diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 3edbe46444..c32a1510ee 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -126,6 +126,11 @@ the specified coordinates. This can be useful for debugging purposes or to create a tiny system with a handful of particles at specified positions. +.. figure:: img/marble_race.jpg + :figwidth: 33% + :align: right + :target: _images/marble_race.jpg + For the *mesh* style, a file with a triangle mesh in `ASCII STL format `_ is read and one or more particles are placed into the area of each triangle. diff --git a/doc/src/img/marble_race.jpg b/doc/src/img/marble_race.jpg new file mode 100644 index 0000000000..f3d238e0f2 Binary files /dev/null and b/doc/src/img/marble_race.jpg differ diff --git a/examples/README b/examples/README index 8d0d7cf1c9..ac3fa4ecc2 100644 --- a/examples/README +++ b/examples/README @@ -86,6 +86,7 @@ mc: MC package models: GCMC, Widom, fix mol/swap mdi: use of the MDI package and MolSSI MDI code coupling library meam: MEAM test for SiC and shear (same as shear examples) melt: rapid melt of 3d LJ system +mesh: create_atoms mesh command micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mliap: examples for using several bundled MLIAP potentials diff --git a/examples/mesh/in.marble_race b/examples/mesh/in.marble_race new file mode 100644 index 0000000000..42eecc856b --- /dev/null +++ b/examples/mesh/in.marble_race @@ -0,0 +1,43 @@ + +units real +lattice sc 5.0 +region box block -110 60 -30 220 -90 130 units box +create_box 2 box +region particles cylinder y 0 -30 47 130 190 units box +create_atoms 1 region particles +region lid cylinder y 0 -30 47 190 200 units box +group mobile type 1 + +create_atoms 2 mesh race_track.stl units box +group mesh type 2 + +mass * 39.95 +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 2 2 0.0 1.0 + +balance 1.1 shift xyz 10 1.01 + +neigh_modify exclude type 2 2 +timestep 1.0 + +fix track mesh setforce 0.0 0.0 0.0 +fix pull mobile addforce 0.0 -0.05 0.0 region particles +fix dir mobile oneway 10 lid -y +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 + +minimize 0.0 0.0 1000 1000 + +reset_timestep 0 time 0.0 + +velocity mobile create 150.0 54634234 +compute ptemp mobile temp +thermo_modify temp ptemp + +thermo 1000 + +# dump 1 all atom 1000 race.lammpstrj +run 10000 + diff --git a/examples/mesh/in.mesh_box b/examples/mesh/in.mesh_box new file mode 100644 index 0000000000..28ce2031f9 --- /dev/null +++ b/examples/mesh/in.mesh_box @@ -0,0 +1,48 @@ + +units real +atom_style hybrid sphere bond + +lattice sc 5.0 +region box block 50 250 50 250 50 250 units box +create_box 2 box +region particles block 110 190 110 190 110 190 units box +create_atoms 1 region particles +region lid block 100 110 50 250 50 250 units box +group mobile type 1 +set type 1 diameter 7.0 + +create_atoms 2 mesh open_box.stl units box radthresh 4.0 +group mesh type 2 + +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 2 2 0.0 1.0 +mass * 39.95 + +neigh_modify exclude type 2 2 + +timestep 1.0 + +run 0 post no + +fix dir mobile oneway 10 lid x +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 +fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box + +reset_timestep 0 time 0.0 +velocity mobile create 150.0 54634234 + +compute ptemp mobile temp +thermo_modify temp ptemp + +thermo 200 +compute ke all ke/atom +#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180 +#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white +#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz + + +run 5000 + diff --git a/examples/mesh/log.8May22.marble_race.g++.1 b/examples/mesh/log.8May22.marble_race.g++.1 new file mode 100644 index 0000000000..b5f5d1c2d0 --- /dev/null +++ b/examples/mesh/log.8May22.marble_race.g++.1 @@ -0,0 +1,156 @@ +LAMMPS (4 May 