 14.510401 + 2050 16738.578 -0.03654435 0 5269.5158 14.510155 + 2100 16738.656 -0.063182323 0 5269.5137 14.510082 + 2150 16738.63 -0.056004395 0 5269.5127 14.510096 + 2200 16738.579 -0.038415873 0 5269.5143 14.510273 + 2250 16738.538 -0.023709094 0 5269.516 14.510414 + 2300 16738.512 -0.013252539 0 5269.5182 14.510501 + 2350 16738.491 -0.0045593284 0 5269.5203 14.510598 + 2400 16738.482 -0.00052242487 0 5269.5217 14.510655 + 2450 16738.486 -0.0023245722 0 5269.5211 14.510627 + 2500 16738.491 -0.005189304 0 5269.5197 14.510606 + 2550 16738.604 -0.044988104 0 5269.5155 14.510185 + 2600 16738.446 0.0009675401 0 5269.5117 14.510521 + 2650 16732.887 1.753125 0 5269.5138 14.598792 + 2700 16738.784 -0.10629556 0 5269.5107 14.499176 + 2750 16734.136 1.359459 0 5269.5135 14.594678 + 2800 16738.608 -0.047184149 0 5269.5147 14.510254 + 2850 16738.509 -0.012527238 0 5269.5181 14.509344 + 2900 16738.487 -0.0026065529 0 5269.521 14.509512 + 2950 16738.498 -0.0082248532 0 5269.519 14.509457 + 3000 16738.683 -0.071294028 0 5269.514 14.509005 + 3050 16717.444 6.5874862 0 5269.4864 14.834144 + 3100 16657.654 25.431253 0 5269.5074 14.467824 + 3150 16739.322 -0.28964062 0 5269.497 13.658821 + 3200 16733.615 1.4969789 0 5269.487 11.998304 + 3250 16737.289 0.35071214 0 5269.4974 11.918931 + 3300 16732.493 1.8663821 0 5269.503 12.109003 + 3350 16738.717 -0.087719164 0 5269.5085 11.979747 + 3400 16738.586 -0.045267897 0 5269.5095 11.97972 + 3450 16738.662 -0.071274216 0 5269.5076 11.979564 + 3500 16738.853 -0.13644992 0 5269.5026 11.979658 + 3550 16729.612 2.7475277 0 5269.4774 12.195939 + 3600 16728.659 3.059607 0 5269.4893 12.241248 + 3650 16738.923 -0.15949792 0 5269.5014 11.991857 + 3700 16738.76 -0.10695054 0 5269.5028 11.992932 + 3750 16738.751 -0.10105954 0 5269.5057 11.993137 + 3800 16738.597 -0.048627545 0 5269.5097 11.993456 + 3850 16738.507 -0.016053927 0 5269.5138 11.992973 + 3900 16738.485 -0.0060825487 0 5269.5169 11.993052 + 3950 16738.475 -0.0014953722 0 5269.5183 11.993119 + 4000 16738.472 -0.00054315391 0 5269.5184 11.99315 + 4050 16738.472 -0.00023792126 0 5269.5187 11.993172 + 4100 16738.472 0 0 5269.5189 11.993188 + 4150 16738.472 0 0 5269.5189 11.993188 + 4200 16738.472 0 0 5269.519 11.993178 + 4250 16738.472 0 0 5269.519 11.993164 + 4300 16738.472 0 0 5269.5191 11.993152 + 4350 16738.473 0 0 5269.5191 11.993147 + 4400 16738.473 0 0 5269.5192 11.993149 + 4450 16738.473 0 0 5269.5192 11.993158 + 4500 16738.473 0 0 5269.5193 11.99317 + 4550 16738.473 0 0 5269.5193 11.993176 + 4600 16738.473 0 0 5269.5194 11.993174 + 4650 16738.473 0 0 5269.5194 11.993167 + 4700 16738.474 0 0 5269.5195 11.993162 + 4750 16738.474 0 0 5269.5195 11.99316 + 4800 16738.474 0 0 5269.5196 11.99316 + 4850 16738.474 0 0 5269.5196 11.993163 + 4900 16738.474 0 0 5269.5197 11.99317 + 4950 16738.474 0 0 5269.5197 11.993176 + 5000 16738.475 0 0 5269.5198 11.993174 + 5050 16738.475 0 0 5269.5198 11.993165 + 5100 16738.475 0 0 5269.5199 11.993155 + 5150 16738.475 0 0 5269.5199 11.99315 + 5200 16738.475 0 0 5269.52 11.993153 + 5250 16738.475 0 0 5269.52 11.993161 + 5300 16738.476 0 0 5269.5201 11.993173 + 5350 16738.476 0 0 5269.5201 11.993185 + 5400 16738.476 0 0 5269.5202 11.993189 + 5450 16738.476 0 0 5269.5202 11.993181 + 5500 16738.476 0 0 5269.5203 11.993165 + 5550 16738.483 -0.0030091905 0 5269.5195 11.993097 + 5600 16738.534 -0.020777802 0 5269.5177 11.992799 + 5650 16738.649 -0.059321662 0 5269.5153 11.993266 + 5700 16409.08 103.75288 0 5269.5745 23.626238 + 5750 16738.578 -0.036776519 0 5269.5155 11.910545 + 5800 16738.484 -0.0047306177 0 5269.518 11.911008 + 5850 16738.477 -0.00022082692 0 5269.5202 11.911078 + 5900 16738.477 -0.00033136078 0 5269.5203 11.91107 + 5950 16738.478 -0.00036902212 0 5269.5203 11.911052 + 6000 16738.477 0 0 5269.5206 11.911044 + 6050 16738.477 0 0 5269.5207 11.911034 + 6100 16738.478 0 0 5269.5207 11.911032 + 6150 16738.478 0 0 5269.5208 11.911037 + 6200 16738.478 0 0 5269.5208 11.911049 + 6250 16738.478 0 0 5269.5209 11.911062 + 6300 16738.478 0 0 5269.5209 11.911068 + 6350 16738.478 0 0 5269.521 11.911065 + 6400 16738.478 0 0 5269.521 11.911058 + 6450 16738.479 0 0 5269.5211 11.911052 + 6500 16738.479 0 0 5269.5211 11.911047 + 6550 16738.479 0 0 5269.5212 11.911046 + 6600 16738.479 0 0 5269.5212 11.911049 + 6650 16738.479 0 0 5269.5213 11.911056 + 6700 16738.479 0 0 5269.5213 11.911062 + 6750 16738.48 0 0 5269.5214 11.91106 + 6800 16738.48 0 0 5269.5214 11.911051 + 6850 16738.48 0 0 5269.5215 11.911044 + 6900 16738.48 0 0 5269.5215 11.911041 + 6950 16738.48 0 0 5269.5216 11.911045 + 7000 16738.48 0 0 5269.5216 11.911053 + 7050 16738.481 0 0 5269.5217 11.911063 + 7100 16738.481 0 0 5269.5217 11.911071 + 7150 16738.481 0 0 5269.5218 11.911072 + 7200 16738.481 0 0 5269.5218 11.911063 + 7250 16738.481 0 0 5269.5219 11.911048 + 7300 16738.481 0 0 5269.5219 11.911036 + 7350 16738.482 0 0 5269.522 11.911031 + 7400 16738.482 0 0 5269.522 11.911035 + 7450 16738.482 0 0 5269.5221 11.911046 + 7500 16738.482 0 0 5269.5221 11.911062 + 7550 16738.482 0 0 5269.5222 11.911077 + 7600 16738.482 0 0 5269.5222 11.911081 + 7650 16738.483 0 0 5269.5223 11.911071 + 7700 16738.483 0 0 5269.5223 11.911054 + 7750 16738.483 0 0 5269.5224 11.911039 + 7800 16738.483 0 0 5269.5224 11.911031 + 7850 16738.483 0 0 5269.5225 11.911031 + 7900 16738.483 0 0 5269.5226 11.911039 + 7950 16738.484 0 0 5269.5226 11.911052 + 8000 16738.484 0 0 5269.5227 11.911065 + 8050 16738.484 0 0 5269.5227 11.91107 + 8100 16738.484 0 0 5269.5228 11.911065 + 8150 16738.484 0 0 5269.5228 11.911056 + 8200 16738.484 0 0 5269.5229 11.911047 + 8250 16738.485 0 0 5269.5229 11.911042 + 8300 16738.485 0 0 5269.523 11.911041 + 8350 16738.485 0 0 5269.523 11.911046 + 8400 16738.485 0 0 5269.5231 11.911055 + 8450 16738.485 0 0 5269.5231 11.911062 + 8500 16738.485 0 0 5269.5232 11.91106 + 8550 16738.486 0 0 5269.5232 11.911053 + 8600 16738.487 -0.00084974055 0 5269.5227 11.911032 + 8650 16738.486 0 0 5269.5233 11.911046 + 8700 16738.486 0 0 5269.5234 11.91105 + 8750 16738.486 0 0 5269.5235 11.911056 + 8800 16738.486 0 0 5269.5235 11.911063 + 8850 16738.487 -0.000227631 0 5269.5234 11.911065 + 8900 16738.487 0 0 5269.5236 11.911068 + 8950 16738.487 0 0 5269.5237 11.911058 + 9000 16738.487 0 0 5269.5237 11.911045 + 9050 16738.487 0 0 5269.5238 11.911036 + 9100 16738.487 0 0 5269.5238 11.911034 + 9150 16738.488 0 0 5269.5239 11.91104 + 9200 16738.488 0 0 5269.5239 11.911052 + 9250 16738.488 0 0 5269.524 11.911068 + 9300 16738.488 0 0 5269.524 11.911079 + 9350 16738.488 0 0 5269.5241 11.911078 + 9400 16738.492 -0.0016306433 0 5269.5235 11.911038 + 9450 16738.492 -0.0032567425 0 5269.522 11.911005 + 9500 16738.495 -0.0036645345 0 5269.5224 11.910982 + 9550 16738.49 -0.001067391 0 5269.5237 11.911012 + 9600 16738.489 0 0 5269.5244 11.911032 + 9650 16738.489 0 0 5269.5244 11.911043 + 9700 16738.49 0 0 5269.5245 11.911058 + 9750 16738.49 0 0 5269.5245 11.911071 + 9800 16738.49 0 0 5269.5246 11.911073 + 9850 16738.49 0 0 5269.5246 11.911065 + 9900 16738.49 0 0 5269.5247 11.911053 + 9950 16738.491 -0.00058544648 0 5269.5243 11.911032 + 10000 16738.493 -0.0015244933 0 5269.5242 11.911015 +Loop time of 2.36483 on 4 procs for 10000 steps with 81 atoms + +Performance: 36535.358 tau/day, 4228.629 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0030635 | 0.0035263 | 0.0040903 | 0.7 | 0.15 +Neigh | 0.0093439 | 0.01002 | 0.010976 | 0.6 | 0.42 +Comm | 0.11912 | 0.12509 | 0.13346 | 1.5 | 5.29 +Output | 0.003411 | 0.0038449 | 0.0050123 | 1.1 | 0.16 +Modify | 2.1961 | 2.2052 | 2.2137 | 0.5 | 93.25 +Other | | 0.01717 | | | 0.73 + +Nlocal: 20.25 ave 27 max 9 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 31.5 ave 51 max 15 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 1 ave 4 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 4 +Ave neighs/atom = 0.049382716 +Neighbor list builds = 998 +Dangerous builds = 997 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.1 b/examples/rigid/log.20Mar22.rigid.poems4.g++.1 new file mode 100644 index 0000000000..e2febc5ed9 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems4.g++.1 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.438428 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699118 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538604 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.029 99.812844 0 3680.6511 -16.185479 + 1450 21771.107 52.159653 0 3680.6775 -2.4756655 + 1500 21520.949 93.503876 0 3680.3286 2.1023573 + 1550 21351.419 121.6813 0 3680.2511 5.5159876 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21873 0 3679.8247 -1.1045277 + 1700 18501.33 596.4807 0 3680.0357 -15.6798 + 1750 18563.64 587.34824 0 3681.2882 33.532308 + 1800 19110.175 494.82517 0 3679.8543 18.024074 + 1850 21364.178 119.23765 0 3679.9339 2.5290144 + 1900 20146.588 322.15509 0 3679.9197 5.7317299 + 1950 20692.676 231.25264 0 3680.0319 4.297803 + 2000 20943.902 189.11251 0 3679.7629 -22.643824 + 2050 19667.823 401.86882 0 3679.8394 3.6241915 + 2100 20280.125 299.81485 0 3679.8357 7.4804047 + 2150 19181.201 483.6306 0 3680.4975 22.63342 + 2200 21301.144 130.54014 0 3680.7308 4.7074288 + 2250 20484.876 266.98315 0 3681.1291 -8.6578278 + 2300 18648.161 573.07329 0 3681.1001 -5.2550954 + 2350 21515.748 95.243054 0 3681.201 -9.386512 + 2400 21462.551 104.18267 0 3681.2745 -29.46442 + 2450 20107.732 330.99437 0 3682.2831 35.38497 + 2500 20771.509 220.47713 0 3682.3953 -12.324858 + 2550 20499.887 265.58494 0 3682.2327 -22.713874 + 2600 21462.182 105.24427 0 3682.2747 -10.175788 + 2650 21004.949 181.51383 0 3682.3387 4.949195 + 2700 18673.552 570.45017 0 3682.7089 21.201437 + 2750 21257.562 139.198 0 3682.1249 -7.5793039 + 2800 21559.645 88.844759 0 3682.119 -6.2360467 + 2850 20865.227 204.46262 0 3682.0004 0.39575069 + 2900 19428.614 443.93293 0 3682.0352 12.796676 + 2950 19630.1 410.18487 0 3681.8681 -0.50572623 + 3000 19663.218 404.06316 0 3681.2661 6.0827093 + 3050 19087.572 500.8452 0 3682.1073 -6.3526476 + 3100 18229.94 643.77681 0 3682.1001 11.453637 + 3150 18927.492 527.51919 0 3682.1011 -1.662863 + 3200 18320.514 628.55895 0 3681.978 21.176126 + 3250 18204.677 647.96462 0 3682.0775 11.331521 + 3300 19231.978 477.02117 0 3682.3509 3.8381593 + 3350 18153.44 656.70376 0 3682.2772 15.135615 + 3400 17476.768 770.0598 0 3682.8545 -3.394312 + 3450 21097.531 166.17241 0 3682.4276 3.74301 + 3500 17605.784 747.54808 0 3681.8454 3.3420627 + 3550 19238.34 476.00608 0 3682.3961 1.1413836 + 3600 18155.288 656.57434 0 3682.4557 3.4360446 + 3650 18735.622 559.2377 0 3681.8413 28.760363 + 3700 15310.261 1134.4215 0 3686.1317 44.207018 + 3750 15377.116 1123.4786 0 3686.3313 7.6773215 + 3800 18798.895 549.05928 0 3682.2084 -12.905825 + 3850 18322.563 628.87744 0 3682.6379 -16.067793 + 3900 19963.049 355.65441 0 3682.8292 3.4694064 + 3950 19925.48 361.2507 0 3682.1641 5.0058567 + 4000 19141.423 492.41081 0 3682.648 -12.782769 + 4050 20022.241 345.61655 0 3682.6568 -3.0149905 + 4100 21348.635 124.95646 0 3683.0624 -4.85779 + 4150 21011.812 181.1132 0 3683.0819 -3.9526196 + 4200 20222.276 312.63945 0 3683.0187 -23.63437 + 4250 20957.757 189.77152 0 3682.731 -1.3712469 + 4300 20070.215 337.5751 0 3682.611 -6.8816517 + 4350 21322.437 129.09228 0 3682.8318 -6.9442178 + 4400 19440.445 442.77531 0 3682.8495 -0.11606236 + 4450 20964.516 188.67174 0 3682.7577 4.8533525 + 4500 13530.08 1428.5497 0 3683.563 12.333187 + 4550 20461.637 272.58882 0 3682.8616 4.5111943 + 4600 17072.994 836.58228 0 3682.0812 5.7611617 + 4650 18860.748 539.82027 0 3683.2782 -2.5558958 + 4700 18373.927 621.04093 0 3683.3621 5.4020702 + 4750 20321.437 296.63662 0 3683.5428 8.9571617 + 4800 21083.122 169.84086 0 3683.6946 10.566368 + 4850 20499.669 267.7012 0 3684.3128 4.2924237 + 4900 20308.781 300.38168 0 3685.1785 -12.396923 + 4950 21043.303 178.56295 0 3685.7801 3.8923762 + 5000 20718.383 232.52208 0 3685.5859 -12.43234 + 5050 21005.749 184.4363 0 3685.3945 -7.6463487 + 5100 20714.133 233.27745 0 3685.6329 -1.6944135 + 5150 19577.452 422.73035 0 3685.639 -21.831219 + 5200 14044.647 1343.9545 0 3684.729 -6.8407194 + 5250 19089.805 504.0893 0 3685.7235 4.05641 + 5300 21094.745 169.94699 0 3685.7378 -0.66593212 + 5350 19907.559 366.77598 0 3684.7024 1.5248525 + 5400 20382.81 289.13263 0 3686.2676 -11.919321 + 5450 19593.693 420.70548 0 3686.3209 -1.1568628 + 5500 20906.08 202.09801 0 3686.4447 -2.4284971 + 5550 16315.465 965.56973 0 3684.8138 -33.178221 + 5600 19714.57 400.39687 0 3686.1586 19.950231 + 5650 20561.724 259.54797 0 3686.502 8.2074524 + 5700 19349.502 460.7789 0 3685.6959 16.252649 + 5750 21006.818 185.56805 0 3686.7044 -11.96089 + 5800 20268.2 307.97547 0 3686.0089 17.322311 + 5850 21018.322 184.16179 0 3687.2154 -14.379909 + 5900 19695.647 404.57094 0 3687.1787 -20.718904 + 5950 21021.687 183.66311 0 3687.2776 -15.206081 + 6000 18947.535 529.30554 0 3687.2281 17.863927 + 6050 15272.373 1141.012 0 3686.4075 -0.43375666 + 6100 17766.197 721.75792 0 3682.7908 11.378913 + 6150 18612.573 584.06688 0 3686.1623 17.543241 + 6200 19005.155 518.97146 0 3686.4973 -16.223107 + 6250 20997.507 187.55499 0 3687.1394 -11.613546 + 6300 19639.901 413.58048 0 3686.8974 14.407136 + 6350 19580.399 423.02818 0 3686.428 -5.5801796 + 6400 14134.119 1332.0662 0 3687.7527 84.864425 + 6450 21598.824 87.419966 0 3687.224 -5.8358352 + 6500 18208.216 649.29108 0 3683.9938 -8.1510884 + 6550 19364.586 459.59813 0 3687.0291 -12.053563 + 6600 20710.927 235.11914 0 3686.9403 -1.0470193 + 6650 21132.334 165.08091 0 3687.1366 1.0785471 + 6700 20217.285 317.589 0 3687.1365 0.055447462 + 6750 21232.279 148.57412 0 3687.2873 -2.4551657 + 6800 20292.683 304.76539 0 3686.8793 -0.42311295 + 6850 19056.291 510.49927 0 3686.5478 6.9533826 + 6900 20429.82 282.23764 0 3687.2076 -4.2360112 + 6950 21281.278 140.27361 0 3687.1533 -0.07475261 + 7000 17173.388 824.54446 0 3686.7758 10.753828 + 7050 18079.7 674.56274 0 3687.846 12.975804 + 7100 16433.233 950.73904 0 3689.6112 -10.5102 + 7150 19033.335 515.59672 0 3687.8193 0.29109447 + 7200 17286.428 809.02352 0 3690.0948 2.3015698 + 7250 16811.962 886.6645 0 3688.6582 -7.4787512 + 7300 15992.461 1023.4849 0 3688.895 -5.2354222 + 7350 19211.451 487.63129 0 3689.5398 8.4351737 + 7400 19065.682 511.95629 0 3689.57 -12.47448 + 7450 21369.265 128.10098 0 3689.6451 2.2930546 + 7500 16807.109 888.64602 0 3689.8308 14.761969 + 7550 18063.046 679.21873 0 3689.7264 3.8950434 + 7600 17794.987 724.55404 0 3690.3851 14.379016 + 7650 17904.751 706.14354 0 3690.2688 23.813776 + 7700 19670.09 411.3021 0 3689.6504 14.099245 + 7750 18082.562 675.23975 0 3689.0001 15.788521 + 7800 17776.135 726.91445 0 3689.6037 6.9780735 + 7850 17062.575 846.33412 0 3690.0966 -8.9289256 + 7900 19059.2 513.07737 0 3689.6107 16.992843 + 7950 16269.685 978.48914 0 3690.1033 11.180179 + 8000 20115.278 336.91405 0 3689.4604 -6.4882518 + 8050 21173.72 161.15229 0 3690.1056 -2.2164491 + 8100 19238.235 484.42784 0 3690.8004 23.412709 + 8150 18438.4 617.58743 0 3690.6542 0.89156316 + 8200 21438.764 117.12721 0 3690.2546 -1.7193227 + 8250 21195.806 157.66607 0 3690.3003 3.820447 + 8300 21177.549 161.13702 0 3690.7286 0.94938203 + 8350 21060.267 181.06887 0 3691.1135 2.8179025 + 8400 20087.113 343.46206 0 3691.3142 8.1484473 + 8450 19298.478 474.87133 0 3691.2843 -16.239664 + 8500 21654.353 82.083485 0 3691.1423 -8.1464138 + 8550 19920.544 371.34795 0 3691.4386 20.765144 + 8600 21692.293 75.655154 0 3691.0373 -13.316763 + 8650 21231.322 151.8989 0 3690.4526 -11.388238 + 8700 19530.647 434.89585 0 3690.0037 2.7433786 + 8750 19720.63 403.07773 0 3689.8493 -6.416414 + 8800 21321.378 136.04091 0 3689.604 1.3661635 + 8850 19811.906 387.80489 0 3689.7893 3.704143 + 8900 19734.167 400.92444 0 3689.9523 2.5685155 + 8950 21076.459 177.18119 0 3689.9244 -11.939513 + 9000 20967.246 195.42966 0 3689.9707 2.0092705 + 9050 21122.023 169.62103 0 3689.9582 2.3791301 + 9100 20169.346 328.27229 0 3689.8299 -3.5017988 + 9150 21418.641 119.84513 0 3689.6187 2.486073 + 9200 20876.042 210.26452 0 3689.6048 -5.3839897 + 9250 21572.38 93.74407 0 3689.1407 -8.3676952 + 9300 20944.78 197.98577 0 3688.7824 1.3278314 + 9350 20706.52 237.48767 0 3688.5744 4.6944204 + 9400 16412.314 953.47251 0 3688.8581 26.134976 + 9450 20461.68 277.76243 0 3688.0424 17.647445 + 9500 20893.994 205.64261 0 3687.9749 -10.642418 + 9550 20503.447 270.63504 0 3687.8761 -17.769897 + 9600 19677.799 408.05887 0 3687.692 -2.7938604 + 9650 17480.971 774.1855 0 3687.6806 0.59827043 + 9700 17799.126 721.50817 0 3688.0292 44.387928 + 9750 20443.384 280.16837 0 3687.399 3.0619324 + 9800 20545.255 263.40108 0 3687.6102 3.6229381 + 9850 20722.819 233.57142 0 3687.3745 0.86462694 + 9900 21128.462 165.09767 0 3686.508 -6.9636843 + 9950 21343.307 130.46714 0 3687.685 -9.7382705 + 10000 20623.887 250.37866 0 3687.6932 2.7529835 +Loop time of 2.28812 on 1 procs for 10000 steps with 81 atoms + +Performance: 37760.318 tau/day, 4370.407 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.094122 | 0.094122 | 0.094122 | 0.0 | 4.11 +Neigh | 0.076427 | 0.076427 | 0.076427 | 0.0 | 3.34 +Comm | 0.0066867 | 0.0066867 | 0.0066867 | 0.0 | 0.29 +Output | 0.003606 | 0.003606 | 0.003606 | 0.0 | 0.16 +Modify | 2.0986 | 2.0986 | 2.0986 | 0.0 | 91.72 +Other | | 0.008698 | | | 0.38 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 62 ave 62 max 62 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 905 ave 905 max 905 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 905 +Ave neighs/atom = 11.17284 +Neighbor list builds = 991 +Dangerous builds = 927 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems4.g++.4 b/examples/rigid/log.20Mar22.rigid.poems4.g++.4 new file mode 100644 index 0000000000..6240237758 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems4.g++.4 @@ -0,0 +1,328 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies.dat +1 clusters, 9 bodies, 8 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045742 + 850 17821.483 711.53827 0 3681.7854 7.4384281 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19374 0 3681.3037 11.787982 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184716 + 1150 20849.582 206.01696 0 3680.9472 -0.86699115 + 1200 21815.003 45.317409 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064083 + 1300 20780.781 217.36511 0 3680.8286 6.0538606 + 1350 20558.971 254.36489 0 3680.8601 -3.6773868 + 1400 21485.03 99.812843 0 3680.6511 -16.185479 + 1450 21771.107 52.159652 0 3680.6775 -2.4756656 + 1500 21520.949 93.503872 0 3680.3286 2.1023574 + 1550 21351.419 121.68131 0 3680.2511 5.5159875 + 1600 20778.804 216.92191 0 3680.0559 15.089203 + 1650 21477.636 100.21877 0 3679.8247 -1.104524 + 1700 18501.329 596.48084 0 3680.0357 -15.679806 + 1750 18563.639 587.34841 0 3681.2882 33.532316 + 1800 19110.174 494.82524 0 3679.8543 18.024079 + 1850 21364.178 119.23767 0 3679.9339 2.5290075 + 1900 20146.588 322.15506 0 3679.9197 5.7317368 + 1950 20692.674 231.25288 0 3680.0319 4.2977982 + 2000 20943.904 189.11229 0 3679.7629 -22.643749 + 2050 19667.815 401.87016 0 3679.8394 3.6240972 + 2100 20280.109 299.81759 0 3679.8357 7.4803647 + 2150 19181.146 483.63975 0 3680.4974 22.634167 + 2200 21301.194 130.53171 0 3680.7308 4.7072523 + 2250 20484.79 266.99736 0 3681.1291 -8.6583002 + 2300 18648.002 573.09962 0 3681.1 -5.2548835 + 2350 21515.851 95.225745 0 3681.2009 -9.3875216 + 2400 21462.37 104.21272 0 3681.2744 -29.459857 + 2450 20108.034 330.94394 0 3682.2829 35.37058 + 2500 20771.818 220.42545 0 3682.3951 -12.318936 + 2550 20502.815 265.09577 0 3682.2316 -22.726822 + 2600 21462.006 105.2733 0 3682.2744 -10.180394 + 2650 21009.656 180.72738 0 3682.3367 4.9580828 + 2700 18680.012 569.37179 0 3682.7071 21.114114 + 2750 21256.19 139.42201 0 3682.1203 -7.4744399 + 2800 21552.267 90.071446 0 3682.1159 -6.2906304 + 2850 20879.958 202.00905 0 3682.0021 0.57990903 + 2900 19018.645 512.35214 0 3682.1262 13.883084 + 2950 19819.365 378.55747 0 3681.785 -0.7348943 + 3000 20269.229 303.35149 0 3681.5563 6.3088075 + 3050 19236.727 475.99457 0 3682.1158 -10.703575 + 3100 18391.55 616.96976 0 3682.2281 9.850079 + 3150 20258.563 305.82076 0 3682.248 7.1951283 + 3200 20716.384 229.15502 0 3681.8856 2.9042294 + 3250 18662.237 572.0784 0 3682.4512 9.2108597 + 3300 19162.278 488.60646 0 3682.3195 3.3306562 + 3350 21235.679 142.98279 0 3682.2626 0.29397483 + 3400 17677.053 736.09247 0 3682.2679 32.75269 + 3450 20852.392 206.65618 0 3682.0548 -4.8319056 + 3500 21182.918 151.46754 0 3681.9539 -5.6330382 + 3550 20589.85 250.40724 0 3682.049 12.582133 + 3600 20973.659 186.28043 0 3681.8903 10.935266 + 3650 17838.632 707.92145 0 3681.0268 -17.200926 + 3700 21538.002 92.744409 0 3682.4114 -0.72124229 + 3750 21390.294 117.90865 0 3682.9576 -7.8431786 + 3800 17921.046 696.50311 0 3683.344 -9.4641531 + 3850 20356.471 290.22624 0 3682.9715 2.4593463 + 3900 20374.077 287.10249 0 3682.782 -1.9519082 + 3950 20563.915 255.29993 0 3682.619 -6.124649 + 4000 20991.467 184.76183 0 3683.3397 1.8954961 + 4050 17805.623 716.24698 0 3683.8509 -20.454944 + 4100 19916.389 363.86301 0 3683.2611 -0.27912557 + 4150 19221.623 480.01232 0 3683.6161 -11.562492 + 4200 20526.82 261.78571 0 3682.9224 -3.9522917 + 4250 20922.813 196.1799 0 3683.3154 0.11947446 + 4300 19956.66 357.78133 0 3683.8914 19.156093 + 4350 19735.73 394.45981 0 3683.7482 14.865775 + 4400 21702.656 67.099805 0 3684.2092 -13.502538 + 4450 18163.055 656.97231 0 3684.1482 -0.6243111 + 4500 17477.718 771.25976 0 3684.2127 -0.4664004 + 4550 20676.507 238.19814 0 3684.2827 -19.444969 + 4600 17322.922 796.77058 0 3683.9242 27.003966 + 4650 11905.158 1704.9151 0 3689.1082 15.574169 + 4700 18689.079 569.80982 0 3684.6563 -14.67311 + 4750 19821.745 381.01914 0 3684.6433 5.0436795 + 4800 20621.335 247.96269 0 3684.8518 -16.407263 + 4850 21923.814 30.965964 0 3684.935 -13.418244 + 4900 18840.555 544.41538 0 3684.5079 11.005357 + 4950 15366.601 1124.2481 0 3685.3482 17.412375 + 5000 18274.314 639.01311 0 3684.732 5.3261109 + 5050 21173.687 155.83673 0 3684.7845 5.4056809 + 5100 21738.219 61.75201 0 3684.7885 -2.631945 + 5150 16597.949 918.84841 0 3685.1732 -10.124101 + 5200 20752.758 225.95919 0 3684.7522 -5.2441372 + 5250 17652.088 741.2645 0 3683.2793 2.0080739 + 5300 19907.523 366.53115 0 3684.4516 8.4266792 + 5350 20104.189 334.14522 0 3684.8433 17.21925 + 5400 21499.848 101.71631 0 3685.0243 -6.1103541 + 5450 21203.533 151.14574 0 3685.068 -5.9468503 + 5500 21076.513 172.45652 0 3685.2088 5.1418181 + 5550 20158.398 325.56609 0 3685.2992 -1.6486034 + 5600 20787.836 221.19563 0 3685.835 -10.66805 + 5650 19687.154 404.77204 0 3685.9644 -23.49128 + 5700 20419.311 282.58328 0 3685.8017 -0.52808211 + 5750 19738.522 395.95893 0 3685.7126 1.3889817 + 5800 18300.025 635.66905 0 3685.6732 23.490447 + 5850 20585.004 255.02032 0 3685.8543 -0.20699939 + 5900 20373.839 290.15881 0 3685.7987 -7.9712187 + 5950 18163.832 659.91192 0 3687.2173 5.4494586 + 6000 21049.247 177.43029 0 3685.6382 2.9138342 + 6050 21239.803 145.77613 0 3685.7433 -1.4927769 + 6100 20686.361 237.86454 0 3685.5913 -0.95516297 + 6150 20461.754 275.31546 0 3685.6079 -3.4166412 + 6200 19264.208 474.73017 0 3685.4316 11.750757 + 6250 21180.813 155.31746 0 3685.4529 2.8188219 + 6300 21047.543 177.4394 0 3685.3632 1.8641486 + 6350 20232.576 313.17716 0 3685.2731 2.8150209 + 6400 20185.616 321.33454 0 3685.6038 -3.8697311 + 6450 18969.632 523.95865 0 3685.5639 0.6725512 + 6500 17592.574 753.49959 0 3685.5952 -1.2557393 + 6550 21279.049 138.42524 0 3684.9335 -1.208945 + 6600 21408.457 116.4143 0 3684.4904 -1.5332953 + 6650 19758.218 391.17316 0 3684.2096 1.8511312 + 6700 20766.943 223.44631 0 3684.6036 -2.3672623 + 6750 20399.631 284.09914 0 3684.0377 -5.4089876 + 6800 21296.628 135.14662 0 3684.5847 -3.8442549 + 6850 20641.481 244.4451 0 3684.692 1.4020639 + 6900 20852.81 209.23009 0 3684.6984 1.8512104 + 6950 20940.555 194.66882 0 3684.7614 -6.554676 + 7000 19496.988 435.28199 0 3684.78 -15.120269 + 7050 19796.829 385.04227 0 3684.5138 -4.1068804 + 7100 19945.264 360.42431 0 3684.635 -4.0629042 + 7150 19431.123 446.12911 0 3684.6497 -6.8321751 + 7200 16864.851 873.80043 0 3684.6089 14.309069 + 7250 20438.75 277.85982 0 3684.3181 -11.41223 + 7300 17688.684 734.01576 0 3682.1298 35.938373 + 7350 21573.419 88.63421 0 3684.204 -3.9032749 + 7400 21198.486 150.72249 0 3683.8034 -7.1477117 + 7450 20586.708 252.93928 0 3684.0572 -7.6634645 + 7500 21815.377 48.180377 0 3684.0765 0.97457507 + 7550 17791.352 718.87564 0 3684.101 28.248235 + 7600 21828.874 45.928597 0 3684.0742 -0.25814944 + 7650 20827.961 212.35674 0 3683.6835 -3.4083384 + 7700 21319.176 130.43547 0 3683.6315 -12.434856 + 7750 20127.904 328.69643 0 3683.3471 -16.975711 + 7800 21741.772 59.679206 0 3683.3078 3.6261863 + 7850 19612.334 414.37418 0 3683.0964 1.3763274 + 7900 20071.318 337.74624 0 3682.9658 -0.40982763 + 7950 17925.664 695.29582 0 3682.9065 17.104439 + 8000 19125.978 492.76383 0 3680.4268 10.807662 + 8050 20233.848 310.42681 0 3682.7347 13.386237 + 8100 20551.619 257.86699 0 3683.1368 -13.97515 + 8150 21578.323 86.88362 0 3683.2708 -9.6811587 + 8200 21154.833 157.72897 0 3683.5344 0.62312375 + 8250 21321.143 129.83967 0 3683.3636 1.9536438 + 8300 21041.696 176.04177 0 3682.9911 4.7475567 + 8350 19883.39 369.32649 0 3683.2247 -7.0959328 + 8400 21626.067 79.062992 0 3683.4075 -14.919059 + 8450 21375.201 120.86836 0 3683.4019 -5.3461514 + 8500 20281.059 303.10304 0 3683.2796 3.7975093 + 8550 21170.533 154.48432 0 3682.9065 -1.1568561 + 8600 17754.931 724.00158 0 3683.1568 14.15254 + 8650 20685.478 235.65879 0 3683.2385 -5.2694179 + 8700 21489.165 101.90509 0 3683.4326 -4.2510612 + 8750 21106.682 165.41638 0 3683.1968 -3.9186708 + 8800 19149.516 491.5843 0 3683.1702 -11.419849 + 8850 21451.865 108.1814 0 3683.4923 -7.8256219 + 8900 19567.4 421.81206 0 3683.0454 -0.71997056 + 8950 20934.097 194.48033 0 3683.4965 -7.0106879 + 9000 18531.559 595.25957 0 3683.8528 3.7449399 + 9050 18868.821 537.22549 0 3682.029 9.9926092 + 9100 19972.527 354.73119 0 3683.4858 -0.30871263 + 9150 19641.651 409.18618 0 3682.7947 -1.3036238 + 9200 20019.08 346.19657 0 3682.7099 6.7425386 + 9250 19259.286 473.04973 0 3682.9308 -24.120659 + 9300 21597.757 82.971857 0 3682.598 -13.748483 + 9350 19348.379 457.23576 0 3681.9656 3.1571402 + 9400 19129.588 493.35235 0 3681.617 8.6293783 + 9450 20337.025 291.20959 0 3680.7138 6.8590795 + 9500 20581.788 249.65891 0 3679.9569 -18.892836 + 9550 19482.069 433.0077 0 3680.0192 23.029778 + 9600 19182.794 482.96871 0 3680.101 -11.081731 + 9650 20086.771 332.5311 0 3680.3263 -18.939681 + 9700 20274.046 300.98818 0 3679.9959 6.7538762 + 9750 18743.595 555.08045 0 3679.0129 8.2757138 + 9800 19464.311 435.66288 0 3679.7148 7.0528759 + 9850 21249.848 138.27382 0 3679.9152 -10.847402 + 9900 21156.214 153.84621 0 3679.8819 -7.8359674 + 9950 21643.134 72.547515 0 3679.7365 -10.507744 + 10000 19587.948 414.64942 0 3679.3075 6.1173553 +Loop time of 2.35562 on 4 procs for 10000 steps with 81 atoms + +Performance: 36678.236 tau/day, 4245.166 timesteps/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 | 0.0055581 | 0.024882 | 0.055326 | 12.0 | 1.06 +Neigh | 0.0073809 | 0.022107 | 0.043683 | 9.2 | 0.94 +Comm | 0.12484 | 0.14528 | 0.1833 | 6.2 | 6.17 +Output | 0.0035526 | 0.0041048 | 0.0055462 | 1.3 | 0.17 +Modify | 2.1078 | 2.1414 | 2.162 | 1.5 | 90.91 +Other | | 0.0178 | | | 0.76 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 41 ave 78 max 11 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 193.5 ave 774 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 774 +Ave neighs/atom = 9.5555556 +Neighbor list builds = 989 +Dangerous builds = 915 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.1 b/examples/rigid/log.20Mar22.rigid.poems5.g++.1 new file mode 100644 index 0000000000..5a18042516 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems5.g++.1 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.666 | 3.666 | 3.666 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086359 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977442 0 3904.4178 9.0928158 + 250 19552.211 283.50525 0 3904.285 15.670465 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47231 0 3902.9213 0.6921524 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05177 0 3902.1317 4.6838621 + 850 19932.48 210.71175 0 3901.9118 3.4716043 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.874422 + 1200 20767.681 56.717094 0 3902.5839 -34.817444 + 1250 20625.583 82.586399 0 3902.1388 11.697329 + 1300 20690.013 71.006478 0 3902.4903 -29.292777 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.559 244.81785 0 3902.8844 6.7138514 + 1450 15690.149 998.342 0 3903.9252 48.124557 + 1500 20234.455 155.92516 0 3903.0465 13.17221 + 1550 20779.631 55.063009 0 3903.1428 -2.639045 + 1600 20642.753 80.233905 0 3902.9659 -2.4688467 + 1650 18785.696 423.90402 0 3902.7365 -5.6466663 + 1700 20965.076 20.760444 0 3903.182 -0.45364296 + 1750 18935.406 396.96067 0 3903.5173 25.913302 + 1800 20581.559 91.756972 0 3903.1567 3.8217234 + 1850 20616.946 85.184849 0 3903.1378 4.1907972 + 1900 16602.053 828.40949 0 3902.8637 -0.49505122 + 1950 20175.526 166.53362 0 3902.7421 5.603825 + 2000 20261.924 150.39322 0 3902.6014 -1.196958 + 2050 20170.339 167.40504 0 3902.6531 -0.80849882 + 2100 19820.132 231.26755 0 3901.6624 3.1476607 + 2150 20666.19 75.838461 0 3902.9106 0.53899287 + 2200 19873.51 222.53286 0 3902.8124 7.9310276 + 2250 18548.063 467.69698 0 3902.5235 16.905356 + 2300 20616.61 84.762399 0 3902.6531 -6.7872951 + 2350 18167.738 538.13635 0 3902.5322 -11.458285 + 2400 20120.227 177.01954 0 3902.9875 -1.2593018 + 2450 20436.599 118.32469 0 3902.8801 -6.5989174 + 2500 18919.923 400.26361 0 3903.9531 32.37476 + 2550 19675.809 259.77151 0 3903.4398 19.437327 + 2600 19739.842 247.86388 0 3903.3901 -7.519784 + 2650 20557.026 96.530313 0 3903.387 0.60211646 + 2700 20666.602 76.099892 0 3903.2484 0.16825503 + 2750 20924.585 28.453883 0 3903.3771 2.4227171 + 2800 20360.659 132.8596 0 3903.352 4.1440877 + 2850 20783.475 54.518625 0 3903.3102 -0.57312067 + 2900 20456.181 115.03745 0 3903.2191 -20.118887 + 2950 20779.493 55.321394 0 3903.3756 -0.26783079 + 3000 20011.867 197.30216 0 3903.2035 -1.4704201 + 3050 20741.875 62.208723 0 3903.2966 -7.5432815 + 3100 21001.754 14.148298 0 3903.362 2.9676438 + 3150 20244.086 154.44639 0 3903.3512 -1.9071213 + 3200 20639.615 81.136426 0 3903.2873 1.4826467 + 3250 20735.244 63.529571 0 3903.3895 2.1127055 + 3300 20142.891 173.22282 0 3903.3878 4.7739415 + 3350 19963.765 206.21899 0 3903.2126 5.5410771 + 3400 16628.667 824.13627 0 3903.519 36.087673 + 3450 19228.218 342.81569 0 3903.5968 3.1057274 + 3500 19759.293 244.57876 0 3903.707 2.2339557 + 3550 19853.21 227.06362 0 3903.584 -1.0882119 + 3600 19673.516 260.64854 0 3903.8923 -10.63775 + 3650 19619.238 270.5393 0 3903.7316 -6.3746003 + 3700 20756.865 59.790243 0 3903.6542 -8.3015766 + 3750 20265.025 150.47347 0 3903.2559 -5.7284695 + 3800 20944.683 24.669276 0 3903.3142 -0.070552298 + 3850 19344.831 320.59492 0 3902.971 13.040749 + 3900 19978.209 203.00247 0 3902.6708 0.15638133 + 3950 19864.118 224.19359 0 3902.734 0.453229 + 4000 17606.216 642.71493 0 3903.1252 -12.656002 + 4050 18017.895 566.54102 0 3903.1883 12.133906 + 4100 20092.963 182.17593 0 3903.095 7.7445947 + 4150 20555.337 96.395074 0 3902.939 -6.5429752 + 4200 20709.781 67.869199 0 3903.0138 -2.8653003 + 4250 18956.203 392.20748 0 3902.6155 -1.6249728 + 4300 17816.204 603.72704 0 3903.0241 23.089239 + 4350 18979.742 388.04678 0 3902.8138 3.2511108 + 4400 20272.085 148.82367 0 3902.9135 1.9518268 + 4450 18820.003 417.74789 0 3902.9337 6.3979299 + 4500 19991.936 200.50131 0 3902.7117 3.5118553 + 4550 20915.092 29.663898 0 3902.8291 -2.3174641 + 4600 20690.37 71.125087 0 3902.6752 -12.008575 + 4650 18893.76 404.50849 0 3903.3529 15.006184 + 4700 18611.123 456.1263 0 3902.6306 -5.3574892 + 4750 20497.821 106.5856 0 3902.4784 0.85039837 + 4800 20803.214 50.120522 0 3902.5675 3.8610873 + 4850 18849.598 411.72635 0 3902.3927 9.2029058 + 4900 18121.714 546.68042 0 3902.5533 9.4522272 + 4950 20377.499 128.99323 0 3902.6041 5.3825395 + 5000 20686.114 72.039749 0 3902.8016 -5.706271 + 5050 20180.449 165.51368 0 3902.634 -16.418461 + 5100 20274.947 148.36657 0 3902.9864 -5.6668309 + 5150 18042.324 560.74137 0 3901.9125 3.6791541 + 5200 20794.666 52.204446 0 3903.0685 -1.4517721 + 5250 19073.55 371.18834 0 3903.3272 -13.457439 + 5300 20821.412 47.364313 0 3903.1813 2.258098 + 5350 20583.073 91.271191 0 3902.9513 5.4323985 + 5400 20490.967 108.41184 0 3903.0353 4.122905 + 5450 18141.79 543.66874 0 3903.2594 -0.19951075 + 5500 20274.012 148.55528 0 3903.002 5.0489974 + 5550 17806.237 605.43454 0 3902.8858 43.80619 + 5600 20999.825 14.341937 0 3903.1983 1.0879933 + 5650 20930.929 27.025347 0 3903.1234 -7.0860209 + 5700 20677.725 73.853093 0 3903.0614 2.6864775 + 5750 20521.264 102.87509 0 3903.1092 2.6940548 + 5800 20792.571 52.596021 0 3903.0721 1.2910217 + 5850 20518.674 103.26595 0 3903.0204 -9.2547271 + 5900 18417.885 491.66696 0 3902.3865 -12.049357 + 5950 17243.837 709.37858 0 3902.6817 -6.2357188 + 6000 20262.525 149.56918 0 3901.8885 -0.28964823 + 6050 19883.554 219.14043 0 3901.2801 2.3071707 + 6100 16548.178 838.47869 0 3902.956 -11.715644 + 6150 19601.177 272.14674 0 3901.9944 -0.9008056 + 6200 20499.796 106.2363 0 3902.4949 0.79071424 + 6250 19601.106 272.50139 0 3902.3359 -1.9306693 + 6300 17210.685 712.70535 0 3899.8692 4.8890923 + 6350 19911.896 214.91041 0 3902.2985 12.691129 + 6400 18834.642 411.87123 0 3899.7678 -1.9447856 + 6450 20216.311 158.39781 0 3902.1591 2.6009109 + 6500 20452.025 114.97122 0 3902.3832 0.14644416 + 6550 19142.589 357.34097 0 3902.2649 2.8968485 + 6600 20412.915 122.08784 0 3902.2573 3.1343105 + 6650 17317.867 699.39994 0 3906.4123 42.25563 + 6700 20479.771 109.8036 0 3902.3537 1.3520625 + 6750 20306.902 142.12484 0 3902.6623 2.2032106 + 6800 20755.367 58.994834 0 3902.5814 -0.90518094 + 6850 20471.259 111.7197 0 3902.6936 1.5799331 + 6900 20702.025 69.15032 0 3902.8586 9.3910371 + 6950 20477.695 110.34414 0 3902.5099 1.8181164 + 7000 20560.727 95.057704 0 3902.5998 -15.686006 + 7050 20336.675 136.39386 0 3902.4448 1.3704327 + 7100 20757.399 58.950153 0 3902.913 -6.4250981 + 7150 20870.958 38.095649 0 3903.088 -4.1962169 + 7200 20706.869 68.489134 0 3903.0944 2.8322659 + 7250 20386.713 127.7432 0 3903.0604 6.0287391 + 7300 18391.773 497.21001 0 3903.0939 19.202343 + 7350 20178.898 166.4993 0 3903.3322 1.5682417 + 7400 16858.704 781.78682 0 3903.7691 21.317514 + 7450 17509.513 660.71963 0 3903.2221 -5.9456143 + 7500 19974.601 204.20412 0 3903.2043 -0.69202711 + 7550 20917.053 29.73415 0 3903.2626 -3.9962577 + 7600 20923.518 28.482703 0 3903.2083 -1.9016251 + 7650 20549.528 97.630612 0 3903.0987 3.5512257 + 7700 20861.441 39.903885 0 3903.1337 2.4426264 + 7750 18843.349 413.64461 0 3903.1537 2.677739 + 7800 20616.054 85.214364 0 3903.0021 3.9639004 + 7850 16478.851 851.93376 0 3903.5728 7.3763128 + 7900 20312.115 141.35103 0 3902.8539 4.6707271 + 7950 20389.623 127.16589 0 3903.0219 3.4414001 + 8000 20452.117 115.30715 0 3902.7362 -1.0162528 + 8050 20857.093 40.791886 0 3903.2164 -15.150068 + 8100 19817.543 233.4997 0 3903.415 0.89346046 + 8150 18649.521 449.9112 0 3903.5262 -0.40053588 + 8200 19619.276 270.37616 0 3903.5754 5.5161492 + 8250 20393.176 127.01336 0 3903.5275 2.122613 + 8300 19145.912 358.00424 0 3903.5435 3.863924 + 8350 19636.311 267.17226 0 3903.5262 -7.1496084 + 8400 19086.332 368.86693 0 3903.3729 7.0968952 + 8450 19494.416 292.89527 0 3902.9723 3.1750935 + 8500 20041.919 191.77756 0 3903.244 0.95215503 + 8550 20357.561 133.15478 0 3903.0736 -0.14020152 + 8600 16998.797 756.07003 0 3903.9954 -16.724408 + 8650 20853.26 41.386996 0 3903.1017 -3.2612965 + 8700 20767.768 57.360884 0 3903.2438 1.1157649 + 8750 20752.546 60.106518 0 3903.1705 0.39130547 + 8800 20574.407 92.99798 0 3903.0734 0.61728166 + 8850 20326.99 138.94203 0 3903.1995 -1.9434522 + 8900 17408.108 679.53222 0 3903.2559 21.935371 + 8950 20471.21 112.2721 0 3903.2368 1.8142747 + 9000 19129.591 360.35257 0 3902.8694 4.5786395 + 9050 20439.668 117.89541 0 3903.0191 2.5585685 + 9100 20780.375 54.788664 0 3903.0062 3.8312459 + 9150 19904.559 216.61504 0 3902.6445 12.150414 + 9200 20961.295 21.52065 0 3903.2419 -0.2120699 + 9250 19315.252 326.44175 0 3903.3402 -19.740867 + 9300 20653.002 78.77764 0 3903.4076 -7.8068233 + 9350 18961.572 391.20947 0 3902.6117 -12.660843 + 9400 16262.179 892.67633 0 3904.191 22.2435 + 9450 17064.394 743.33301 0 3903.406 36.139436 + 9500 18075.588 555.06436 0 3902.3954 24.598176 + 9550 20487.738 109.06287 0 3903.0884 2.6320759 + 9600 20358.609 133.36993 0 3903.4828 0.76449113 + 9650 19849.022 228.46312 0 3904.208 9.5547064 + 9700 20448.112 116.8757 0 3903.5632 -1.0845697 + 9750 20472.78 112.51661 0 3903.7722 -0.30676738 + 9800 19491.99 293.35361 0 3902.9814 -20.10857 + 9850 19895.603 218.42479 0 3902.7957 -0.18235641 + 9900 19704.336 254.55068 0 3903.5019 14.553184 + 9950 17689.462 627.9788 0 3903.805 4.9918088 + 10000 20184.205 165.29396 0 3903.1097 2.9472364 +Loop time of 2.28393 on 1 procs for 10000 steps with 81 atoms + +Performance: 37829.498 tau/day, 4378.414 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.052911 | 0.052911 | 0.052911 | 0.0 | 2.32 +Neigh | 0.056658 | 0.056658 | 0.056658 | 0.0 | 2.48 +Comm | 0.0087389 | 0.0087389 | 0.0087389 | 0.0 | 0.38 +Output | 0.0037996 | 0.0037996 | 0.0037996 | 0.0 | 0.17 +Modify | 2.1537 | 2.1537 | 2.1537 | 0.0 | 94.30 +Other | | 0.008147 | | | 0.36 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 113 ave 113 max 113 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 582 ave 582 max 582 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 582 +Ave neighs/atom = 7.1851852 +Neighbor list builds = 993 +Dangerous builds = 950 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.20Mar22.rigid.poems5.g++.4 b/examples/rigid/log.20Mar22.rigid.poems5.g++.4 new file mode 100644 index 0000000000..cbf8b05490 --- /dev/null +++ b/examples/rigid/log.20Mar22.rigid.poems5.g++.4 @@ -0,0 +1,329 @@ +LAMMPS (17 Feb 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid +Reading data file ... + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + read_data CPU = 0.000 seconds + +velocity all create 100.0 4928459 + + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems file connected-bodies2.dat +2 clusters, 9 bodies, 7 joints, 81 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- fix poems command: + +@Article{Mukherjee08, + author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson}, + title = {Substructured molecular dynamics using multibody dynamics algorithms}, + journal = {Intl.~J.~Non-linear Mechanics}, + year = 2008, + volume = 43, + pages = {1045--1055} +} + +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 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, 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) = 3.514 | 3.545 | 3.639 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12774.759 1538.7382 0 3904.4344 18.086358 + 100 19803.641 237.21132 0 3904.5523 -3.1528278 + 150 20259.6 152.62072 0 3904.3985 -4.6173524 + 200 20705.978 69.977039 0 3904.4174 9.0928122 + 250 19552.211 283.50525 0 3904.285 15.670466 + 300 19266.324 333.5792 0 3901.4169 7.2119197 + 350 20738.325 63.738945 0 3904.1694 -23.03999 + 400 20616.682 86.082444 0 3903.9864 -13.783584 + 450 19831.326 230.13858 0 3902.6063 0.42074361 + 500 20365.825 131.47271 0 3902.9217 0.69215592 + 550 20794.102 52.163238 0 3902.9229 4.5895354 + 600 20853.873 40.899172 0 3902.7275 2.3593042 + 650 19255.802 336.29509 0 3902.1844 10.341742 + 700 18526.969 471.02462 0 3901.9448 -0.61898691 + 750 18960.662 391.26068 0 3902.4944 12.04731 + 800 20142.432 172.05197 0 3902.1319 4.6838632 + 850 19932.48 210.71175 0 3901.9118 3.4716031 + 900 20243.528 153.13972 0 3901.9411 3.6490762 + 950 20388.132 126.88722 0 3902.4671 -4.4518463 + 1000 20076.333 184.61915 0 3902.4586 -2.272315 + 1050 20859.506 39.696993 0 3902.5684 6.45166 + 1100 15284.661 1072.1908 0 3902.6836 21.194042 + 1150 19658.317 261.99809 0 3902.4272 -2.8744219 + 1200 20767.681 56.717095 0 3902.5839 -34.817444 + 1250 20625.583 82.586198 0 3902.1386 11.697328 + 1300 20690.013 71.006478 0 3902.4903 -29.29278 + 1350 20936.019 26.022786 0 3903.0634 1.0316025 + 1400 19753.56 244.81784 0 3902.8844 6.7138497 + 1450 15690.149 998.34213 0 3903.9252 48.124569 + 1500 20234.455 155.92516 0 3903.0465 13.172207 + 1550 20779.631 55.063019 0 3903.1428 -2.6390455 + 1600 20642.753 80.233821 0 3902.9659 -2.4688431 + 1650 18785.698 423.90364 0 3902.7365 -5.6466892 + 1700 20965.076 20.760451 0 3903.182 -0.45366172 + 1750 18935.412 396.95958 0 3903.5173 25.913174 + 1800 20581.554 91.757912 0 3903.1567 3.8218442 + 1850 20616.949 85.184789 0 3903.1382 4.1907933 + 1900 16601.896 828.43849 0 3902.8638 -0.49468175 + 1950 20175.564 166.52646 0 3902.7421 5.6035728 + 2000 20262.525 150.28224 0 3902.6017 -1.1967705 + 2050 20168.994 167.65314 0 3902.6521 -0.80723928 + 2100 19810.955 232.96524 0 3901.6605 3.1936531 + 2150 20667.232 75.645145 0 3902.9103 0.54812734 + 2200 19863.772 224.34646 0 3902.8228 7.9294465 + 2250 18808.943 419.2084 0 3902.3461 14.344526 + 2300 20573.665 92.761842 0 3902.6999 -6.7671703 + 2350 19075.104 369.95414 0 3902.3809 -9.5353568 + 2400 20273.873 148.53775 0 3902.9586 -1.93796 + 2450 20087.769 182.30216 0 3902.2593 2.131796 + 2500 20711.602 67.530554 0 3903.0124 2.6280244 + 2550 19971.224 204.75926 0 3903.134 3.1760522 + 2600 20620.084 85.027145 0 3903.5612 -0.92888063 + 2650 19737.546 248.65474 0 3903.7559 -3.3218688 + 2700 20650.724 79.522243 0 3903.7303 -7.5918025 + 2750 19863.245 225.2505 0 3903.6292 9.2140221 + 2800 18992.457 386.73547 0 3903.8572 2.6244537 + 2850 18703.899 440.48356 0 3904.1685 14.561348 + 2900 17939.805 581.74599 0 3903.932 -8.0863089 + 2950 20867.516 39.38186 0 3903.7367 3.0985423 + 3000 19767.994 242.8847 0 3903.6243 1.5943109 + 3050 20397.448 126.31591 0 3903.6212 -0.14982775 + 3100 20978.114 19.126395 0 3903.9623 -9.6797253 + 3150 18303.556 513.8514 0 3903.3989 4.5940322 + 3200 19156.505 356.46608 0 3903.9671 10.071308 + 3250 17484.205 666.52199 0 3904.3377 -4.1641768 + 3300 18069.94 557.75947 0 3904.0447 11.868707 + 3350 20855.645 41.964632 0 3904.1212 5.4186293 + 3400 18011.986 568.76255 0 3904.3155 25.262783 + 3450 18669.69 446.92755 0 3904.2776 -4.194499 + 3500 20248.799 154.22147 0 3903.9991 3.9211572 + 3550 20226.024 158.64726 0 3904.2072 1.5299114 + 3600 20267.02 151.25631 0 3904.4082 -8.9821729 + 3650 20522.946 103.65382 0 3904.1994 -14.433796 + 3700 20892.319 35.294614 0 3904.2426 -21.264596 + 3750 19942.202 211.02993 0 3904.0304 -1.6428817 + 3800 20421.678 122.08118 0 3903.8734 1.7137935 + 3850 17899.53 588.82593 0 3903.5536 -24.450276 + 3900 20721.119 66.486999 0 3903.7312 -7.1772088 + 3950 20946.484 24.799445 0 3903.778 -0.4028037 + 4000 20985.362 17.608355 0 3903.7865 4.7522266 + 4050 19969.779 205.46466 0 3903.5719 18.941639 + 4100 20479.578 110.56561 0 3903.08 2.3715952 + 4150 18110.701 549.53348 0 3903.367 1.133321 + 4200 19321.098 325.58216 0 3903.5634 -3.7574942 + 4250 20734.436 63.87616 0 3903.5865 0.48350623 + 4300 19446.823 302.1727 0 3903.4362 4.0462392 + 4350 20494.669 108.1918 0 3903.501 2.9789077 + 4400 20379.244 129.61413 0 3903.5482 4.0881089 + 4450 19710.564 253.4251 0 3903.5295 5.3334683 + 4500 20744.753 61.785082 0 3903.406 4.0015409 + 4550 19948.024 208.76984 0 3902.8484 2.705423 + 4600 18367.368 502.69569 0 3904.0602 21.476471 + 4650 20559.367 96.133242 0 3903.4234 2.2549454 + 4700 20940.135 25.547808 0 3903.3505 -8.9042666 + 4750 20128.703 175.82088 0 3903.3584 -8.1450176 + 4800 20632.27 82.543887 0 3903.3347 -0.55649542 + 4850 19864.539 224.63792 0 3903.2563 7.1553461 + 4900 19332.037 323.15561 0 3903.1625 17.020214 + 4950 19055.575 373.68069 0 3902.4908 10.149457 + 5000 20219.484 159.21383 0 3903.5627 3.1806346 + 5050 17557.761 652.32864 0 3903.7659 10.733736 + 5100 20615.337 85.795304 0 3903.4503 -3.6035636 + 5150 20759.853 59.155843 0 3903.573 2.0152286 + 5200 20082.007 184.39375 0 3903.2839 -5.3745109 + 5250 18689.521 442.59842 0 3903.6208 -9.8911164 + 5300 20038.496 192.34221 0 3903.1749 -2.1437039 + 5350 19897.455 218.70142 0 3903.4154 0.64582116 + 5400 18732.385 434.21543 0 3903.1755 12.98676 + 5450 19831.487 230.79099 0 3903.2886 11.439958 + 5500 20079.89 184.6953 0 3903.1935 4.0906279 + 5550 20453.497 115.47128 0 3903.1559 7.8844436 + 5600 16673.041 815.52661 0 3903.1267 -20.17797 + 5650 19691.378 256.6412 0 3903.1928 3.7103317 + 5700 20345.743 135.29997 0 3903.0302 5.6373816 + 5750 20769.613 56.906603 0 3903.1312 -17.564762 + 5800 20713.369 67.38314 0 3903.1922 -5.340631 + 5850 20799.947 51.348865 0 3903.1909 -2.7827653 + 5900 19581.933 273.51588 0 3899.7997 12.347375 + 5950 20444.438 116.909 0 3902.9161 -0.74896654 + 6000 18970.948 389.99664 0 3903.1352 26.642912 + 6050 19414.753 307.13217 0 3902.4568 25.86316 + 6100 20780.042 54.586474 0 3902.7424 1.5387425 + 6150 20885.872 35.091585 0 3902.8456 -8.251884 + 6200 19825.81 231.40943 0 3902.8558 6.7196589 + 6250 20578.278 92.255994 0 3903.0481 -5.9647091 + 6300 20093.43 181.8699 0 3902.8754 -9.9906069 + 6350 20605.294 87.180289 0 3902.9755 -3.5643876 + 6400 19737.257 247.84828 0 3902.8958 -4.2783347 + 6450 19884.717 220.81633 0 3903.1714 3.8758905 + 6500 18719.372 436.94802 0 3903.4984 1.7865904 + 6550 20096.883 181.63346 0 3903.2784 2.395512 + 6600 20888.673 35.003062 0 3903.2758 2.7728947 + 6650 20437.85 118.16373 0 3902.9507 8.1456757 + 6700 19241.051 339.73065 0 3902.8882 13.740454 + 6750 20407.542 123.94326 0 3903.1177 7.6285942 + 6800 20536.785 99.976706 0 3903.0851 8.3496632 + 6850 20625.328 83.579677 0 3903.0849 6.5074992 + 6900 20705.37 68.944625 0 3903.2724 3.1905177 + 6950 18872.424 408.67134 0 3903.5647 6.2638845 + 7000 20072.762 186.18051 0 3903.3586 -22.780407 + 7050 20461.879 114.07495 0 3903.3117 -11.495523 + 7100 19811.566 234.50237 0 3903.3108 1.1212695 + 7150 20742.918 61.884088 0 3903.1651 -3.7907508 + 7200 20911.192 30.599903 0 3903.0429 -7.0262304 + 7250 20879.755 36.30274 0 3902.9241 -5.8018787 + 7300 20682.32 72.703261 0 3902.7626 -3.3446789 + 7350 19401.046 309.70672 0 3902.493 3.4836528 + 7400 20220.542 157.83897 0 3902.3838 2.3400031 + 7450 17691.193 625.47764 0 3901.6244 25.239568 + 7500 19745.294 245.02566 0 3901.5615 5.3622843 + 7550 19685.719 256.70983 0 3902.2133 3.4560563 + 7600 18830.192 415.10021 0 3902.1727 -0.10282681 + 7650 19613.136 270.18979 0 3902.2521 8.2241536 + 7700 20989.015 15.636879 0 3902.4915 1.2955204 + 7750 20301.583 142.90625 0 3902.4586 0.12548373 + 7800 18360.147 502.50342 0 3902.5307 17.117272 + 7850 20796.478 51.032537 0 3902.2321 -3.0993883 + 7900 20284.267 145.64296 0 3901.9887 -1.2682383 + 7950 20280.983 146.13471 0 3901.8723 3.5999841 + 8000 20915.869 28.730821 0 3902.0399 2.4987291 + 8050 20745.162 60.19981 0 3901.8964 4.0643481 + 8100 20509.039 103.70462 0 3901.6748 1.0771863 + 8150 20212.97 158.64893 0 3901.7916 3.0000215 + 8200 20323.463 138.25912 0 3901.8634 -1.2802945 + 8250 19997.284 198.37183 0 3901.5727 -2.6431964 + 8300 20138.402 171.75824 0 3901.092 1.7669897 + 8350 20367.568 130.22531 0 3901.9972 -1.2153731 + 8400 19945.534 208.35675 0 3901.9741 1.6021151 + 8450 20112.534 177.18642 0 3901.7298 2.2413008 + 8500 20686.7 71.116816 0 3901.9873 2.2888545 + 8550 18081.94 553.83586 0 3902.3432 7.8257937 + 8600 18320.081 505.67086 0 3898.2784 16.554878 + 8650 20235.305 154.43021 0 3901.709 3.1740823 + 8700 20355.413 132.22512 0 3901.746 4.3436482 + 8750 20087.188 182.11349 0 3901.9631 10.422134 + 8800 20400.795 124.09819 0 3902.0232 2.1179177 + 8850 20678.731 72.825797 0 3902.2204 -3.4491441 + 8900 20372.643 129.5072 0 3902.2189 -8.2166415 + 8950 20851.731 40.899364 0 3902.331 -5.8382839 + 9000 20318.076 139.61775 0 3902.2243 -4.1960802 + 9050 16879.415 776.53739 0 3902.3549 -14.429475 + 9100 19135.149 358.68223 0 3902.2284 -15.50479 + 9150 20689.556 70.939656 0 3902.339 -2.9876179 + 9200 19949.801 207.54882 0 3901.9564 6.4259245 + 9250 20207.027 160.2813 0 3902.3233 1.7402195 + 9300 20030.005 192.99466 0 3902.2548 5.300728 + 9350 19795.291 236.24003 0 3902.0347 5.8677745 + 9400 18232.093 526.18752 0 3902.501 19.344893 + 9450 18789.641 422.30568 0 3901.8687 -7.5185247 + 9500 16332.599 874.10423 0 3898.6597 16.241378 + 9550 18572.572 462.19972 0 3901.5649 -10.777359 + 9600 19859.645 223.32209 0 3901.0341 0.89631957 + 9650 19092.741 365.35768 0 3901.0504 6.7830005 + 9700 18391.154 495.72792 0 3901.4972 6.0683847 + 9750 17790.092 608.60997 0 3903.0714 8.2090184 + 9800 17681.783 628.99951 0 3903.4038 14.231747 + 9850 17804.412 605.54067 0 3902.654 22.308453 + 9900 19134.472 359.37911 0 3902.7999 8.5633158 + 9950 20099.055 180.28604 0 3902.3332 4.7905855 + 10000 20035.447 192.30744 0 3902.5754 1.8299201 +Loop time of 2.34062 on 4 procs for 10000 steps with 81 atoms + +Performance: 36913.309 tau/day, 4272.374 timesteps/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 | 0.0052865 | 0.014915 | 0.039366 | 11.6 | 0.64 +Neigh | 0.0080708 | 0.016504 | 0.03345 | 7.7 | 0.71 +Comm | 0.1357 | 0.14237 | 0.15111 | 1.5 | 6.08 +Output | 0.0033429 | 0.0037922 | 0.0050931 | 1.2 | 0.16 +Modify | 2.1033 | 2.1433 | 2.1609 | 1.6 | 91.57 +Other | | 0.01973 | | | 0.84 + +Nlocal: 20.25 ave 36 max 0 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 35.25 ave 47 max 24 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 137.5 ave 252 max 0 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 550 +Ave neighs/atom = 6.7901235 +Neighbor list builds = 994 +Dangerous builds = 956 +Total wall time: 0:00:02 diff --git a/examples/rigid/log.27Nov18.rigid.poems.g++.1 b/examples/rigid/log.27Nov18.rigid.poems.g++.1 deleted file mode 100644 index e279b8a73e..0000000000 --- a/examples/rigid/log.27Nov18.rigid.poems.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 3.292 | 3.292 | 3.292 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699149 - 1200 21815.003 45.317414 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064078 - 1300 20780.781 217.36506 0 3680.8286 6.0538616 - 1350 20558.971 254.36482 0 3680.8601 -3.6773952 - 1400 21485.029 99.812921 0 3680.6511 -16.185473 - 1450 21771.107 52.15961 0 3680.6775 -2.4756673 - 1500 21520.948 93.503927 0 3680.3286 2.1023576 - 1550 21351.418 121.68137 0 3680.2511 5.5159947 - 1600 20778.805 216.92177 0 3680.0559 15.089188 - 1650 21477.638 100.21836 0 3679.8247 -1.1045746 - 1700 18501.339 596.47914 0 3680.0357 -15.679679 - 1750 18563.642 587.34785 0 3681.2882 33.532209 - 1800 19110.185 494.8234 0 3679.8543 18.024046 - 1850 21364.191 119.23545 0 3679.9339 2.5291103 - 1900 20146.626 322.14867 0 3679.9197 5.7313218 - 1950 20692.672 231.25325 0 3680.0319 4.2977763 - 2000 20943.904 189.11235 0 3679.7629 -22.645121 - 2050 19668.057 401.82994 0 3679.8394 3.6251916 - 2100 20280.442 299.76155 0 3679.8353 7.4807949 - 2150 19181.86 483.522 0 3680.4987 22.620507 - 2200 21300.161 130.70534 0 3680.7322 4.7102665 - 2250 20486.943 266.63931 0 3681.1299 -8.6456512 - 2300 18653.122 572.24819 0 3681.1018 -5.2637122 - 2350 21513.523 95.614901 0 3681.2021 -9.3621767 - 2400 21466.272 103.56446 0 3681.2765 -29.561368 - 2450 20100.105 332.27123 0 3682.2887 35.744287 - 2500 20764.395 221.6677 0 3682.4001 -12.468906 - 2550 20435.699 276.31055 0 3682.2603 -22.413697 - 2600 21466.467 104.53618 0 3682.2807 -10.078508 - 2650 20814.737 213.23892 0 3682.3617 5.1390411 - 2700 18565.761 588.3578 0 3682.6513 22.27664 - 2750 20772.36 220.1607 0 3682.2206 -7.9448198 - 2800 21018.563 179.10058 0 3682.1945 -7.0717829 - 2850 16789.412 884.21472 0 3682.4501 33.279015 - 2900 19304.363 464.75282 0 3682.1466 7.947554 - 2950 20513.758 263.07578 0 3682.0355 2.2361434 - 3000 20617.309 245.95251 0 3682.1706 -0.75213689 - 3050 18567.52 587.90473 0 3682.4914 -4.0112006 - 3100 18696.577 566.20617 0 3682.3023 -1.4814167 - 3150 19864.606 371.56078 0 3682.3284 8.9362836 - 3200 18902.643 532.04614 0 3682.4867 0.76630303 - 3250 21110.454 163.86212 0 3682.271 -1.6253894 - 3300 19369.939 454.05833 0 3682.3816 4.9066544 - 3350 19082.603 501.69905 0 3682.133 3.5982292 - 3400 19527.779 426.918 0 3681.5478 6.9612143 - 3450 19892.953 366.19989 0 3681.6921 3.0050426 - 3500 19708.981 396.84552 0 3681.6756 7.0757635 - 3550 20256.096 306.23937 0 3682.2554 -1.752138 - 3600 21289.889 133.93823 0 3682.253 -3.7462615 - 3650 18333.877 627.18028 0 3682.8264 -15.276791 - 3700 19829.133 377.33753 0 3682.1931 -6.269648 - 3750 20771.635 220.07171 0 3682.0109 -28.479036 - 3800 18373.813 619.79253 0 3682.0947 29.594781 - 3850 19320.99 461.92786 0 3682.0928 -5.3212101 - 3900 16119.825 995.68064 0 3682.3182 -8.4683118 - 3950 15556.948 1091.3655 0 3684.1902 20.98273 - 4000 20000.464 348.24891 0 3681.6596 7.1589745 - 4050 18870.219 536.59924 0 3681.6358 -3.7997025 - 4100 19889.518 367.49253 0 3682.4122 -14.091266 - 4150 15789.623 1051.3399 0 3682.9438 -4.4152389 - 4200 20548.889 256.83493 0 3681.6498 0.92234153 - 4250 20681.925 235.46113 0 3682.4487 -11.515773 - 4300 19330.404 460.80975 0 3682.5437 -22.351775 - 4350 19369.443 453.35405 0 3681.5945 29.418242 - 4400 20762.165 222.24133 0 3682.6021 2.6627047 - 4450 19984.657 350.71294 0 3681.4891 28.88731 - 4500 21167.58 154.25344 0 3682.1834 -3.0784322 - 4550 18133.576 660.73671 0 3682.9995 2.5305835 - 4600 19935.069 360.36826 0 3682.8798 2.4575034 - 4650 21413.76 113.86464 0 3682.8246 -5.1271547 - 4700 21716.333 63.609419 0 3682.9982 -2.4708049 - 4750 21352.947 124.36961 0 3683.1941 -0.29026265 - 4800 19043.788 508.8617 0 3682.8264 14.797006 - 4850 20516.121 263.78758 0 3683.1411 7.1348281 - 4900 20624.5 245.81827 0 3683.235 0.34708051 - 4950 20317.197 296.68937 0 3682.8889 -0.55065946 - 5000 18346.865 625.37246 0 3683.1832 7.3371413 - 5050 18867.53 538.49153 0 3683.0799 1.9249866 - 5100 18790.276 551.17224 0 3682.885 2.2333017 - 5150 20241.365 311.84683 0 3685.4076 -3.998004 - 5200 17685.058 739.76418 0 3687.2739 3.2835025 - 5250 18496.626 604.58166 0 3687.3526 -10.185776 - 5300 18420.042 617.82026 0 3687.8273 -16.392458 - 5350 18767.338 559.0349 0 3686.9246 4.5320767 - 5400 20423.245 284.90517 0 3688.7794 -8.6356656 - 5450 21080.398 176.18494 0 3689.5846 -16.450038 - 5500 16684.424 909.12643 0 3689.8637 49.94555 - 5550 20132.31 335.03663 0 3690.4216 -16.018038 - 5600 20430.923 285.17562 0 3690.3295 -5.0773675 - 5650 20479.943 276.55962 0 3689.8834 5.4334564 - 5700 20061.532 345.95553 0 3689.5441 -16.230658 - 5750 20523.759 268.92217 0 3689.5487 -4.4128812 - 5800 18900.356 537.65462 0 3687.7139 13.605549 - 5850 20280.502 310.27193 0 3690.3556 -4.7884959 - 5900 19050.26 515.66087 0 3690.7042 7.8864722 - 5950 19566.917 430.2997 0 3691.4525 31.715268 - 6000 18878.118 544.75449 0 3691.1076 -4.2415329 - 6050 19308.682 471.70734 0 3689.821 -10.561614 - 6100 18776.194 560.04764 0 3689.4133 -7.7286747 - 6150 21475.064 110.1508 0 3689.3281 -3.6506391 - 6200 19975 360.82675 0 3689.9934 10.282021 - 6250 21396.341 123.5341 0 3689.5909 -5.7215163 - 6300 18533.423 600.87422 0 3689.778 15.408027 - 6350 20653.152 247.19253 0 3689.3846 8.5607784 - 6400 19716.537 403.41487 0 3689.5044 13.165575 - 6450 21120.66 168.79838 0 3688.9084 -0.50382728 - 6500 19700.345 404.7155 0 3688.1064 13.941375 - 6550 10818.393 1892.037 0 3695.1025 38.423155 - 6600 18684.478 574.84755 0 3688.9273 5.9176985 - 6650 19219.732 486.04269 0 3689.3314 18.287659 - 6700 20058.587 344.88255 0 3687.9804 6.5372086 - 6750 21279.318 142.77333 0 3689.3264 2.498188 - 6800 20671.545 244.25024 0 3689.5078 -4.1356416 - 6850 21203.598 155.82001 0 3689.753 -0.0083061182 - 6900 21699.344 73.301497 0 3689.8588 -8.0309898 - 6950 20951.212 197.19403 0 3689.0627 0.76668303 - 7000 20166.275 329.02869 0 3690.0746 2.0083318 - 7050 21554.944 97.465792 0 3689.9564 -3.2420086 - 7100 20817.494 220.25476 0 3689.8372 0.17206182 - 7150 21481.11 109.84029 0 3690.0253 -3.6814741 - 7200 21266.824 145.53099 0 3690.0016 -2.060543 - 7250 19434.684 450.81331 0 3689.9273 9.4822765 - 7300 21246.525 148.96573 0 3690.0532 3.3208839 - 7350 19749.269 398.60049 0 3690.1454 1.0929662 - 7400 20354.792 297.70261 0 3690.168 1.547159 - 7450 19996.859 357.16723 0 3689.977 -0.68412025 - 7500 20179.628 326.53243 0 3689.8038 -2.4805507 - 7550 18765.184 561.65039 0 3689.1811 -1.7976428 - 7600 19457.496 447.04428 0 3689.9603 -1.9055522 - 7650 18206.823 655.57276 0 3690.0433 1.2797964 - 7700 19152.344 497.77422 0 3689.8315 18.145069 - 7750 21387.484 125.48654 0 3690.0673 -2.9915772 - 7800 18127.052 668.61425 0 3689.7896 9.044869 - 7850 21419.557 120.08889 0 3690.015 6.2651717 - 7900 21817.182 53.739819 0 3689.9368 -4.2387416 - 7950 18215.195 654.15494 0 3690.0208 -54.628049 - 8000 21523.503 102.58018 0 3689.8307 -4.84236 - 8050 20720.799 236.28689 0 3689.7535 -9.3725225 - 8100 21196.483 157.3232 0 3690.0704 -7.7222497 - 8150 20869.667 211.65308 0 3689.9309 -6.8438295 - 8200 17790.052 725.72497 0 3690.7336 -25.697688 - 8250 19634.94 417.71929 0 3690.2094 8.861604 - 8300 19135.784 500.92443 0 3690.2218 -3.1245167 - 8350 20191.718 324.93312 0 3690.2195 6.5736107 - 8400 20695.239 241.02378 0 3690.2302 -14.592221 - 8450 21793.857 57.609525 0 3689.9191 -11.509747 - 8500 21271.088 144.43102 0 3689.6124 -0.091587085 - 8550 20064.337 345.21754 0 3689.2737 9.5058471 - 8600 20282.86 308.2307 0 3688.7074 2.265529 - 8650 21223.055 151.24306 0 3688.419 1.7296834 - 8700 18875.342 542.42055 0 3688.3108 6.367148 - 8750 20922.65 201.55122 0 3688.6595 3.4208578 - 8800 21406.54 120.8539 0 3688.6106 1.8253729 - 8850 19868.524 377.05623 0 3688.477 16.327796 - 8900 20025.322 348.94892 0 3686.5025 17.063406 - 8950 21224.374 151.3567 0 3688.7524 -0.11028753 - 9000 21318.309 135.862 0 3688.9135 -0.50826819 - 9050 17538.618 768.00136 0 3691.1043 37.978645 - 9100 21247.861 147.84641 0 3689.1566 -6.7773259 - 9150 18455.677 613.08767 0 3689.0339 -3.4844751 - 9200 19486.859 441.03829 0 3688.8482 -18.602827 - 9250 21774.926 59.710446 0 3688.8648 -13.379919 - 9300 17628.877 750.72321 0 3688.8694 27.797974 - 9350 19827.334 383.85708 0 3688.4128 6.5459021 - 9400 20020.126 351.61742 0 3688.3051 -14.332562 - 9450 21596.338 88.904175 0 3688.2939 1.5779716 - 9500 18981.418 524.60141 0 3688.1711 5.4352409 - 9550 18652.616 579.05144 0 3687.8208 25.600729 - 9600 21198.037 155.23097 0 3688.2371 -3.3586596 - 9650 19958.317 361.32544 0 3687.7115 4.2910178 - 9700 19129.101 499.5993 0 3687.7828 13.267102 - 9750 21913.967 35.689587 0 3688.0174 -7.3222905 - 9800 21314.694 135.43794 0 3687.8869 -9.5613518 - 9850 20899.743 204.82802 0 3688.1185 -2.6321428 - 9900 20288.244 306.5013 0 3687.8753 3.6196618 - 9950 19271.015 475.88527 0 3687.7211 -1.8196764 - 10000 21122.24 167.82714 0 3688.2005 -3.8464842 -Loop time of 6.61148 on 1 procs for 10000 steps with 81 atoms - -Performance: 13068.179 tau/day, 1512.521 timesteps/s -97.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14595 | 0.14595 | 0.14595 | 0.0 | 2.21 -Neigh | 0.10704 | 0.10704 | 0.10704 | 0.0 | 1.62 -Comm | 0.013317 | 0.013317 | 0.013317 | 0.0 | 0.20 -Output | 0.0047956 | 0.0047956 | 0.0047956 | 0.0 | 0.07 -Modify | 6.3318 | 6.3318 | 6.3318 | 0.0 | 95.77 -Other | | 0.008603 | | | 0.13 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 95 ave 95 max 95 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 744 ave 744 max 744 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 744 -Ave neighs/atom = 9.18519 -Neighbor list builds = 992 -Dangerous builds = 941 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:06 diff --git a/examples/rigid/log.27Nov18.rigid.poems.g++.4 b/examples/rigid/log.27Nov18.rigid.poems.g++.4 deleted file mode 100644 index 55ecca3067..0000000000 --- a/examples/rigid/log.27Nov18.rigid.poems.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 3.263 | 3.357 | 3.638 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384276 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184718 - 1150 20849.582 206.01695 0 3680.9472 -0.8669916 - 1200 21815.003 45.317417 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064076 - 1300 20780.781 217.36504 0 3680.8286 6.0538619 - 1350 20558.972 254.3648 0 3680.8601 -3.6773987 - 1400 21485.029 99.812949 0 3680.6511 -16.185471 - 1450 21771.108 52.15959 0 3680.6775 -2.4756681 - 1500 21520.948 93.503949 0 3680.3286 2.1023578 - 1550 21351.418 121.6814 0 3680.2511 5.5159978 - 1600 20778.805 216.92171 0 3680.0559 15.089182 - 1650 21477.639 100.2182 0 3679.8247 -1.1045944 - 1700 18501.343 596.47853 0 3680.0357 -15.67963 - 1750 18563.643 587.34767 0 3681.2882 33.532167 - 1800 19110.19 494.82264 0 3679.8543 18.024034 - 1850 21364.196 119.23454 0 3679.9339 2.5291491 - 1900 20146.643 322.14595 0 3679.9197 5.731152 - 1950 20692.67 231.25357 0 3680.0319 4.2977641 - 2000 20943.904 189.11223 0 3679.763 -22.645645 - 2050 19668.152 401.81407 0 3679.8394 3.6255896 - 2100 20280.572 299.73976 0 3679.8351 7.4809355 - 2150 19182.121 483.47905 0 3680.4992 22.615309 - 2200 21299.76 130.77281 0 3680.7327 4.7114154 - 2250 20487.784 266.4995 0 3681.1302 -8.6406776 - 2300 18655.125 571.91487 0 3681.1023 -5.2671669 - 2350 21512.614 95.766913 0 3681.2025 -9.3523428 - 2400 21467.773 103.31519 0 3681.2773 -29.600307 - 2450 20096.937 332.80159 0 3682.2911 35.890912 - 2500 20761.446 222.16118 0 3682.4022 -12.528127 - 2550 20409.6 280.67234 0 3682.2723 -22.277373 - 2600 21469.964 103.95529 0 3682.2826 -10.038267 - 2650 20708.138 231.00516 0 3682.3615 5.3659502 - 2700 18584.743 585.07862 0 3682.5357 21.785261 - 2750 20503.019 264.91491 0 3682.0847 -4.5583917 - 2800 20584.075 251.44664 0 3682.1258 -6.5084595 - 2850 17277.076 802.33356 0 3681.8462 15.519513 - 2900 19392.956 449.92915 0 3682.0885 -4.3829957 - 2950 18371.786 620.29835 0 3682.2626 7.2117592 - 3000 20412.015 280.25302 0 3682.2555 0.32492606 - 3050 20858.248 205.65269 0 3682.0273 4.5055715 - 3100 21561.094 88.438447 0 3681.9541 -3.7523733 - 3150 15471.278 1103.4497 0 3681.9961 -14.576367 - 3200 15386.973 1117.8815 0 3682.377 15.051163 - 3250 19741.037 392.04755 0 3682.2204 -2.6610995 - 3300 20870.191 203.58229 0 3681.9475 -4.7795545 - 3350 16648.228 907.66571 0 3682.3704 -8.9242511 - 3400 20104.016 331.58603 0 3682.2554 6.4783858 - 3450 21421.316 112.28228 0 3682.5015 -8.3484987 - 3500 19284.533 467.80739 0 3681.8962 -12.835452 - 3550 20160.125 322.4476 0 3682.4684 1.6574827 - 3600 16682.415 902.73752 0 3683.14 22.383296 - 3650 16762.19 890.14636 0 3683.8446 16.119412 - 3700 17858.568 707.37212 0 3683.8 -1.6582504 - 3750 20029.881 345.15986 0 3683.4733 -3.1415889 - 3800 20734 227.99158 0 3683.6582 -7.9580418 - 3850 20741.089 226.39408 0 3683.2423 8.3055765 - 3900 18671.251 571.42296 0 3683.2981 -3.7468858 - 3950 19547.209 423.14256 0 3681.0108 5.8312279 - 4000 19739.799 393.58799 0 3683.5544 18.604884 - 4050 20014.121 347.8176 0 3683.5044 9.93387 - 4100 20503.654 266.08691 0 3683.3626 8.1304118 - 4150 18309.702 632.29807 0 3683.9151 -0.0021480359 - 4200 20509.423 265.60353 0 3683.8408 -2.1658857 - 4250 21805.541 50.325935 0 3684.5828 1.082842 - 4300 21420.551 114.90431 0 3684.9962 -1.7985998 - 4350 20256.928 308.74187 0 3684.8966 -11.669472 - 4400 21633.488 79.629274 0 3685.2106 -0.96131785 - 4450 20793.327 219.66955 0 3685.2241 1.3752349 - 4500 18719.484 564.86754 0 3684.7816 2.6308699 - 4550 20966.335 190.68308 0 3685.0722 -18.587627 - 4600 19428.962 446.59618 0 3684.7565 -4.4051672 - 4650 18408.956 616.85009 0 3685.0095 2.777272 - 4700 19215.779 482.57562 0 3685.2054 19.441016 - 4750 20155.927 326.13401 0 3685.4553 6.1734993 - 4800 20918.085 199.31832 0 3685.6659 3.4407437 - 4850 20236.958 312.07276 0 3684.899 3.2612893 - 4900 21419.89 115.36879 0 3685.3505 -4.675951 - 4950 19707.901 401.14828 0 3685.7985 -10.730734 - 5000 19407.201 450.64394 0 3685.1775 17.518981 - 5050 21527.598 97.655186 0 3685.5882 -9.2294707 - 5100 21581.933 88.595517 0 3685.5843 -20.669485 - 5150 21161.214 158.48503 0 3685.3541 -2.7587502 - 5200 21166.679 157.24762 0 3685.0275 -18.180044 - 5250 20909.576 200.23507 0 3685.1644 -16.617303 - 5300 21911.746 33.236563 0 3685.1942 -5.8313967 - 5350 20857.303 208.87453 0 3685.0916 12.176312 - 5400 20958.96 191.96694 0 3685.1269 3.6116429 - 5450 20433.179 279.61178 0 3685.1415 13.324529 - 5500 19604.675 416.88499 0 3684.3308 21.536484 - 5550 18171.145 655.92915 0 3684.4534 -9.2269804 - 5600 19799.907 385.12116 0 3685.1056 22.202165 - 5650 19711.882 399.30581 0 3684.6194 15.93063 - 5700 17908.833 699.52405 0 3684.3295 0.35530356 - 5750 18606.518 583.538 0 3684.6243 -4.4540843 - 5800 21814.053 48.974627 0 3684.6501 -1.5206358 - 5850 18029.107 679.9357 0 3684.7868 12.137677 - 5900 21090.739 169.64502 0 3684.7682 -1.5051545 - 5950 21086.26 170.29075 0 3684.6674 -2.8164474 - 6000 21285.771 136.95608 0 3684.5846 -26.582739 - 6050 21203.994 150.87822 0 3684.8772 -2.6617226 - 6100 21481.553 104.57796 0 3684.8368 -16.524974 - 6150 20354.4 292.57675 0 3684.9767 2.7960207 - 6200 21326.591 130.75243 0 3685.1843 -1.5929194 - 6250 21505.087 101.07817 0 3685.2593 -3.7821931 - 6300 21296.273 135.6593 0 3685.0382 -0.55635908 - 6350 21295.389 135.86485 0 3685.0964 5.6614093 - 6400 16552.242 926.02655 0 3684.7336 14.177218 - 6450 20148.951 327.1151 0 3685.2736 7.4561085 - 6500 20962.151 191.79415 0 3685.486 -4.5436711 - 6550 21710.328 67.433972 0 3685.8219 -5.7678572 - 6600 20698.571 234.79099 0 3684.5528 -2.1984068 - 6650 17892.287 704.05484 0 3686.1026 11.525836 - 6700 21272.999 141.26589 0 3686.7657 0.44088069 - 6750 19558.993 426.46448 0 3686.2966 -16.907401 - 6800 20350.247 295.23951 0 3686.9474 1.1284348 - 6850 18665.05 573.5326 0 3684.3742 17.088712 - 6900 19769.199 392.1551 0 3687.0216 6.7562425 - 6950 19439.159 446.99138 0 3686.8512 -6.0105763 - 7000 19379.907 456.53471 0 3686.5192 -9.0505095 - 7050 19983.754 356.02523 0 3686.651 -5.6274314 - 7100 19867.737 375.47627 0 3686.7658 17.315482 - 7150 19258.794 477.47344 0 3687.2724 14.316676 - 7200 21282.428 139.96051 0 3687.0318 -0.77043459 - 7250 19828.603 381.98919 0 3686.7564 6.5142869 - 7300 20574.582 257.8245 0 3686.9215 -3.6547118 - 7350 21613.467 84.771568 0 3687.0161 -7.5188826 - 7400 21817.009 50.844944 0 3687.0131 -14.888864 - 7450 14937.538 1197.4257 0 3687.0154 1.7540499 - 7500 18326.914 632.40374 0 3686.8894 8.3397357 - 7550 13611.007 1418.4727 0 3686.9739 -19.379482 - 7600 19173.985 491.9482 0 3687.6123 17.229001 - 7650 16911.504 867.33649 0 3685.9204 -21.042834 - 7700 21752.116 61.143705 0 3686.4963 -10.344487 - 7750 20208.337 318.26355 0 3686.3197 13.385814 - 7800 21649.909 77.950987 0 3686.2692 -1.7911084 - 7850 20139.64 329.50319 0 3686.1098 -5.5805093 - 7900 21355.026 126.7642 0 3685.9352 -7.7062172 - 7950 21336.178 129.88925 0 3685.9188 -2.059298 - 8000 21047.596 177.71546 0 3685.6482 0.37963466 - 8050 19217.351 482.62331 0 3685.5152 6.5582595 - 8100 20499.057 268.7173 0 3685.2268 -1.1959737 - 8150 21494.301 102.83829 0 3685.2219 -1.6427647 - 8200 20074.928 339.19817 0 3685.0195 6.285123 - 8250 17335.157 793.47566 0 3682.6685 22.877381 - 8300 17340.544 794.62619 0 3684.7168 3.9147755 - 8350 20529.345 262.51162 0 3684.0691 4.031768 - 8400 18884.747 537.47827 0 3684.9361 22.853404 - 8450 20341.86 293.10484 0 3683.4148 0.33856656 - 8500 19300.282 467.58127 0 3684.2949 12.35507 - 8550 21631.936 78.254534 0 3683.5772 -10.992959 - 8600 20204.913 316.83233 0 3684.3178 20.74228 - 8650 21018.189 181.32054 0 3684.352 1.8412068 - 8700 20161.304 323.97907 0 3684.1964 -2.646629 - 8750 19081.79 504.00155 0 3684.2998 -10.088053 - 8800 20834.489 211.76247 0 3684.1773 14.896336 - 8850 20929.355 196.18335 0 3684.4092 -1.2602398 - 8900 21491.074 102.47788 0 3684.3235 -1.4696758 - 8950 20474.735 271.69461 0 3684.1504 -6.9489258 - 9000 21128.641 162.40732 0 3683.8474 -7.7928168 - 9050 18421.801 614.46442 0 3684.7646 24.40313 - 9100 19301.292 466.98873 0 3683.8707 4.4687046 - 9150 21575.705 88.213763 0 3684.1646 -0.94696984 - 9200 20004.776 350.05448 0 3684.1838 -7.3466605 - 9250 21384.079 120.14472 0 3684.1578 -8.3773844 - 9300 21980.599 20.702393 0 3684.1356 -12.666293 - 9350 21686.606 69.517984 0 3683.9524 -8.8366533 - 9400 20732.704 228.46247 0 3683.9131 -6.4080307 - 9450 19798.859 384.34696 0 3684.1568 7.6198484 - 9500 20270.695 305.22664 0 3683.6758 1.5862486 - 9550 16496.156 935.28481 0 3684.6441 15.001468 - 9600 20642.429 241.08853 0 3681.4934 -9.2159382 - 9650 21292.587 135.4474 0 3684.2119 -0.54770976 - 9700 18888.158 536.60518 0 3684.6315 5.3236926 - 9750 18750.018 559.35922 0 3684.3623 -9.9424949 - 9800 20544.772 259.71076 0 3683.8394 8.732202 - 9850 16698.125 901.90076 0 3684.9216 9.9553329 - 9900 21450.963 109.58687 0 3684.7474 -4.8001999 - 9950 20664.461 240.66995 0 3684.7468 -3.4840781 - 10000 18951.367 526.45428 0 3685.0155 21.512727 -Loop time of 8.99246 on 4 procs for 10000 steps with 81 atoms - -Performance: 9608.051 tau/day, 1112.043 timesteps/s -93.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.01308 | 0.038162 | 0.084123 | 14.4 | 0.42 -Neigh | 0.017227 | 0.032774 | 0.061983 | 10.0 | 0.36 -Comm | 1.329 | 1.5822 | 1.8017 | 13.5 | 17.60 -Output | 0.014984 | 0.029676 | 0.046035 | 6.6 | 0.33 -Modify | 6.8022 | 7.1104 | 7.4356 | 8.6 | 79.07 -Other | | 0.1992 | | | 2.22 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 46.25 ave 95 max 14 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 249.25 ave 997 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 997 -Ave neighs/atom = 12.3086 -Neighbor list builds = 993 -Dangerous builds = 943 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:09 diff --git a/examples/rigid/log.27Nov18.rigid.poems2.g++.1 b/examples/rigid/log.27Nov18.rigid.poems2.g++.1 deleted file mode 100644 index 071e9bcc52..0000000000 --- a/examples/rigid/log.27Nov18.rigid.poems2.g++.1 +++ /dev/null @@ -1,342 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) -WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) -WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 3.854 | 3.854 | 3.854 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47585 0 3765.6103 -17.923459 - 1500 19223.688 204.15175 0 3764.0939 -1.6134531 - 1550 18147.996 404.12677 0 3764.8668 8.4194779 - 1600 18615.043 317.42467 0 3764.6548 -2.3288934 - 1650 20120.654 38.887913 0 3764.935 -8.7620277 - 1700 19450.907 162.98272 0 3765.0025 2.3254731 - 1750 19374.632 177.37966 0 3765.2744 8.9328774 - 1800 19424.404 167.93966 0 3765.0514 0.081230261 - 1850 17936.249 442.84231 0 3764.3699 6.6010636 - 1900 19982.595 64.406198 0 3764.8868 -2.9529813 - 1950 16215.852 761.91287 0 3764.8485 13.994708 - 2000 18584.422 322.12049 0 3763.68 7.1654003 - 2050 20107.965 41.025754 0 3764.723 -0.3109069 - 2100 20002.333 60.593017 0 3764.7288 -6.7919784 - 2150 16949.762 626.59623 0 3765.441 3.508941 - 2200 20010.953 58.808279 0 3764.5403 -10.862172 - 2250 18982.73 247.00892 0 3762.3292 -0.53807815 - 2300 18401.298 354.87973 0 3762.5274 1.0920554 - 2350 19390.524 172.9415 0 3763.7793 -3.3524932 - 2400 16080.801 786.38838 0 3764.3146 -16.200514 - 2450 18870.412 268.74976 0 3763.2705 11.197736 - 2500 19688.29 117.58223 0 3763.5618 4.382644 - 2550 18870.825 268.78678 0 3763.384 -5.6623656 - 2600 17019.35 611.70808 0 3763.4395 6.3109641 - 2650 18753.285 291.0596 0 3763.8902 2.4120296 - 2700 19742.456 107.20901 0 3763.2193 -0.33061303 - 2750 19522.438 148.16759 0 3763.4339 -1.6254851 - 2800 18304.801 372.55152 0 3762.3295 22.6368 - 2850 18465.36 343.48495 0 3762.9961 4.4169272 - 2900 20151.999 31.372926 0 3763.2245 1.2013699 - 2950 15498.143 892.80071 0 3762.8272 13.263724 - 3000 18728.301 294.65113 0 3762.855 8.1897838 - 3050 18538.466 330.25223 0 3763.3015 8.5865739 - 3100 19081.409 229.5907 0 3763.1849 -4.8573813 - 3150 18498.802 337.11548 0 3762.8195 1.0555321 - 3200 19925.897 73.358029 0 3763.339 -7.7325108 - 3250 19780.108 100.23785 0 3763.2209 -5.5974972 - 3300 19221.043 203.82387 0 3763.2763 4.2703251 - 3350 19025.292 240.11329 0 3763.3156 5.7708328 - 3400 18153.696 401.52086 0 3763.3164 21.076943 - 3450 18611.375 316.50396 0 3763.0548 -3.5484945 - 3500 19931.319 71.969274 0 3762.9543 1.8764978 - 3550 19747.562 106.05439 0 3763.0103 -2.5506186 - 3600 18491.39 338.4134 0 3762.7449 -4.0527808 - 3650 19757.998 104.19207 0 3763.0806 1.4865598 - 3700 20108.003 39.345514 0 3763.0498 0.062827129 - 3750 19222.505 203.28065 0 3763.0039 0.33719277 - 3800 19286.383 191.08831 0 3762.6406 -0.1826802 - 3850 19450.083 161.09138 0 3762.9587 -0.2708263 - 3900 18002.304 429.25655 0 3763.0166 -4.6832439 - 3950 17186.829 582.26502 0 3765.0111 55.816834 - 4000 16826.434 645.84974 0 3761.856 19.675962 - 4050 19227.526 202.18151 0 3762.8344 -0.2596098 - 4100 19908.792 76.084531 0 3762.8978 -2.796813 - 4150 17821.329 462.63065 0 3762.8768 13.069155 - 4200 19917.133 74.574998 0 3762.9329 -6.4181155 - 4250 19012.618 241.96787 0 3762.823 4.0847974 - 4300 19077.34 229.98133 0 3762.8221 4.324323 - 4350 19361.128 177.47406 0 3762.8681 -7.377974 - 4400 18565.044 324.95107 0 3762.9223 2.5229032 - 4450 19352.406 178.98756 0 3762.7665 0.10862717 - 4500 18482.218 340.15496 0 3762.788 12.518301 - 4550 18359.732 362.83749 0 3762.7879 3.7500902 - 4600 19623.618 128.71624 0 3762.7196 -1.1328521 - 4650 17565.707 509.99904 0 3762.9078 1.7135935 - 4700 19876.052 81.892814 0 3762.6431 0.32476108 - 4750 19022.676 239.92262 0 3762.6403 -0.24613022 - 4800 18862.685 269.24248 0 3762.3324 6.2733979 - 4850 19899.174 77.426145 0 3762.4584 0.42535238 - 4900 18250.865 382.72867 0 3762.5185 23.308462 - 4950 18895.847 263.22651 0 3762.4575 8.0634675 - 5000 19096.705 225.69358 0 3762.1204 3.6816481 - 5050 16546.294 698.91312 0 3763.0416 17.453618 - 5100 19501.208 151.20999 0 3762.5449 -1.1231291 - 5150 19479.879 155.00669 0 3762.3917 -3.983378 - 5200 17397.818 541.23039 0 3763.0485 6.1109992 - 5250 18564.869 324.10557 0 3762.0442 9.2244762 - 5300 16271.663 747.52374 0 3760.7947 -6.5256602 - 5350 19831.418 89.851887 0 3762.3367 -2.3453958 - 5400 18723.697 294.67435 0 3762.0256 4.6822081 - 5450 19547.28 142.21934 0 3762.086 -5.5243408 - 5500 19415.447 166.68729 0 3762.1404 -9.5658991 - 5550 18492.721 337.54773 0 3762.1256 6.5184903 - 5600 19391.389 171.14375 0 3762.1416 -0.53835361 - 5650 18503.465 334.62751 0 3761.1951 4.6580363 - 5700 18153.344 399.91064 0 3761.6409 12.851587 - 5750 18342.297 365.14769 0 3761.8694 2.7148176 - 5800 19583.241 135.64969 0 3762.1758 -1.089608 - 5850 15967.283 804.18382 0 3761.088 11.278762 - 5900 19040.271 235.35509 0 3761.3312 5.1352158 - 5950 17920.962 443.17951 0 3761.8762 4.9621366 - 6000 19100.92 224.3946 0 3761.602 -9.537589 - 6050 17982.119 432.3251 0 3762.3472 -2.851617 - 6100 16233.096 755.46191 0 3761.5908 25.113316 - 6150 18316.543 370.01118 0 3761.9635 -1.7445703 - 6200 18483.464 339.13282 0 3761.9966 -2.0857447 - 6250 18609.406 315.56032 0 3761.7467 -12.289208 - 6300 17167.919 582.68212 0 3761.9264 -3.8263397 - 6350 17870.329 452.58116 0 3761.9013 -3.3843134 - 6400 19309.717 186.11786 0 3761.9913 -4.9462739 - 6450 17964.073 435.39924 0 3762.0794 12.272972 - 6500 18772.847 285.61959 0 3762.0727 6.7928648 - 6550 18915.116 259.41365 0 3762.213 -4.1449761 - 6600 19446.628 161.18763 0 3762.415 -2.1906581 - 6650 16348.787 734.99282 0 3762.546 -9.9624546 - 6700 19066.684 231.43863 0 3762.3061 -5.362833 - 6750 14890.323 1004.547 0 3762.0143 37.373013 - 6800 18235.19 385.253 0 3762.1401 0.21012662 - 6850 16447.997 716.11276 0 3762.0382 -9.2095411 - 6900 18343.362 364.81902 0 3761.7379 10.417932 - 6950 16014.084 797.13348 0 3762.7046 6.7906777 - 7000 19120.393 221.29236 0 3762.1059 -1.3461375 - 7050 18055.409 418.30136 0 3761.8957 1.5772317 - 7100 18407.231 353.41868 0 3762.1652 0.61071769 - 7150 18728.136 293.64021 0 3761.8136 5.1649654 - 7200 17706.628 483.07628 0 3762.0815 18.000708 - 7250 19349.505 178.89673 0 3762.1385 2.540201 - 7300 20016.293 55.389159 0 3762.1101 -1.5793163 - 7350 19398.573 169.86661 0 3762.1949 -5.060123 - 7400 19466.526 157.37407 0 3762.2862 1.7158273 - 7450 18440.348 347.09196 0 3761.9712 12.781963 - 7500 19989.907 60.555934 0 3762.3906 -1.5033319 - 7550 19667.28 120.27403 0 3762.363 -3.3502366 - 7600 18497.707 336.15863 0 3761.66 1.7887539 - 7650 17901.957 447.17282 0 3762.3501 0.016725252 - 7700 19758.725 103.3129 0 3762.3361 -23.534448 - 7750 19443.957 161.6532 0 3762.386 -10.323924 - 7800 19776.178 100.1773 0 3762.4324 6.0854422 - 7850 19242.512 198.86705 0 3762.2952 5.2823659 - 7900 19499.929 151.30366 0 3762.4017 12.299911 - 7950 19630.317 127.19541 0 3762.4393 8.0799632 - 8000 19872.384 82.421129 0 3762.4923 2.2126691 - 8050 17747.038 476.27982 0 3762.7683 -7.7042786 - 8100 18832.654 274.78106 0 3762.3095 13.882157 - 8150 19949.814 68.09711 0 3762.5072 -0.54410896 - 8200 17555.866 511.02517 0 3762.1115 6.2471175 - 8250 17800.1 465.9992 0 3762.314 13.583485 - 8300 19755.224 103.89732 0 3762.2721 -1.487243 - 8350 17583.61 506.17539 0 3762.3995 -9.7819128 - 8400 18529.003 330.75623 0 3762.0532 14.731228 - 8450 20155.902 29.797078 0 3762.3716 -8.5711085 - 8500 18047.548 420.54645 0 3762.685 7.3875118 - 8550 19790.794 97.493375 0 3762.4553 -3.3427911 - 8600 19997.902 59.172074 0 3762.4874 3.3479688 - 8650 19987.319 61.148363 0 3762.5037 -1.889232 - 8700 19363.91 176.41833 0 3762.3276 -9.4291288 - 8750 18712.689 296.3979 0 3761.7107 5.9221369 - 8800 19783.17 98.860518 0 3762.4105 -3.5262066 - 8850 18796.049 281.60057 0 3762.3504 -8.2913002 - 8900 16738.277 662.62261 0 3762.3035 8.5838631 - 8950 17869.613 452.25006 0 3761.4377 11.561101 - 9000 18682.512 302.27997 0 3762.0043 3.8878724 - 9050 17513.759 518.50265 0 3761.7914 23.05778 - 9100 17500.686 521.57944 0 3762.4473 -2.8435751 - 9150 19645.683 124.43597 0 3762.5254 -3.0193092 - 9200 18898.897 262.76552 0 3762.5612 3.5891701 - 9250 20114.279 37.614866 0 3762.4813 -0.58120871 - 9300 19562.613 139.54073 0 3762.2468 -3.2630158 - 9350 19679.811 118.05865 0 3762.468 -3.4644363 - 9400 19297.384 188.84527 0 3762.4349 0.40498037 - 9450 18267.029 379.52581 0 3762.309 -0.13762867 - 9500 19951.072 67.63844 0 3762.2814 -7.575539 - 9550 19134.562 218.46835 0 3761.9057 -1.9626244 - 9600 19089.093 227.29178 0 3762.3089 -1.94158 - 9650 16964.603 620.71289 0 3762.3061 16.987042 - 9700 18846.881 271.3129 0 3761.4761 3.4458802 - 9750 19309.225 186.0142 0 3761.7966 9.4048627 - 9800 16359.704 733.51007 0 3763.0849 15.870164 - 9850 19958.532 66.203725 0 3762.2282 6.0043645 - 9900 19864.564 83.502384 0 3762.1253 -0.65360617 - 9950 18996.789 244.25101 0 3762.1749 -2.4961826 - 10000 17933.494 441.33587 0 3762.3532 -6.0731708 -Loop time of 6.84978 on 1 procs for 10000 steps with 81 atoms - -Performance: 12613.550 tau/day, 1459.902 timesteps/s -96.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.1054 | 0.1054 | 0.1054 | 0.0 | 1.54 -Neigh | 0.081336 | 0.081336 | 0.081336 | 0.0 | 1.19 -Comm | 0.017124 | 0.017124 | 0.017124 | 0.0 | 0.25 -Output | 0.0050254 | 0.0050254 | 0.0050254 | 0.0 | 0.07 -Modify | 6.6313 | 6.6313 | 6.6313 | 0.0 | 96.81 -Other | | 0.00962 | | | 0.14 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 612 ave 612 max 612 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 612 -Ave neighs/atom = 7.55556 -Neighbor list builds = 989 -Dangerous builds = 906 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:06 diff --git a/examples/rigid/log.27Nov18.rigid.poems2.g++.4 b/examples/rigid/log.27Nov18.rigid.poems2.g++.4 deleted file mode 100644 index 36856d97ec..0000000000 --- a/examples/rigid/log.27Nov18.rigid.poems2.g++.4 +++ /dev/null @@ -1,342 +0,0 @@ -LAMMPS (27 Nov 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) -WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) -WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, 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) = 3.825 | 3.919 | 4.201 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47585 0 3765.6103 -17.923459 - 1500 19223.688 204.15176 0 3764.0939 -1.6134529 - 1550 18147.996 404.12677 0 3764.8668 8.4194781 - 1600 18615.043 317.42468 0 3764.6548 -2.3288926 - 1650 20120.654 38.887908 0 3764.935 -8.7620288 - 1700 19450.907 162.98267 0 3765.0025 2.3254739 - 1750 19374.631 177.3797 0 3765.2744 8.9328773 - 1800 19424.404 167.93965 0 3765.0514 0.081228843 - 1850 17936.227 442.84645 0 3764.3699 6.6011251 - 1900 19982.595 64.406244 0 3764.8868 -2.952971 - 1950 16215.818 761.91942 0 3764.8486 13.994877 - 2000 18584.433 322.11846 0 3763.6801 7.1653695 - 2050 20107.965 41.025796 0 3764.723 -0.31089763 - 2100 20002.329 60.593879 0 3764.7288 -6.7919882 - 2150 16949.817 626.58598 0 3765.4409 3.5087505 - 2200 20010.954 58.8082 0 3764.5403 -10.862143 - 2250 18982.732 247.00854 0 3762.3293 -0.53812607 - 2300 18401.276 354.88369 0 3762.5274 1.0921058 - 2350 19390.535 172.93951 0 3763.7793 -3.3524354 - 2400 16080.475 786.44896 0 3764.3146 -16.201558 - 2450 18870.293 268.77171 0 3763.2704 11.199749 - 2500 19688.508 117.54164 0 3763.5617 4.3806994 - 2550 18870.328 268.87896 0 3763.3841 -5.6641099 - 2600 17020.211 611.54841 0 3763.4394 6.3081434 - 2650 18748.838 291.88478 0 3763.8917 2.4175163 - 2700 19743.991 106.92945 0 3763.224 -0.33916964 - 2750 19525.446 147.60906 0 3763.4324 -1.6251174 - 2800 18257.411 381.40184 0 3762.4038 23.39495 - 2850 18496.796 337.65425 0 3762.9868 4.3657735 - 2900 20163.418 29.253902 0 3763.2203 1.4431917 - 2950 16823.317 646.69817 0 3762.1273 4.9041552 - 3000 19223.007 203.2529 0 3763.069 4.0414458 - 3050 17391.02 542.93746 0 3763.4968 15.139863 - 3100 19205.6 206.57791 0 3763.1705 4.8519241 - 3150 19835.659 90.247763 0 3763.5179 -14.900053 - 3200 18962.776 251.5838 0 3763.2089 -13.706561 - 3250 19418.837 167.29058 0 3763.3716 -2.0866468 - 3300 18628.291 313.69067 0 3763.3742 5.9919715 - 3350 17465.974 529.14439 0 3763.5841 14.122593 - 3400 18488.661 339.6186 0 3763.4448 21.526798 - 3450 19163.152 214.26098 0 3762.9928 4.1888096 - 3500 18000.27 429.81789 0 3763.2011 5.4734485 - 3550 19582.423 136.71887 0 3763.0935 -2.5335675 - 3600 19634.325 127.2219 0 3763.208 -1.9728322 - 3650 19428.114 165.40707 0 3763.2059 -2.3318779 - 3700 19861.116 85.356944 0 3763.3414 -3.9097609 - 3750 19337.239 182.43992 0 3763.4102 -3.3559651 - 3800 19493.146 153.40349 0 3763.2453 -0.71089657 - 3850 18607.616 317.74889 0 3763.6037 3.475832 - 3900 19719.59 111.5553 0 3763.3313 0.58876668 - 3950 19756.661 104.5522 0 3763.1931 3.7526698 - 4000 17904.708 447.1673 0 3762.854 12.270654 - 4050 19588.087 135.80435 0 3763.2279 0.94578945 - 4100 19065.901 232.38235 0 3763.1048 -2.7495195 - 4150 18775.075 286.2257 0 3763.0915 -3.7039858 - 4200 18800.725 281.46601 0 3763.0817 0.15619543 - 4250 19732.687 108.90618 0 3763.1075 3.0865861 - 4300 18278.151 377.63653 0 3762.4794 1.5768601 - 4350 17915.757 445.4804 0 3763.2133 -3.7040484 - 4400 15987.794 802.41575 0 3763.1183 22.252078 - 4450 19302.37 188.69495 0 3763.2079 0.91081327 - 4500 20039.32 52.304099 0 3763.2893 -2.0828905 - 4550 19535.953 145.4374 0 3763.2064 -3.3804255 - 4600 19700.723 114.79823 0 3763.0803 -1.1761163 - 4650 17804.641 465.85788 0 3763.0136 7.5947192 - 4700 19913.881 75.240289 0 3762.996 -2.1100557 - 4750 19982.484 62.535995 0 3762.996 -4.5821237 - 4800 17400.76 540.21707 0 3762.58 -5.8418778 - 4850 19199.88 206.90989 0 3762.4433 3.4536341 - 4900 19173.92 212.11327 0 3762.8392 5.0387071 - 4950 19236.635 200.57537 0 3762.9152 -1.4932783 - 5000 19077.616 230.04967 0 3762.9415 4.3742655 - 5050 19893.763 78.909747 0 3762.94 -1.5796711 - 5100 18884.746 265.68301 0 3762.8583 2.2767949 - 5150 17417.096 537.54036 0 3762.9286 -2.8632555 - 5200 18247.844 383.60092 0 3762.8312 10.384179 - 5250 19494.107 152.60532 0 3762.6251 -4.7617287 - 5300 18739.781 292.46206 0 3762.7919 23.210048 - 5350 19310.938 186.62363 0 3762.7232 14.895327 - 5400 19540.39 144.14287 0 3762.7336 6.094624 - 5450 20074.459 45.247888 0 3762.7403 -2.0871835 - 5500 19986.377 61.668045 0 3762.849 -2.4551918 - 5550 19038.904 237.07578 0 3762.7987 5.4250813 - 5600 19439.124 163.1438 0 3762.9816 4.1291468 - 5650 19480.321 155.58325 0 3763.0501 -3.5308058 - 5700 19869.291 83.651379 0 3763.1497 -7.8661592 - 5750 19991.447 61.068554 0 3763.1884 -6.8473586 - 5800 19454.072 160.36805 0 3762.9739 1.527662 - 5850 17994.409 430.95597 0 3763.2539 -5.6078082 - 5900 19209.794 205.74997 0 3763.1193 8.4113055 - 5950 19046.427 236.06321 0 3763.1793 10.463356 - 6000 19409.899 168.95271 0 3763.3785 2.542067 - 6050 18068.174 417.35443 0 3763.3125 10.498199 - 6100 19549.253 143.21885 0 3763.4509 2.3075797 - 6150 18464.719 344.0303 0 3763.4228 0.46469762 - 6200 19811.205 94.62725 0 3763.3689 1.2382763 - 6250 18715.36 297.26445 0 3763.0718 -3.4541762 - 6300 17115.664 594.09913 0 3763.6666 4.2065564 - 6350 18155.927 400.71764 0 3762.9264 1.1521258 - 6400 19873.093 83.169067 0 3763.3716 0.16383592 - 6450 19991.88 61.13218 0 3763.3321 -1.3008128 - 6500 19434.416 164.40698 0 3763.3728 -13.593422 - 6550 19855.253 86.645329 0 3763.544 -0.85704037 - 6600 19251.141 198.41152 0 3763.4376 4.3027745 - 6650 19741.815 107.69047 0 3763.582 4.994835 - 6700 19633.466 127.69333 0 3763.5203 6.3677145 - 6750 16231.353 757.83705 0 3763.6431 -1.5978692 - 6800 18863.396 270.1114 0 3763.3329 -11.915909 - 6850 19644.779 125.29421 0 3763.2163 -1.151217 - 6900 18883.642 266.06889 0 3763.0397 -4.3950749 - 6950 19042.364 236.54144 0 3762.9052 5.5718878 - 7000 18351.868 364.38028 0 3762.8743 7.8958273 - 7050 19981.031 62.840667 0 3763.0316 -5.8572298 - 7100 19796.372 97.073665 0 3763.0685 -3.5178361 - 7150 19805.385 95.235221 0 3762.899 -2.5481726 - 7200 18722.055 295.86113 0 3762.9084 13.826356 - 7250 19537.304 144.54234 0 3762.5616 1.2288666 - 7300 18787.328 283.49504 0 3762.6299 9.0044469 - 7350 18886.005 265.52121 0 3762.9295 6.6791881 - 7400 19891.864 79.239278 0 3762.9178 -2.3882842 - 7450 18164.752 399.07065 0 3762.9137 3.9400481 - 7500 18702.612 299.582 0 3763.0286 4.7987316 - 7550 19884.986 80.231665 0 3762.6365 -0.75016515 - 7600 19549.059 142.16243 0 3762.3586 -2.1035756 - 7650 18223.668 387.9047 0 3762.658 -17.064339 - 7700 19428.4 164.79531 0 3762.6473 -2.8342541 - 7750 19239.584 199.93029 0 3762.8163 3.1746033 - 7800 19458.005 159.46176 0 3762.7961 1.714515 - 7850 18320.308 369.77051 0 3762.4202 2.1422976 - 7900 18817.415 278.04812 0 3762.7546 0.94492621 - 7950 19892.761 79.115928 0 3762.9606 1.4948501 - 8000 19592.344 134.7639 0 3762.9758 -1.8520224 - 8050 19316.109 185.70579 0 3762.7631 -4.8061205 - 8100 19867.017 83.850395 0 3762.9277 -3.496391 - 8150 19129.936 220.29802 0 3762.8789 -2.8357376 - 8200 18449.554 346.30415 0 3762.8883 1.4417837 - 8250 18405.197 354.49049 0 3762.8602 6.7020283 - 8300 18310.437 372.25376 0 3763.0755 3.9043508 - 8350 18842.702 273.55075 0 3762.94 -10.987272 - 8400 18574.308 323.33378 0 3763.0204 12.008785 - 8450 15368.628 918.21692 0 3764.2591 34.80292 - 8500 18432.887 349.54013 0 3763.0378 0.00064258465 - 8550 15777.73 841.79263 0 3763.5945 15.473699 - 8600 17205.381 576.4515 0 3762.6331 2.3985544 - 8650 19773.742 101.48276 0 3763.2869 2.3978892 - 8700 19059.824 232.99716 0 3762.5941 5.2611349 - 8750 19006.086 243.41125 0 3763.0568 4.7880403 - 8800 19492.691 153.0188 0 3762.7763 1.9118755 - 8850 19625.883 128.44474 0 3762.8675 3.4157389 - 8900 19916.97 74.635094 0 3762.9629 -10.157254 - 8950 16012.956 798.16801 0 3763.5302 16.904998 - 9000 19364.051 177.00354 0 3762.9389 -13.373346 - 9050 19133.929 219.61882 0 3762.9389 -7.3824392 - 9100 18657.168 307.85939 0 3762.8905 9.3071421 - 9150 17975.904 434.21548 0 3763.0867 6.9609506 - 9200 19075.282 230.41699 0 3762.8767 7.0961232 - 9250 20115.276 37.578674 0 3762.6298 1.8678552 - 9300 18195.486 393.20682 0 3762.7413 13.272552 - 9350 19617.155 129.85893 0 3762.6653 -2.0849447 - 9400 19276.325 193.03425 0 3762.724 -2.8963555 - 9450 18642.803 310.4759 0 3762.8467 3.407984 - 9500 19175.951 211.72785 0 3762.8298 -0.39025564 - 9550 17669.191 490.85942 0 3762.9319 5.3867954 - 9600 18481.199 340.29485 0 3762.7391 8.9004886 - 9650 20091.442 42.504743 0 3763.1422 -1.3206133 - 9700 19651.405 124.04835 0 3763.1975 1.4000525 - 9750 19138.245 219.03637 0 3763.1558 5.8352794 - 9800 19189.146 209.67958 0 3763.2251 6.214691 - 9850 19899.376 78.096337 0 3763.166 -0.75102404 - 9900 19447.247 161.27279 0 3762.6149 -6.4166376 - 9950 19807.083 95.152663 0 3763.1309 -0.88933698 - 10000 18972.157 249.56342 0 3762.9258 1.9189241 -Loop time of 9.05599 on 4 procs for 10000 steps with 81 atoms - -Performance: 9540.646 tau/day, 1104.241 timesteps/s -94.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.009043 | 0.030098 | 0.048276 | 8.1 | 0.33 -Neigh | 0.012702 | 0.02622 | 0.04009 | 6.1 | 0.29 -Comm | 0.99902 | 1.2924 | 1.6008 | 24.3 | 14.27 -Output | 0.0057414 | 0.010684 | 0.024912 | 7.9 | 0.12 -Modify | 7.2674 | 7.5881 | 7.9123 | 10.6 | 83.79 -Other | | 0.1085 | | | 1.20 - -Nlocal: 20.25 ave 37 max 0 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 17.75 ave 33 max 4 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 144.75 ave 356 max 0 min -Histogram: 2 0 0 0 0 0 1 0 0 1 - -Total # of neighbors = 579 -Ave neighs/atom = 7.14815 -Neighbor list builds = 994 -Dangerous builds = 958 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:09 diff --git a/examples/rigid/unconnected-bodies.dat b/examples/rigid/unconnected-bodies.dat new file mode 100644 index 0000000000..d185963c20 --- /dev/null +++ b/examples/rigid/unconnected-bodies.dat @@ -0,0 +1,14 @@ +# Body definition file for POEMS fix +# 9 individual rigid bodies + +# Format +# Body-ID Body-Type Atom-ID1 Atom-ID2 ... +1 1 1 2 3 4 5 6 7 8 9 +2 2 10 11 12 13 14 15 16 17 18 +3 1 19 20 21 22 23 24 25 26 27 +4 2 28 29 30 31 32 33 34 35 36 +5 3 37 38 39 40 41 42 43 44 45 +6 1 46 47 48 49 50 51 52 53 54 +7 2 55 56 57 58 59 60 61 62 63 +8 1 64 65 66 67 68 69 70 71 72 +9 2 73 74 75 76 77 78 79 80 81 diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index 201e40b5b8..d2df9b0159 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -20,57 +19,58 @@ #include "fix_poems.h" -#include -#include - -#include "workspace.h" #include "atom.h" +#include "citeme.h" +#include "comm.h" #include "domain.h" -#include "update.h" -#include "respa.h" -#include "modify.h" +#include "error.h" #include "force.h" #include "group.h" -#include "comm.h" -#include "citeme.h" -#include "memory.h" -#include "error.h" #include "math_eigen.h" +#include "memory.h" +#include "modify.h" +#include "respa.h" +#include "text_file_reader.h" +#include "update.h" +#include "workspace.h" + +#include +#include +#include using namespace LAMMPS_NS; using namespace FixConst; -#define MAXBODY 2 // currently 2 since only linear chains allowed +#define MAXBODY 2 // currently 2 since only linear chains allowed #define DELTA 128 #define TOLERANCE 1.0e-6 #define EPSILON 1.0e-7 static const char cite_fix_poems[] = - "fix poems command:\n\n" - "@Article{Mukherjee08,\n" - " author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},\n" - " title = {Substructured molecular dynamics using multibody dynamics algorithms},\n" - " journal = {Intl.~J.~Non-linear Mechanics},\n" - " year = 2008,\n" - " volume = 43,\n" - " pages = {1045--1055}\n" - "}\n\n"; + "fix poems command:\n\n" + "@Article{Mukherjee08,\n" + " author = {R. M. Mukherjee, P. S. Crozier, S. J. Plimpton, K. S. Anderson},\n" + " title = {Substructured molecular dynamics using multibody dynamics algorithms},\n" + " journal = {Intl.~J.~Non-linear Mechanics},\n" + " year = 2008,\n" + " volume = 43,\n" + " pages = {1045--1055}\n" + "}\n\n"; /* ---------------------------------------------------------------------- define rigid bodies and joints, initiate POEMS ------------------------------------------------------------------------- */ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), step_respa(nullptr), natom2body(nullptr), - atom2body(nullptr), displace(nullptr), nrigid(nullptr), masstotal(nullptr), - xcm(nullptr), vcm(nullptr), fcm(nullptr), inertia(nullptr), ex_space(nullptr), - ey_space(nullptr), ez_space(nullptr), angmom(nullptr), omega(nullptr), - torque(nullptr), sum(nullptr), all(nullptr), jointbody(nullptr), - xjoint(nullptr), freelist(nullptr), poems(nullptr) + Fix(lmp, narg, arg), step_respa(nullptr), natom2body(nullptr), atom2body(nullptr), + displace(nullptr), nrigid(nullptr), masstotal(nullptr), xcm(nullptr), vcm(nullptr), + fcm(nullptr), inertia(nullptr), ex_space(nullptr), ey_space(nullptr), ez_space(nullptr), + angmom(nullptr), omega(nullptr), torque(nullptr), sum(nullptr), all(nullptr), + jointbody(nullptr), xjoint(nullptr), freelist(nullptr), poems(nullptr) { if (lmp->citeme) lmp->citeme->add(cite_fix_poems); - int i,j,ibody; + int i, j, ibody; time_integrate = 1; rigid_flag = 1; @@ -79,8 +79,6 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : thermo_virial = 1; dof_flag = 1; - MPI_Comm_rank(world,&me); - // perform initial allocation of atom-based arrays // register with atom class @@ -109,19 +107,18 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : // set natom2body, atom2body for all atoms and nbody = # of rigid bodies // atoms must also be in fix group to be in a body - if (narg < 4) error->all(FLERR,"Illegal fix poems command"); + if (narg < 4) error->all(FLERR, "Illegal fix poems command"); // group = arg has list of groups - if (strcmp(arg[3],"group") == 0) { - nbody = narg-4; - if (nbody <= 0) error->all(FLERR,"Illegal fix poems command"); + if (strcmp(arg[3], "group") == 0) { + nbody = narg - 4; + if (nbody <= 0) error->all(FLERR, "Illegal fix poems command"); int *igroups = new int[nbody]; for (ibody = 0; ibody < nbody; ibody++) { - igroups[ibody] = group->find(arg[ibody+4]); - if (igroups[ibody] == -1) - error->all(FLERR,"Could not find fix poems group ID"); + igroups[ibody] = group->find(arg[ibody + 4]); + if (igroups[ibody] == -1) error->all(FLERR, "Could not find fix poems group ID"); } int *mask = atom->mask; @@ -135,13 +132,13 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : } } - delete [] igroups; + delete[] igroups; - // file = read bodies from file - // file read doesn't pay attention to fix group, - // so after read, reset natom2body = 0 if atom is not in fix group + // file = read bodies from file + // file read doesn't pay attention to fix group, + // so after read, reset natom2body = 0 if atom is not in fix group - } else if (strcmp(arg[3],"file") == 0) { + } else if (strcmp(arg[3], "file") == 0) { readfile(arg[4]); @@ -149,17 +146,16 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : for (int i = 0; i < nlocal; i++) if (!(mask[i] & groupbit)) natom2body[i] = 0; - // each molecule in fix group is a rigid body - // maxmol = largest molecule ID - // ncount = # of atoms in each molecule (have to sum across procs) - // nbody = # of non-zero ncount values - // use nall as incremented ptr to set atom2body[] values for each atom + // each molecule in fix group is a rigid body + // maxmol = largest molecule ID + // ncount = # of atoms in each molecule (have to sum across procs) + // nbody = # of non-zero ncount values + // use nall as incremented ptr to set atom2body[] values for each atom - } else if (strcmp(arg[3],"molecule") == 0) { - if (narg != 4) error->all(FLERR,"Illegal fix poems command"); + } else if (strcmp(arg[3], "molecule") == 0) { + if (narg != 4) error->all(FLERR, "Illegal fix poems command"); if (atom->molecular == Atom::ATOMIC) - error->all(FLERR, - "Must use a molecular atom style with fix poems molecule"); + error->all(FLERR, "Must use a molecular atom style with fix poems molecule"); int *mask = atom->mask; tagint *molecule = atom->molecule; @@ -167,29 +163,30 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : tagint maxmol_tag = -1; for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag,molecule[i]); + if (mask[i] & groupbit) maxmol_tag = MAX(maxmol_tag, molecule[i]); tagint itmp; - MPI_Allreduce(&maxmol_tag,&itmp,1,MPI_LMP_TAGINT,MPI_MAX,world); - if (itmp+1 > MAXSMALLINT) - error->all(FLERR,"Too many molecules for fix poems"); + MPI_Allreduce(&maxmol_tag, &itmp, 1, MPI_LMP_TAGINT, MPI_MAX, world); + if (itmp + 1 > MAXSMALLINT) error->all(FLERR, "Too many molecules for fix poems"); int maxmol = (int) itmp; int *ncount; - memory->create(ncount,maxmol+1,"rigid:ncount"); + memory->create(ncount, maxmol + 1, "rigid:ncount"); for (i = 0; i <= maxmol; i++) ncount[i] = 0; for (i = 0; i < nlocal; i++) if (mask[i] & groupbit) ncount[molecule[i]]++; int *nall; - memory->create(nall,maxmol+1,"rigid:ncount"); - MPI_Allreduce(ncount,nall,maxmol+1,MPI_INT,MPI_SUM,world); + memory->create(nall, maxmol + 1, "rigid:ncount"); + MPI_Allreduce(ncount, nall, maxmol + 1, MPI_INT, MPI_SUM, world); nbody = 0; for (i = 0; i <= maxmol; i++) - if (nall[i]) nall[i] = nbody++; - else nall[i] = -1; + if (nall[i]) + nall[i] = nbody++; + else + nall[i] = -1; for (i = 0; i < nlocal; i++) { natom2body[i] = 0; @@ -202,38 +199,38 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : memory->destroy(ncount); memory->destroy(nall); - } else error->all(FLERR,"Illegal fix poems command"); + } else + error->all(FLERR, "Illegal fix poems command"); // error if no bodies // error if any atom in too many bodies - if (nbody == 0) error->all(FLERR,"No rigid bodies defined"); + if (nbody == 0) error->all(FLERR, "No rigid bodies defined"); int flag = 0; for (int i = 0; i < nlocal; i++) if (natom2body[i] > MAXBODY) flag = 1; int flagall; - MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world); - if (flagall) - error->all(FLERR,"Atom in too many rigid bodies - boost MAXBODY"); + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); + if (flagall) error->all(FLERR, "Atom in too many rigid bodies - boost MAXBODY"); // create all nbody-length arrays nrigid = new int[nbody]; masstotal = new double[nbody]; - memory->create(xcm,nbody,3,"poems:xcm"); - memory->create(vcm,nbody,3,"poems:vcm"); - memory->create(fcm,nbody,3,"poems:fcm"); - memory->create(inertia,nbody,3,"poems:inertia"); - memory->create(ex_space,nbody,3,"poems:ex_space"); - memory->create(ey_space,nbody,3,"poems:ey_space"); - memory->create(ez_space,nbody,3,"poems:ez_space"); - memory->create(angmom,nbody,3,"poems:angmom"); - memory->create(omega,nbody,3,"poems:omega"); - memory->create(torque,nbody,3,"poems:torque"); + memory->create(xcm, nbody, 3, "poems:xcm"); + memory->create(vcm, nbody, 3, "poems:vcm"); + memory->create(fcm, nbody, 3, "poems:fcm"); + memory->create(inertia, nbody, 3, "poems:inertia"); + memory->create(ex_space, nbody, 3, "poems:ex_space"); + memory->create(ey_space, nbody, 3, "poems:ey_space"); + memory->create(ez_space, nbody, 3, "poems:ez_space"); + memory->create(angmom, nbody, 3, "poems:angmom"); + memory->create(omega, nbody, 3, "poems:omega"); + memory->create(torque, nbody, 3, "poems:torque"); - memory->create(sum,nbody,6,"poems:sum"); - memory->create(all,nbody,6,"poems:all"); + memory->create(sum, nbody, 6, "poems:sum"); + memory->create(all, nbody, 6, "poems:all"); // nrigid[n] = # of atoms in Nth rigid body // double count joint atoms as being in multiple bodies @@ -243,14 +240,13 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : for (ibody = 0; ibody < nbody; ibody++) ncount[ibody] = 0; for (i = 0; i < nlocal; i++) - for (j = 0; j < natom2body[i]; j++) - ncount[atom2body[i][j]]++; + for (j = 0; j < natom2body[i]; j++) ncount[atom2body[i][j]]++; - MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world); - delete [] ncount; + MPI_Allreduce(ncount, nrigid, nbody, MPI_INT, MPI_SUM, world); + delete[] ncount; for (ibody = 0; ibody < nbody; ibody++) - if (nrigid[ibody] <= 1) error->all(FLERR,"One or zero atoms in rigid body"); + if (nrigid[ibody] <= 1) error->all(FLERR, "One or zero atoms in rigid body"); // build list of joint connections and check for cycles and trees @@ -277,9 +273,9 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) : for (ibody = 0; ibody < nbody; ibody++) nsum += nrigid[ibody]; nsum -= njoint; - if (me == 0) - utils::logmesg(lmp,"{} clusters, {} bodies, {} joints, {} atoms\n", - ncluster,nbody,njoint,nsum); + if (comm->me == 0) + utils::logmesg(lmp, "{} clusters, {} bodies, {} joints, {} atoms\n", ncluster, nbody, njoint, + nsum); } /* ---------------------------------------------------------------------- @@ -291,7 +287,7 @@ FixPOEMS::~FixPOEMS() // if atom class still exists: // unregister this fix so atom class doesn't invoke it any more - if (atom) atom->delete_callback(id,Atom::GROW); + if (atom) atom->delete_callback(id, Atom::GROW); // delete locally stored arrays @@ -301,8 +297,8 @@ FixPOEMS::~FixPOEMS() // delete nbody-length arrays - delete [] nrigid; - delete [] masstotal; + delete[] nrigid; + delete[] masstotal; memory->destroy(xcm); memory->destroy(vcm); memory->destroy(fcm); @@ -321,7 +317,7 @@ FixPOEMS::~FixPOEMS() memory->destroy(jointbody); memory->destroy(xjoint); - delete [] freelist; + delete[] freelist; // delete POEMS object @@ -347,39 +343,29 @@ int FixPOEMS::setmask() void FixPOEMS::init() { - int i,ibody; + int i, ibody; // warn if more than one POEMS fix // if earlyflag, warn if any post-force fixes come after POEMS fix - int count = 0; - for (int i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"poems") == 0) count++; - if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems"); + if (modify->get_fix_by_style("poems").size() > 1) + if (comm->me == 0) error->warning(FLERR, "More than one fix poems"); if (earlyflag) { - int pflag = 0; - for (i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1; - if (pflag && (modify->fmask[i] & POST_FORCE) && - !modify->fix[i]->rigid_flag) { - if (comm->me == 0) - error->warning(FLERR,std::string("Fix ") + modify->fix[i]->id - + std::string(" alters forces after fix poems")); - } + bool pflag = false; + for (auto ifix : modify->get_fix_list()) { + if (utils::strmatch(ifix->style, "^poems")) pflag = true; + if (pflag && (ifix->setmask() & POST_FORCE) && !ifix->rigid_flag) + if (comm->me == 0) error->warning(FLERR, "Fix {} alters forces after fix poems", ifix->id); } } // error if npt,nph fix comes before rigid fix - - for (i = 0; i < modify->nfix; i++) { - if (strcmp(modify->fix[i]->style,"npt") == 0) break; - if (strcmp(modify->fix[i]->style,"nph") == 0) break; - } - if (i < modify->nfix) { - for (int j = i; j < modify->nfix; j++) - if (strcmp(modify->fix[j]->style,"poems") == 0) - error->all(FLERR,"POEMS fix must come before NPT/NPH fix"); + bool pflag = false; + for (auto ifix : modify->get_fix_list()) { + if (!pflag && utils::strmatch(ifix->style, "np[th]")) + error->all(FLERR, "POEMS fix must come before NPT/NPH fix"); + if (utils::strmatch(ifix->style, "^poems")) pflag = true; } // timestep info @@ -390,7 +376,7 @@ void FixPOEMS::init() // rRESPA info - if (utils::strmatch(update->integrate_style,"^respa")) { + if (utils::strmatch(update->integrate_style, "^respa")) { step_respa = ((Respa *) update->integrate)->step; nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -409,7 +395,7 @@ void FixPOEMS::init() double yprd = domain->yprd; double zprd = domain->zprd; - int xbox,ybox,zbox; + int xbox, ybox, zbox; double massone; for (ibody = 0; ibody < nbody; ibody++) @@ -422,23 +408,22 @@ void FixPOEMS::init() ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; massone = mass[type[i]]; - sum[ibody][0] += (x[i][0] + xbox*xprd) * massone; - sum[ibody][1] += (x[i][1] + ybox*yprd) * massone; - sum[ibody][2] += (x[i][2] + zbox*zprd) * massone; + sum[ibody][0] += (x[i][0] + xbox * xprd) * massone; + sum[ibody][1] += (x[i][1] + ybox * yprd) * massone; + sum[ibody][2] += (x[i][2] + zbox * zprd) * massone; sum[ibody][3] += massone; - sum[ibody][4] += massone * - (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]); + sum[ibody][4] += massone * (v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2]); } } - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sum[0], all[0], 6 * nbody, MPI_DOUBLE, MPI_SUM, world); total_ke = 0.0; for (ibody = 0; ibody < nbody; ibody++) { masstotal[ibody] = all[ibody][3]; - xcm[ibody][0] = all[ibody][0]/masstotal[ibody]; - xcm[ibody][1] = all[ibody][1]/masstotal[ibody]; - xcm[ibody][2] = all[ibody][2]/masstotal[ibody]; + xcm[ibody][0] = all[ibody][0] / masstotal[ibody]; + xcm[ibody][1] = all[ibody][1] / masstotal[ibody]; + xcm[ibody][2] = all[ibody][2] / masstotal[ibody]; total_ke += 0.5 * all[ibody][4]; } @@ -446,7 +431,7 @@ void FixPOEMS::init() // only count joint atoms in 1st body // dx,dy,dz = coords relative to center-of-mass - double dx,dy,dz; + double dx, dy, dz; for (ibody = 0; ibody < nbody; ibody++) for (i = 0; i < 6; i++) sum[ibody][i] = 0.0; @@ -458,31 +443,31 @@ void FixPOEMS::init() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - xcm[ibody][0]; - dy = x[i][1] + ybox*yprd - xcm[ibody][1]; - dz = x[i][2] + zbox*zprd - xcm[ibody][2]; + dx = x[i][0] + xbox * xprd - xcm[ibody][0]; + dy = x[i][1] + ybox * yprd - xcm[ibody][1]; + dz = x[i][2] + zbox * zprd - xcm[ibody][2]; massone = mass[type[i]]; - sum[ibody][0] += massone * (dy*dy + dz*dz); - sum[ibody][1] += massone * (dx*dx + dz*dz); - sum[ibody][2] += massone * (dx*dx + dy*dy); - sum[ibody][3] -= massone * dx*dy; - sum[ibody][4] -= massone * dy*dz; - sum[ibody][5] -= massone * dx*dz; + sum[ibody][0] += massone * (dy * dy + dz * dz); + sum[ibody][1] += massone * (dx * dx + dz * dz); + sum[ibody][2] += massone * (dx * dx + dy * dy); + sum[ibody][3] -= massone * dx * dy; + sum[ibody][4] -= massone * dy * dz; + sum[ibody][5] -= massone * dx * dz; } } - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sum[0], all[0], 6 * nbody, MPI_DOUBLE, MPI_SUM, world); // inertia = 3 eigenvalues = principal moments of inertia // ex_space,ey_space,ez_space = 3 eigenvectors = principal axes of rigid body - double **tensor,**evectors; - memory->create(tensor,3,3,"fix_rigid:tensor"); - memory->create(evectors,3,3,"fix_rigid:evectors"); + double **tensor, **evectors; + memory->create(tensor, 3, 3, "fix_rigid:tensor"); + memory->create(evectors, 3, 3, "fix_rigid:evectors"); int ierror; - double ez0,ez1,ez2; + double ez0, ez1, ez2; for (ibody = 0; ibody < nbody; ibody++) { tensor[0][0] = all[ibody][0]; @@ -492,8 +477,8 @@ void FixPOEMS::init() tensor[1][2] = tensor[2][1] = all[ibody][4]; tensor[0][2] = tensor[2][0] = all[ibody][5]; - ierror = MathEigen::jacobi3(tensor,inertia[ibody],evectors); - if (ierror) error->all(FLERR,"Insufficient Jacobi rotations for POEMS body"); + ierror = MathEigen::jacobi3(tensor, inertia[ibody], evectors); + if (ierror) error->all(FLERR, "Insufficient Jacobi rotations for POEMS body"); ex_space[ibody][0] = evectors[0][0]; ex_space[ibody][1] = evectors[1][0]; @@ -511,26 +496,21 @@ void FixPOEMS::init() // this is b/c POEMS cannot yet handle degenerate bodies double max; - max = MAX(inertia[ibody][0],inertia[ibody][1]); - max = MAX(max,inertia[ibody][2]); + max = MAX(inertia[ibody][0], inertia[ibody][1]); + max = MAX(max, inertia[ibody][2]); - if (inertia[ibody][0] < EPSILON*max || - inertia[ibody][1] < EPSILON*max || - inertia[ibody][2] < EPSILON*max) - error->all(FLERR,"Rigid body has degenerate moment of inertia"); + if (inertia[ibody][0] < EPSILON * max || inertia[ibody][1] < EPSILON * max || + inertia[ibody][2] < EPSILON * max) + error->all(FLERR, "Rigid body has degenerate moment of inertia"); // enforce 3 evectors as a right-handed coordinate system // flip 3rd evector if needed - ez0 = ex_space[ibody][1]*ey_space[ibody][2] - - ex_space[ibody][2]*ey_space[ibody][1]; - ez1 = ex_space[ibody][2]*ey_space[ibody][0] - - ex_space[ibody][0]*ey_space[ibody][2]; - ez2 = ex_space[ibody][0]*ey_space[ibody][1] - - ex_space[ibody][1]*ey_space[ibody][0]; + ez0 = ex_space[ibody][1] * ey_space[ibody][2] - ex_space[ibody][2] * ey_space[ibody][1]; + ez1 = ex_space[ibody][2] * ey_space[ibody][0] - ex_space[ibody][0] * ey_space[ibody][2]; + ez2 = ex_space[ibody][0] * ey_space[ibody][1] - ex_space[ibody][1] * ey_space[ibody][0]; - if (ez0*ez_space[ibody][0] + ez1*ez_space[ibody][1] + - ez2*ez_space[ibody][2] < 0.0) { + if (ez0 * ez_space[ibody][0] + ez1 * ez_space[ibody][1] + ez2 * ez_space[ibody][2] < 0.0) { ez_space[ibody][0] = -ez_space[ibody][0]; ez_space[ibody][1] = -ez_space[ibody][1]; ez_space[ibody][2] = -ez_space[ibody][2]; @@ -553,17 +533,15 @@ void FixPOEMS::init() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - xcm[ibody][0]; - dy = x[i][1] + ybox*yprd - xcm[ibody][1]; - dz = x[i][2] + zbox*zprd - xcm[ibody][2]; + dx = x[i][0] + xbox * xprd - xcm[ibody][0]; + dy = x[i][1] + ybox * yprd - xcm[ibody][1]; + dz = x[i][2] + zbox * zprd - xcm[ibody][2]; - displace[i][0] = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] + - dz*ex_space[ibody][2]; - displace[i][1] = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] + - dz*ey_space[ibody][2]; - displace[i][2] = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] + - dz*ez_space[ibody][2]; - } else displace[i][0] = displace[i][1] = displace[i][2] = 0.0; + displace[i][0] = dx * ex_space[ibody][0] + dy * ex_space[ibody][1] + dz * ex_space[ibody][2]; + displace[i][1] = dx * ey_space[ibody][0] + dy * ey_space[ibody][1] + dz * ey_space[ibody][2]; + displace[i][2] = dx * ez_space[ibody][0] + dy * ez_space[ibody][1] + dz * ez_space[ibody][2]; + } else + displace[i][0] = displace[i][1] = displace[i][2] = 0.0; } // test for valid principal moments & axes @@ -577,7 +555,7 @@ void FixPOEMS::init() for (ibody = 0; ibody < nbody; ibody++) for (i = 0; i < 6; i++) sum[ibody][i] = 0.0; - double ddx,ddy,ddz; + double ddx, ddy, ddz; for (i = 0; i < nlocal; i++) { if (natom2body[i]) { @@ -586,38 +564,34 @@ void FixPOEMS::init() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - xcm[ibody][0]; - dy = x[i][1] + ybox*yprd - xcm[ibody][1]; - dz = x[i][2] + zbox*zprd - xcm[ibody][2]; + dx = x[i][0] + xbox * xprd - xcm[ibody][0]; + dy = x[i][1] + ybox * yprd - xcm[ibody][1]; + dz = x[i][2] + zbox * zprd - xcm[ibody][2]; massone = mass[type[i]]; - ddx = dx*ex_space[ibody][0] + dy*ex_space[ibody][1] + - dz*ex_space[ibody][2]; - ddy = dx*ey_space[ibody][0] + dy*ey_space[ibody][1] + - dz*ey_space[ibody][2]; - ddz = dx*ez_space[ibody][0] + dy*ez_space[ibody][1] + - dz*ez_space[ibody][2]; + ddx = dx * ex_space[ibody][0] + dy * ex_space[ibody][1] + dz * ex_space[ibody][2]; + ddy = dx * ey_space[ibody][0] + dy * ey_space[ibody][1] + dz * ey_space[ibody][2]; + ddz = dx * ez_space[ibody][0] + dy * ez_space[ibody][1] + dz * ez_space[ibody][2]; - sum[ibody][0] += massone * (ddy*ddy + ddz*ddz); - sum[ibody][1] += massone * (ddx*ddx + ddz*ddz); - sum[ibody][2] += massone * (ddx*ddx + ddy*ddy); - sum[ibody][3] -= massone * ddx*ddy; - sum[ibody][4] -= massone * ddy*ddz; - sum[ibody][5] -= massone * ddx*ddz; + sum[ibody][0] += massone * (ddy * ddy + ddz * ddz); + sum[ibody][1] += massone * (ddx * ddx + ddz * ddz); + sum[ibody][2] += massone * (ddx * ddx + ddy * ddy); + sum[ibody][3] -= massone * ddx * ddy; + sum[ibody][4] -= massone * ddy * ddz; + sum[ibody][5] -= massone * ddx * ddz; } } - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sum[0], all[0], 6 * nbody, MPI_DOUBLE, MPI_SUM, world); for (ibody = 0; ibody < nbody; ibody++) { - if (fabs(all[ibody][0]-inertia[ibody][0]) > TOLERANCE || - fabs(all[ibody][1]-inertia[ibody][1]) > TOLERANCE || - fabs(all[ibody][2]-inertia[ibody][2]) > TOLERANCE) - error->all(FLERR,"Bad principal moments"); - if (fabs(all[ibody][3]) > TOLERANCE || - fabs(all[ibody][4]) > TOLERANCE || + if (fabs(all[ibody][0] - inertia[ibody][0]) > TOLERANCE || + fabs(all[ibody][1] - inertia[ibody][1]) > TOLERANCE || + fabs(all[ibody][2] - inertia[ibody][2]) > TOLERANCE) + error->all(FLERR, "Bad principal moments"); + if (fabs(all[ibody][3]) > TOLERANCE || fabs(all[ibody][4]) > TOLERANCE || fabs(all[ibody][5]) > TOLERANCE) - error->all(FLERR,"Bad principal moments"); + error->all(FLERR, "Bad principal moments"); } } @@ -628,7 +602,7 @@ void FixPOEMS::init() void FixPOEMS::setup(int vflag) { - int i,n,ibody; + int i, n, ibody; // vcm = velocity of center-of-mass of each rigid body // angmom = angular momentum of each rigid body @@ -645,8 +619,8 @@ void FixPOEMS::setup(int vflag) double yprd = domain->yprd; double zprd = domain->zprd; - int xbox,ybox,zbox; - double massone,dx,dy,dz; + int xbox, ybox, zbox; + double massone, dx, dy, dz; for (ibody = 0; ibody < nbody; ibody++) for (i = 0; i < 6; i++) sum[ibody][i] = 0.0; @@ -659,25 +633,25 @@ void FixPOEMS::setup(int vflag) xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - xcm[ibody][0]; - dy = x[i][1] + ybox*yprd - xcm[ibody][1]; - dz = x[i][2] + zbox*zprd - xcm[ibody][2]; + dx = x[i][0] + xbox * xprd - xcm[ibody][0]; + dy = x[i][1] + ybox * yprd - xcm[ibody][1]; + dz = x[i][2] + zbox * zprd - xcm[ibody][2]; sum[ibody][0] += v[i][0] * massone; sum[ibody][1] += v[i][1] * massone; sum[ibody][2] += v[i][2] * massone; - sum[ibody][3] += dy * massone*v[i][2] - dz * massone*v[i][1]; - sum[ibody][4] += dz * massone*v[i][0] - dx * massone*v[i][2]; - sum[ibody][5] += dx * massone*v[i][1] - dy * massone*v[i][0]; + sum[ibody][3] += dy * massone * v[i][2] - dz * massone * v[i][1]; + sum[ibody][4] += dz * massone * v[i][0] - dx * massone * v[i][2]; + sum[ibody][5] += dx * massone * v[i][1] - dy * massone * v[i][0]; } } - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sum[0], all[0], 6 * nbody, MPI_DOUBLE, MPI_SUM, world); for (ibody = 0; ibody < nbody; ibody++) { - vcm[ibody][0] = all[ibody][0]/masstotal[ibody]; - vcm[ibody][1] = all[ibody][1]/masstotal[ibody]; - vcm[ibody][2] = all[ibody][2]/masstotal[ibody]; + vcm[ibody][0] = all[ibody][0] / masstotal[ibody]; + vcm[ibody][1] = all[ibody][1] / masstotal[ibody]; + vcm[ibody][2] = all[ibody][2] / masstotal[ibody]; angmom[ibody][0] = all[ibody][3]; angmom[ibody][1] = all[ibody][4]; angmom[ibody][2] = all[ibody][5]; @@ -690,8 +664,8 @@ void FixPOEMS::setup(int vflag) // set velocities from angmom & omega for (ibody = 0; ibody < nbody; ibody++) - omega_from_mq(angmom[ibody],ex_space[ibody],ey_space[ibody], - ez_space[ibody],inertia[ibody],omega[ibody]); + omega_from_mq(angmom[ibody], ex_space[ibody], ey_space[ibody], ez_space[ibody], inertia[ibody], + omega[ibody]); set_v(); // guestimate virial as 2x the set_v contribution @@ -701,8 +675,7 @@ void FixPOEMS::setup(int vflag) for (n = 0; n < 6; n++) virial[n] *= 2.0; if (vflag_atom) { for (i = 0; i < nlocal; i++) - for (n = 0; n < 6; n++) - vatom[i][n] *= 2.0; + for (n = 0; n < 6; n++) vatom[i][n] *= 2.0; } } @@ -713,10 +686,9 @@ void FixPOEMS::setup(int vflag) // setup for POEMS - poems->MakeSystem(nbody,masstotal,inertia,xcm,vcm,omega, - ex_space,ey_space,ez_space, - njoint,jointbody,xjoint,nfree,freelist, - dthalf,dtv,force->ftm2v,total_ke); + poems->MakeSystem(nbody, masstotal, inertia, xcm, vcm, omega, ex_space, ey_space, ez_space, + njoint, jointbody, xjoint, nfree, freelist, dthalf, dtv, force->ftm2v, + total_ke); } /* ---------------------------------------------------------------------- @@ -728,7 +700,7 @@ void FixPOEMS::initial_integrate(int vflag) { // perform POEMS integration - poems->LobattoOne(xcm,vcm,omega,torque,fcm,ex_space,ey_space,ez_space); + poems->LobattoOne(xcm, vcm, omega, torque, fcm, ex_space, ey_space, ez_space); // virial setup before call to set_xv @@ -753,9 +725,9 @@ void FixPOEMS::post_force(int /* vflag */) void FixPOEMS::compute_forces_and_torques() { - int i,ibody; - int xbox,ybox,zbox; - double dx,dy,dz; + int i, ibody; + int xbox, ybox, zbox; + double dx, dy, dz; imageint *image = atom->image; double **x = atom->x; @@ -780,17 +752,17 @@ void FixPOEMS::compute_forces_and_torques() xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - dx = x[i][0] + xbox*xprd - xcm[ibody][0]; - dy = x[i][1] + ybox*yprd - xcm[ibody][1]; - dz = x[i][2] + zbox*zprd - xcm[ibody][2]; + dx = x[i][0] + xbox * xprd - xcm[ibody][0]; + dy = x[i][1] + ybox * yprd - xcm[ibody][1]; + dz = x[i][2] + zbox * zprd - xcm[ibody][2]; - sum[ibody][3] += dy*f[i][2] - dz*f[i][1]; - sum[ibody][4] += dz*f[i][0] - dx*f[i][2]; - sum[ibody][5] += dx*f[i][1] - dy*f[i][0]; + sum[ibody][3] += dy * f[i][2] - dz * f[i][1]; + sum[ibody][4] += dz * f[i][0] - dx * f[i][2]; + sum[ibody][5] += dx * f[i][1] - dy * f[i][0]; } } - MPI_Allreduce(sum[0],all[0],6*nbody,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sum[0], all[0], 6 * nbody, MPI_DOUBLE, MPI_SUM, world); for (ibody = 0; ibody < nbody; ibody++) { fcm[ibody][0] = all[ibody][0]; @@ -823,7 +795,7 @@ void FixPOEMS::final_integrate() // perform POEMS integration - poems->LobattoTwo(vcm,omega,torque,fcm); + poems->LobattoTwo(vcm, omega, torque, fcm); // set velocities of atoms in rigid bodies // virial is already setup from initial_integrate @@ -839,15 +811,17 @@ void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) dtf = 0.5 * step_respa[ilevel] * force->ftm2v; dthalf = 0.5 * step_respa[ilevel]; - if (ilevel == 0) initial_integrate(vflag); - else final_integrate(); + if (ilevel == 0) + initial_integrate(vflag); + else + final_integrate(); } /* ---------------------------------------------------------------------- */ void FixPOEMS::post_force_respa(int vflag, int ilevel, int /* iloop */) { - if (ilevel == nlevels_respa-1) post_force(vflag); + if (ilevel == nlevels_respa - 1) post_force(vflag); } /* ---------------------------------------------------------------------- */ @@ -896,27 +870,27 @@ int FixPOEMS::dof(int igroup) if (natom2body[i]) ncount[atom2body[i][0]]++; int *nall = new int[nbody]; - MPI_Allreduce(ncount,nall,nbody,MPI_INT,MPI_SUM,world); + MPI_Allreduce(ncount, nall, nbody, MPI_INT, MPI_SUM, world); // remove 3N - 6 dof for each rigid body if at least 2 atoms are in igroup int n = 0; for (int ibody = 0; ibody < nbody; ibody++) - if (nall[ibody] > 2) n += 3*nall[ibody] - 6; + if (nall[ibody] > 2) n += 3 * nall[ibody] - 6; // subtract 3 additional dof for each joint if atom is also in igroup int m = 0; for (int i = 0; i < nlocal; i++) - if (natom2body[i] > 1 && (mask[i] & groupbit)) m += 3*(natom2body[i]-1); + if (natom2body[i] > 1 && (mask[i] & groupbit)) m += 3 * (natom2body[i] - 1); int mall; - MPI_Allreduce(&m,&mall,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&m, &mall, 1, MPI_INT, MPI_SUM, world); n += mall; // delete local memory - delete [] ncount; - delete [] nall; + delete[] ncount; + delete[] nall; return n; } @@ -936,72 +910,55 @@ void FixPOEMS::deform(int /* flag */) {} /* ---------------------------------------------------------------------- */ -void FixPOEMS::readfile(char *file) +void FixPOEMS::readfile(const char *file) { - FILE *fp; - if (me == 0) { - fp = fopen(file,"r"); - if (fp == nullptr) - error->one(FLERR,"Cannot open fix poems file {}: {}", - file, utils::getsyserror()); + // read and parse file with bodies on rank 0 and then broadcast and process data + std::vector> bodies; + int maxbody = 0; + + if (comm->me == 0) { + try { + TextFileReader reader(file, "POEMS rigid bodies"); + while (true) { + std::vector onebody; + auto values = reader.next_values(0); + values.skip(2); // ignore body id and body type + while (values.has_next()) onebody.push_back(values.next_bigint()); + maxbody = MAX(maxbody, (int) onebody.size()); + bodies.push_back(onebody); + } + } catch (EOFException &) { + // reached end of file + printf("reached EOF\n"); + } catch (std::exception &e) { + error->one(FLERR, "Error reading file with POEMS body definitions: {}", e.what()); + } } - nbody = 0; - char *line = nullptr; - int maxline = 0; - char *ptr; - int nlocal = atom->nlocal; - int i,id,nlen; + nbody = bodies.size(); + MPI_Bcast(&nbody, 1, MPI_INT, 0, world); + MPI_Bcast(&maxbody, 1, MPI_INT, 0, world); + bigint *buf = new bigint[maxbody + 1]; + const int nlocal = atom->nlocal; - while (true) { - if (me == 0) nlen = readline(fp,&line,&maxline); - MPI_Bcast(&nlen,1,MPI_INT,0,world); - if (nlen == 0) break; - MPI_Bcast(line,nlen,MPI_CHAR,0,world); - - ptr = strtok(line," ,\t\n\0"); - if (ptr == nullptr || ptr[0] == '#') continue; - ptr = strtok(nullptr," ,\t\n\0"); - - while ((ptr = strtok(nullptr," ,\t\n\0"))) { - id = atoi(ptr); - i = atom->map(id); - if (i < 0 || i >= nlocal) continue; - if (natom2body[i] < MAXBODY) atom2body[i][natom2body[i]] = nbody; - natom2body[i]++; + for (int i = 0; i < nbody; ++i) { + if (comm->me == 0) { + buf[0] = bodies[i].size(); + memcpy(buf + 1, bodies[i].data(), bodies[i].size() * sizeof(bigint)); + } + MPI_Bcast(buf, maxbody + 1, MPI_LMP_BIGINT, 0, world); + + // convert global atom ids to local atom indices and fill data structures + for (int j = 1; j <= buf[0]; ++j) { + int k = atom->map(buf[j]); + if (k < 0 || k >= nlocal) continue; + if (natom2body[k] < MAXBODY) atom2body[k][natom2body[k]] = i; + natom2body[k]++; } - nbody++; } - memory->destroy(line); - if (me == 0) fclose(fp); -} - -/* ---------------------------------------------------------------------- */ - -int FixPOEMS::readline(FILE *fp, char **pline, int *pmaxline) -{ - int n = 0; - char *line = *pline; - int maxline = *pmaxline; - - while (true) { - if (n+1 >= maxline) { - maxline += DELTA; - memory->grow(line,maxline,"fix_poems:line"); - } - if (fgets(&line[n],maxline-n,fp) == nullptr) { - n = 0; - break; - } - n = strlen(line); - if (n < maxline-1 || line[n-1] == '\n') break; - } - - *pmaxline = maxline; - *pline = line; - return n; + delete[] buf; } /* ---------------------------------------------------------------------- @@ -1010,7 +967,7 @@ int FixPOEMS::readline(FILE *fp, char **pline, int *pmaxline) void FixPOEMS::jointbuild() { - int i,j; + int i, j; // convert atom2body into list of joint atoms on this proc // mjoint = # of joint atoms in this proc @@ -1023,11 +980,11 @@ void FixPOEMS::jointbuild() int mjoint = 0; for (i = 0; i < nlocal; i++) { if (natom2body[i] <= 1) continue; - mjoint += natom2body[i]-1; + mjoint += natom2body[i] - 1; } tagint **mylist = nullptr; - if (mjoint) memory->create(mylist,mjoint,3,"poems:mylist"); + if (mjoint) memory->create(mylist, mjoint, 3, "poems:mylist"); mjoint = 0; for (i = 0; i < nlocal; i++) { @@ -1042,50 +999,48 @@ void FixPOEMS::jointbuild() // jlist = mylist concatenated across all procs via MPI_Allgatherv - MPI_Allreduce(&mjoint,&njoint,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&mjoint, &njoint, 1, MPI_INT, MPI_SUM, world); tagint **jlist = nullptr; - if (njoint) memory->create(jlist,njoint,3,"poems:jlist"); + if (njoint) memory->create(jlist, njoint, 3, "poems:jlist"); int nprocs; - MPI_Comm_size(world,&nprocs); + MPI_Comm_size(world, &nprocs); int *recvcounts = new int[nprocs]; - int tmp = 3*mjoint; - MPI_Allgather(&tmp,1,MPI_INT,recvcounts,1,MPI_INT,world); + int tmp = 3 * mjoint; + MPI_Allgather(&tmp, 1, MPI_INT, recvcounts, 1, MPI_INT, world); int *displs = new int[nprocs]; displs[0] = 0; - for (i = 1; i < nprocs; i++) displs[i] = displs[i-1] + recvcounts[i-1]; + for (i = 1; i < nprocs; i++) displs[i] = displs[i - 1] + recvcounts[i - 1]; // allgather the local joint lists // 2 versions in case mjoint is 0 on this proc if (njoint) { if (mjoint) - MPI_Allgatherv(mylist[0],3*mjoint,MPI_LMP_TAGINT,jlist[0], - recvcounts,displs,MPI_LMP_TAGINT,world); + MPI_Allgatherv(mylist[0], 3 * mjoint, MPI_LMP_TAGINT, jlist[0], recvcounts, displs, + MPI_LMP_TAGINT, world); else - MPI_Allgatherv(nullptr,3*mjoint,MPI_LMP_TAGINT,jlist[0], - recvcounts,displs,MPI_LMP_TAGINT,world); + MPI_Allgatherv(nullptr, 3 * mjoint, MPI_LMP_TAGINT, jlist[0], recvcounts, displs, + MPI_LMP_TAGINT, world); } - delete [] recvcounts; - delete [] displs; + delete[] recvcounts; + delete[] displs; // warning if no joints - if (njoint == 0 && me == 0) - error->warning(FLERR, - "No joints between rigid bodies, use fix rigid instead"); + if (njoint == 0 && comm->me == 0) + error->warning(FLERR, "No joints between rigid bodies, use fix rigid instead"); // sort joint list in ascending order by body indices // check for loops in joint connections between rigid bodies // check for trees = same body in more than 2 joints - sortlist(njoint,jlist); + sortlist(njoint, jlist); - if (loopcheck(nbody,njoint,jlist)) - error->all(FLERR,"Cyclic loop in joint connections"); + if (loopcheck(nbody, njoint, jlist)) error->all(FLERR, "Cyclic loop in joint connections"); int *bodyflag = new int[nbody]; for (i = 0; i < nbody; i++) bodyflag[i] = 0; @@ -1094,9 +1049,8 @@ void FixPOEMS::jointbuild() bodyflag[jlist[i][1]]++; } for (i = 0; i < nbody; i++) - if (bodyflag[i] > 2) - error->all(FLERR,"Tree structure in joint connections"); - delete [] bodyflag; + if (bodyflag[i] > 2) error->all(FLERR, "Tree structure in joint connections"); + delete[] bodyflag; // allocate and setup joint arrays // jointbody stores body indices from 1 to Nbody to pass to POEMS @@ -1107,9 +1061,9 @@ void FixPOEMS::jointbuild() xjoint = nullptr; double **myjoint = nullptr; if (njoint) { - memory->create(jointbody,njoint,2,"poems:jointbody"); - memory->create(xjoint,njoint,3,"poems:xjoint"); - memory->create(myjoint,njoint,3,"poems:myjoint"); + memory->create(jointbody, njoint, 2, "poems:jointbody"); + memory->create(xjoint, njoint, 3, "poems:xjoint"); + memory->create(myjoint, njoint, 3, "poems:myjoint"); } double **x = atom->x; @@ -1122,11 +1076,11 @@ void FixPOEMS::jointbuild() myjoint[i][0] = x[j][0]; myjoint[i][1] = x[j][1]; myjoint[i][2] = x[j][2]; - } else myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0; + } else + myjoint[i][0] = myjoint[i][1] = myjoint[i][2] = 0.0; } - if (njoint) - MPI_Allreduce(myjoint[0],xjoint[0],3*njoint,MPI_DOUBLE,MPI_SUM,world); + if (njoint) MPI_Allreduce(myjoint[0], xjoint[0], 3 * njoint, MPI_DOUBLE, MPI_SUM, world); // compute freelist of nfree single unconnected bodies // POEMS could do this itself @@ -1134,19 +1088,21 @@ void FixPOEMS::jointbuild() int *mark = new int[nbody]; for (i = 0; i < nbody; i++) mark[i] = 1; for (i = 0; i < njoint; i++) { - mark[jointbody[i][0]-1] = 0; - mark[jointbody[i][1]-1] = 0; + mark[jointbody[i][0] - 1] = 0; + mark[jointbody[i][1] - 1] = 0; } nfree = 0; for (i = 0; i < nbody; i++) if (mark[i]) nfree++; - if (nfree) freelist = new int[nfree]; - else freelist = nullptr; + if (nfree) + freelist = new int[nfree]; + else + freelist = nullptr; nfree = 0; for (i = 0; i < nbody; i++) if (mark[i]) freelist[nfree++] = i + 1; - delete [] mark; + delete[] mark; // free memory local to this routine @@ -1162,35 +1118,35 @@ void FixPOEMS::jointbuild() void FixPOEMS::sortlist(int n, tagint **list) { - int i,j,flag; - tagint v0,v1,v2; + int i, j, flag; + tagint v0, v1, v2; int inc = 1; - while (inc <= n) inc = 3*inc + 1; + while (inc <= n) inc = 3 * inc + 1; do { inc /= 3; - for (i = inc+1; i <= n; i++) { - v0 = list[i-1][0]; - v1 = list[i-1][1]; - v2 = list[i-1][2]; + for (i = inc + 1; i <= n; i++) { + v0 = list[i - 1][0]; + v1 = list[i - 1][1]; + v2 = list[i - 1][2]; j = i; flag = 0; - if (list[j-inc-1][0] > v0 || - (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1; + if (list[j - inc - 1][0] > v0 || (list[j - inc - 1][0] == v0 && list[j - inc - 1][1] > v1)) + flag = 1; while (flag) { - list[j-1][0] = list[j-inc-1][0]; - list[j-1][1] = list[j-inc-1][1]; - list[j-1][2] = list[j-inc-1][2]; + list[j - 1][0] = list[j - inc - 1][0]; + list[j - 1][1] = list[j - inc - 1][1]; + list[j - 1][2] = list[j - inc - 1][2]; j -= inc; if (j <= inc) break; flag = 0; - if (list[j-inc-1][0] > v0 || - (list[j-inc-1][0] == v0 && list[j-inc-1][1] > v1)) flag = 1; + if (list[j - inc - 1][0] > v0 || (list[j - inc - 1][0] == v0 && list[j - inc - 1][1] > v1)) + flag = 1; } - list[j-1][0] = v0; - list[j-1][1] = v1; - list[j-1][2] = v2; + list[j - 1][0] = v0; + list[j - 1][1] = v1; + list[j - 1][2] = v2; } } while (inc > 1); } @@ -1202,7 +1158,7 @@ void FixPOEMS::sortlist(int n, tagint **list) int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist) { - int i,j,k; + int i, j, k; // ecount[i] = # of vertices connected to vertex i via edge // elistfull[i][*] = list of vertices connected to vertex i @@ -1215,10 +1171,10 @@ int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist) } int emax = 0; - for (i = 0; i < nvert; i++) emax = MAX(emax,ecount[i]); + for (i = 0; i < nvert; i++) emax = MAX(emax, ecount[i]); int **elistfull; - memory->create(elistfull,nvert,emax,"poems:elistfull"); + memory->create(elistfull, nvert, emax, "poems:elistfull"); for (i = 0; i < nvert; i++) ecount[i] = 0; for (i = 0; i < nedge; i++) { elistfull[elist[i][0]][ecount[elist[i][0]]++] = elist[i][1]; @@ -1270,11 +1226,11 @@ int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist) // free memory local to this routine - delete [] ecount; + delete[] ecount; memory->destroy(elistfull); - delete [] parent; - delete [] mark; - delete [] stack; + delete[] parent; + delete[] mark; + delete[] stack; return 0; } @@ -1289,21 +1245,27 @@ int FixPOEMS::loopcheck(int nvert, int nedge, tagint **elist) and divide by principal moments ------------------------------------------------------------------------- */ -void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez, - double *inertia, double *w) +void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez, double *inertia, + double *w) { double wbody[3]; - if (inertia[0] == 0.0) wbody[0] = 0.0; - else wbody[0] = (m[0]*ex[0] + m[1]*ex[1] + m[2]*ex[2]) / inertia[0]; - if (inertia[1] == 0.0) wbody[1] = 0.0; - else wbody[1] = (m[0]*ey[0] + m[1]*ey[1] + m[2]*ey[2]) / inertia[1]; - if (inertia[2] == 0.0) wbody[2] = 0.0; - else wbody[2] = (m[0]*ez[0] + m[1]*ez[1] + m[2]*ez[2]) / inertia[2]; + if (inertia[0] == 0.0) + wbody[0] = 0.0; + else + wbody[0] = (m[0] * ex[0] + m[1] * ex[1] + m[2] * ex[2]) / inertia[0]; + if (inertia[1] == 0.0) + wbody[1] = 0.0; + else + wbody[1] = (m[0] * ey[0] + m[1] * ey[1] + m[2] * ey[2]) / inertia[1]; + if (inertia[2] == 0.0) + wbody[2] = 0.0; + else + wbody[2] = (m[0] * ez[0] + m[1] * ez[1] + m[2] * ez[2]) / inertia[2]; - w[0] = wbody[0]*ex[0] + wbody[1]*ey[0] + wbody[2]*ez[0]; - w[1] = wbody[0]*ex[1] + wbody[1]*ey[1] + wbody[2]*ez[1]; - w[2] = wbody[0]*ex[2] + wbody[1]*ey[2] + wbody[2]*ez[2]; + w[0] = wbody[0] * ex[0] + wbody[1] * ey[0] + wbody[2] * ez[0]; + w[1] = wbody[0] * ex[1] + wbody[1] * ey[1] + wbody[2] * ez[1]; + w[2] = wbody[0] * ex[2] + wbody[1] * ey[2] + wbody[2] * ez[2]; } /* ---------------------------------------------------------------------- @@ -1315,8 +1277,8 @@ void FixPOEMS::omega_from_mq(double *m, double *ex, double *ey, double *ez, void FixPOEMS::set_xv() { int ibody; - int xbox,ybox,zbox; - double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone; + int xbox, ybox, zbox; + double x0, x1, x2, v0, v1, v2, fc0, fc1, fc2, massone; double vr[6]; imageint *image = atom->image; @@ -1345,9 +1307,9 @@ void FixPOEMS::set_xv() // save old positions and velocities for virial if (evflag) { - x0 = x[i][0] + xbox*xprd; - x1 = x[i][1] + ybox*yprd; - x2 = x[i][2] + zbox*zprd; + x0 = x[i][0] + xbox * xprd; + x1 = x[i][1] + ybox * yprd; + x2 = x[i][2] + zbox * zprd; v0 = v[i][0]; v1 = v[i][1]; @@ -1357,29 +1319,23 @@ void FixPOEMS::set_xv() // x = displacement from center-of-mass, based on body orientation // v = vcm + omega around center-of-mass - x[i][0] = ex_space[ibody][0]*displace[i][0] + - ey_space[ibody][0]*displace[i][1] + - ez_space[ibody][0]*displace[i][2]; - x[i][1] = ex_space[ibody][1]*displace[i][0] + - ey_space[ibody][1]*displace[i][1] + - ez_space[ibody][1]*displace[i][2]; - x[i][2] = ex_space[ibody][2]*displace[i][0] + - ey_space[ibody][2]*displace[i][1] + - ez_space[ibody][2]*displace[i][2]; + x[i][0] = ex_space[ibody][0] * displace[i][0] + ey_space[ibody][0] * displace[i][1] + + ez_space[ibody][0] * displace[i][2]; + x[i][1] = ex_space[ibody][1] * displace[i][0] + ey_space[ibody][1] * displace[i][1] + + ez_space[ibody][1] * displace[i][2]; + x[i][2] = ex_space[ibody][2] * displace[i][0] + ey_space[ibody][2] * displace[i][1] + + ez_space[ibody][2] * displace[i][2]; - v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] + - vcm[ibody][0]; - v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] + - vcm[ibody][1]; - v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] + - vcm[ibody][2]; + v[i][0] = omega[ibody][1] * x[i][2] - omega[ibody][2] * x[i][1] + vcm[ibody][0]; + v[i][1] = omega[ibody][2] * x[i][0] - omega[ibody][0] * x[i][2] + vcm[ibody][1]; + v[i][2] = omega[ibody][0] * x[i][1] - omega[ibody][1] * x[i][0] + vcm[ibody][2]; // add center of mass to displacement // map back into periodic box via xbox,ybox,zbox - x[i][0] += xcm[ibody][0] - xbox*xprd; - x[i][1] += xcm[ibody][1] - ybox*yprd; - x[i][2] += xcm[ibody][2] - zbox*zprd; + x[i][0] += xcm[ibody][0] - xbox * xprd; + x[i][1] += xcm[ibody][1] - ybox * yprd; + x[i][2] += xcm[ibody][2] - zbox * zprd; // virial = unwrapped coords dotted into body constraint force // body constraint force = implied force due to v change minus f external @@ -1389,18 +1345,18 @@ void FixPOEMS::set_xv() if (evflag) { massone = mass[type[i]]; - fc0 = massone*(v[i][0] - v0)/dtf - f[i][0]; - fc1 = massone*(v[i][1] - v1)/dtf - f[i][1]; - fc2 = massone*(v[i][2] - v2)/dtf - f[i][2]; + fc0 = massone * (v[i][0] - v0) / dtf - f[i][0]; + fc1 = massone * (v[i][1] - v1) / dtf - f[i][1]; + fc2 = massone * (v[i][2] - v2) / dtf - f[i][2]; - vr[0] = 0.5*fc0*x0; - vr[1] = 0.5*fc1*x1; - vr[2] = 0.5*fc2*x2; - vr[3] = 0.5*fc1*x0; - vr[4] = 0.5*fc2*x0; - vr[5] = 0.5*fc2*x1; + vr[0] = 0.5 * fc0 * x0; + vr[1] = 0.5 * fc1 * x1; + vr[2] = 0.5 * fc2 * x2; + vr[3] = 0.5 * fc1 * x0; + vr[4] = 0.5 * fc2 * x0; + vr[5] = 0.5 * fc2 * x1; - v_tally(1,&i,1.0,vr); + v_tally(1, &i, 1.0, vr); } } } @@ -1413,9 +1369,9 @@ void FixPOEMS::set_xv() void FixPOEMS::set_v() { int ibody; - int xbox,ybox,zbox; - double dx,dy,dz; - double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone; + int xbox, ybox, zbox; + double dx, dy, dz; + double x0, x1, x2, v0, v1, v2, fc0, fc1, fc2, massone; double vr[6]; double *mass = atom->mass; @@ -1437,15 +1393,12 @@ void FixPOEMS::set_v() if (natom2body[i] == 0) continue; ibody = atom2body[i][0]; - dx = ex_space[ibody][0]*displace[i][0] + - ey_space[ibody][0]*displace[i][1] + - ez_space[ibody][0]*displace[i][2]; - dy = ex_space[ibody][1]*displace[i][0] + - ey_space[ibody][1]*displace[i][1] + - ez_space[ibody][1]*displace[i][2]; - dz = ex_space[ibody][2]*displace[i][0] + - ey_space[ibody][2]*displace[i][1] + - ez_space[ibody][2]*displace[i][2]; + dx = ex_space[ibody][0] * displace[i][0] + ey_space[ibody][0] * displace[i][1] + + ez_space[ibody][0] * displace[i][2]; + dy = ex_space[ibody][1] * displace[i][0] + ey_space[ibody][1] * displace[i][1] + + ez_space[ibody][1] * displace[i][2]; + dz = ex_space[ibody][2] * displace[i][0] + ey_space[ibody][2] * displace[i][1] + + ez_space[ibody][2] * displace[i][2]; // save old velocities for virial @@ -1455,9 +1408,9 @@ void FixPOEMS::set_v() v2 = v[i][2]; } - v[i][0] = omega[ibody][1]*dz - omega[ibody][2]*dy + vcm[ibody][0]; - v[i][1] = omega[ibody][2]*dx - omega[ibody][0]*dz + vcm[ibody][1]; - v[i][2] = omega[ibody][0]*dy - omega[ibody][1]*dx + vcm[ibody][2]; + v[i][0] = omega[ibody][1] * dz - omega[ibody][2] * dy + vcm[ibody][0]; + v[i][1] = omega[ibody][2] * dx - omega[ibody][0] * dz + vcm[ibody][1]; + v[i][2] = omega[ibody][0] * dy - omega[ibody][1] * dx + vcm[ibody][2]; // virial = unwrapped coords dotted into body constraint force // body constraint force = implied force due to v change minus f external @@ -1467,26 +1420,26 @@ void FixPOEMS::set_v() if (evflag) { massone = mass[type[i]]; - fc0 = massone*(v[i][0] - v0)/dtf - f[i][0]; - fc1 = massone*(v[i][1] - v1)/dtf - f[i][1]; - fc2 = massone*(v[i][2] - v2)/dtf - f[i][2]; + fc0 = massone * (v[i][0] - v0) / dtf - f[i][0]; + fc1 = massone * (v[i][1] - v1) / dtf - f[i][1]; + fc2 = massone * (v[i][2] - v2) / dtf - f[i][2]; xbox = (image[i] & IMGMASK) - IMGMAX; ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX; zbox = (image[i] >> IMG2BITS) - IMGMAX; - x0 = x[i][0] + xbox*xprd; - x1 = x[i][1] + ybox*yprd; - x2 = x[i][2] + zbox*zprd; + x0 = x[i][0] + xbox * xprd; + x1 = x[i][1] + ybox * yprd; + x2 = x[i][2] + zbox * zprd; - vr[0] = 0.5*fc0*x0; - vr[1] = 0.5*fc1*x1; - vr[2] = 0.5*fc2*x2; - vr[3] = 0.5*fc1*x0; - vr[4] = 0.5*fc2*x0; - vr[5] = 0.5*fc2*x1; + vr[0] = 0.5 * fc0 * x0; + vr[1] = 0.5 * fc1 * x1; + vr[2] = 0.5 * fc2 * x2; + vr[3] = 0.5 * fc1 * x0; + vr[4] = 0.5 * fc2 * x0; + vr[5] = 0.5 * fc2 * x1; - v_tally(1,&i,1.0,vr); + v_tally(1, &i, 1.0, vr); } } } @@ -1497,9 +1450,9 @@ void FixPOEMS::set_v() void FixPOEMS::grow_arrays(int nmax) { - memory->grow(natom2body,nmax,"fix_poems:natom2body"); - memory->grow(atom2body,nmax,MAXBODY,"fix_poems:atom2body"); - memory->grow(displace,nmax,3,"fix_poems:displace"); + memory->grow(natom2body, nmax, "fix_poems:natom2body"); + memory->grow(atom2body, nmax, MAXBODY, "fix_poems:atom2body"); + memory->grow(displace, nmax, 3, "fix_poems:displace"); } /* ---------------------------------------------------------------------- @@ -1522,9 +1475,9 @@ void FixPOEMS::copy_arrays(int i, int j, int /* delflag */) double FixPOEMS::memory_usage() { int nmax = atom->nmax; - double bytes = (double)nmax * sizeof(int); - bytes += (double)nmax*MAXBODY * sizeof(int); - bytes += (double)nmax*3 * sizeof(double); + double bytes = (double) nmax * sizeof(int); + bytes += (double) nmax * MAXBODY * sizeof(int); + bytes += (double) nmax * 3 * sizeof(double); return bytes; } @@ -1535,9 +1488,8 @@ double FixPOEMS::memory_usage() int FixPOEMS::pack_exchange(int i, double *buf) { int m = 0; - buf[m++] = static_cast (natom2body[i]); - for (int j = 0; j < natom2body[i]; j++) - buf[m++] = static_cast (atom2body[i][j]); + buf[m++] = static_cast(natom2body[i]); + for (int j = 0; j < natom2body[i]; j++) buf[m++] = static_cast(atom2body[i][j]); buf[m++] = displace[i][0]; buf[m++] = displace[i][1]; buf[m++] = displace[i][2]; @@ -1551,9 +1503,8 @@ int FixPOEMS::pack_exchange(int i, double *buf) int FixPOEMS::unpack_exchange(int nlocal, double *buf) { int m = 0; - natom2body[nlocal] = static_cast (buf[m++]); - for (int i = 0; i < natom2body[nlocal]; i++) - atom2body[nlocal][i] = static_cast (buf[m++]); + natom2body[nlocal] = static_cast(buf[m++]); + for (int i = 0; i < natom2body[nlocal]; i++) atom2body[nlocal][i] = static_cast(buf[m++]); displace[nlocal][0] = buf[m++]; displace[nlocal][1] = buf[m++]; displace[nlocal][2] = buf[m++]; @@ -1564,11 +1515,14 @@ int FixPOEMS::unpack_exchange(int nlocal, double *buf) int FixPOEMS::modify_param(int narg, char **arg) { - if (strcmp(arg[0],"bodyforces") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); - if (strcmp(arg[1],"early") == 0) earlyflag = 1; - else if (strcmp(arg[1],"late") == 0) earlyflag = 0; - else error->all(FLERR,"Illegal fix_modify command"); + if (strcmp(arg[0], "bodyforces") == 0) { + if (narg < 2) error->all(FLERR, "Illegal fix_modify command"); + if (strcmp(arg[1], "early") == 0) + earlyflag = 1; + else if (strcmp(arg[1], "late") == 0) + earlyflag = 0; + else + error->all(FLERR, "Illegal fix_modify command"); return 2; } diff --git a/src/POEMS/fix_poems.h b/src/POEMS/fix_poems.h index 0b610189bd..cb12a46fb0 100644 --- a/src/POEMS/fix_poems.h +++ b/src/POEMS/fix_poems.h @@ -53,7 +53,6 @@ class FixPOEMS : public Fix { void reset_dt() override; private: - int me; double dtv, dtf, dthalf; double *step_respa; int nlevels_respa; @@ -101,8 +100,7 @@ class FixPOEMS : public Fix { // internal class functions void compute_forces_and_torques(); - void readfile(char *); - int readline(FILE *, char **, int *); + void readfile(const char *); void jointbuild(); void sortlist(int, tagint **); int loopcheck(int, int, tagint **);