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +units real +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block -110 60 -30 220 -90 130 units box +create_box 2 box +Created orthogonal box = (-110 -30 -90) to (60 220 130) + 1 by 1 by 1 MPI processor grid +region particles cylinder y 0 -30 47 130 190 units box +create_atoms 1 region particles +Created 3601 atoms + using lattice units in orthogonal box = (-110 -30 -90) to (60 220 130) + create_atoms CPU = 0.001 seconds +region lid cylinder y 0 -30 47 190 200 units box +group mobile type 1 +3601 atoms in group mobile + +create_atoms 2 mesh race_track.stl units box +Reading STL object Georgs Murmelbahn from file race_track.stl + read 9472 triangles with 1.00 atoms per triangle +Created 9472 atoms + using box units in orthogonal box = (-110 -30 -90) to (60 220 130) + create_atoms CPU = 0.040 seconds +group mesh type 2 +9472 atoms in group mesh + +mass * 39.95 +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 1 2 0.2339 7.008 7.8662140345520858986 +pair_coeff 2 2 0.0 1.0 + +balance 1.1 shift xyz 10 1.01 +Balancing ... +Generated 0 of 1 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 = 10.76 + ghost atom cutoff = 10.76 + binsize = 5.38, bins = 32 47 41 + 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 + +neigh_modify exclude type 2 2 +timestep 1.0 + +fix track mesh setforce 0.0 0.0 0.0 +fix pull mobile addforce 0.0 -0.05 0.0 region particles +fix dir mobile oneway 10 lid -y +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 + +minimize 0.0 0.0 1000 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 4.803 | 4.803 | 4.803 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 737062.81 0 737062.81 21986.781 9350000 + 67 0 -2063.91 0 -2063.91 -5.0227698 9350000 +Loop time of 0.518872 on 1 procs for 67 steps with 13073 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + 737062.806250078 -2063.90998808136 -2063.90998808136 + Force two-norm initial, final = 689296.27 22.226599 + Force max component initial, final = 336546.89 0.90593277 + Final line search alpha, max atom move = 1.2850327e-11 1.1641532e-11 + Iterations, force evaluations = 67 393 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.38371 | 0.38371 | 0.38371 | 0.0 | 73.95 +Neigh | 0.038019 | 0.038019 | 0.038019 | 0.0 | 7.33 +Comm | 0.001586 | 0.001586 | 0.001586 | 0.0 | 0.31 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0.033492 | 0.033492 | 0.033492 | 0.0 | 6.45 +Other | | 0.06206 | | | 11.96 + +Nlocal: 13073 ave 13073 max 13073 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 590 ave 590 max 590 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 66778 ave 66778 max 66778 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 66778 +Ave neighs/atom = 5.1080854 +Neighbor list builds = 5 +Dangerous builds = 0 + +reset_timestep 0 time 0.0 + +velocity mobile create 150.0 54634234 +compute ptemp mobile temp +thermo_modify temp ptemp +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520) + +thermo 1000 + +# dump 1 all atom 1000 race.lammpstrj +run 10000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.678 | 3.678 | 3.678 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 150 -2063.91 0 -454.27256 2.8467694 9350000 + 1000 197.01825 -1960.8576 0 153.32871 13.788868 9350000 + 2000 216.32291 -2037.8959 0 283.44712 13.915645 9350000 + 3000 239.06547 -2059.8437 0 505.54782 14.550975 9350000 + 4000 266.60476 -2076.3375 0 784.57583 17.457495 9350000 + 5000 299.6816 -2109.6562 0 1106.202 19.375766 9350000 + 6000 335.17037 -2129.5487 0 1467.1364 24.636144 9350000 + 7000 367.9265 -2101.7855 0 1846.4029 33.591291 9350000 + 8000 404.7304 -2144.8541 0 2198.2739 43.134333 9350000 + 9000 435.75368 -2180.3183 0 2495.7179 53.466409 9350000 + 10000 457.96804 -2194.6681 0 2719.7486 64.521177 9350000 +Loop time of 12.1468 on 1 procs for 10000 steps with 13073 atoms + +Performance: 71.130 ns/day, 0.337 hours/ns, 823.265 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.4112 | 9.4112 | 9.4112 | 0.0 | 77.48 +Neigh | 1.1197 | 1.1197 | 1.1197 | 0.0 | 9.22 +Comm | 0.042153 | 0.042153 | 0.042153 | 0.0 | 0.35 +Output | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.00 +Modify | 1.2618 | 1.2618 | 1.2618 | 0.0 | 10.39 +Other | | 0.3115 | | | 2.56 + +Nlocal: 13073 ave 13073 max 13073 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 590 ave 590 max 590 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 112709 ave 112709 max 112709 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 112709 +Ave neighs/atom = 8.62151 +Neighbor list builds = 129 +Dangerous builds = 0 + +Total wall time: 0:00:12 diff --git a/examples/mesh/log.8May22.marble_race.g++.4 b/examples/mesh/log.8May22.marble_race.g++.4 new file mode 100644 index 0000000000..a728e292cf --- /dev/null +++ b/examples/mesh/log.8May22.marble_race.g++.4 @@ -0,0 +1,163 @@ +LAMMPS (4 May 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +units real +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block -110 60 -30 220 -90 130 units box +create_box 2 box +Created orthogonal box = (-110 -30 -90) to (60 220 130) + 1 by 2 by 2 MPI processor grid +region particles cylinder y 0 -30 47 130 190 units box +create_atoms 1 region particles +Created 3601 atoms + using lattice units in orthogonal box = (-110 -30 -90) to (60 220 130) + create_atoms CPU = 0.001 seconds +region lid cylinder y 0 -30 47 190 200 units box +group mobile type 1 +3601 atoms in group mobile + +create_atoms 2 mesh race_track.stl units box +Reading STL object Georgs Murmelbahn from file race_track.stl + read 9472 triangles with 1.00 atoms per triangle +Created 9472 atoms + using box units in orthogonal box = (-110 -30 -90) to (60 220 130) + create_atoms CPU = 0.069 seconds +group mesh type 2 +9472 atoms in group mesh + +mass * 39.95 +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 1 2 0.2339 7.008 7.8662140345520858986 +pair_coeff 2 2 0.0 1.0 + +balance 1.1 shift xyz 10 1.01 +Balancing ... +Generated 0 of 1 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 = 10.76 + ghost atom cutoff = 10.76 + binsize = 5.38, bins = 32 47 41 + 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 + rebalancing time: 0.001 seconds + iteration count = 17 + initial/final maximal load/proc = 6175 4316 + initial/final imbalance factor = 1.8893903 1.3205844 + x cuts: 0 1 + y cuts: 0 0.5859375 1 + z cuts: 0 0.36376953 1 + +neigh_modify exclude type 2 2 +timestep 1.0 + +fix track mesh setforce 0.0 0.0 0.0 +fix pull mobile addforce 0.0 -0.05 0.0 region particles +fix dir mobile oneway 10 lid -y +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 + +minimize 0.0 0.0 1000 1000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.54 | 4.57 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 0 737062.81 0 737062.81 21986.781 9350000 + 67 0 -2063.91 0 -2063.91 -5.0227698 9350000 +Loop time of 0.375696 on 4 procs for 67 steps with 13073 atoms + +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = linesearch alpha is zero + Energy initial, next-to-last, final = + 737062.806250145 -2063.90998808134 -2063.90998808134 + Force two-norm initial, final = 689296.27 22.226599 + Force max component initial, final = 336546.89 0.90593277 + Final line search alpha, max atom move = 1.2850327e-11 1.1641532e-11 + Iterations, force evaluations = 67 393 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0026793 | 0.10176 | 0.30773 | 39.0 | 27.09 +Neigh | 0.0083945 | 0.011206 | 0.01705 | 3.3 | 2.98 +Comm | 0.0076602 | 0.21941 | 0.32088 | 27.2 | 58.40 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0.0035482 | 0.0090038 | 0.018889 | 6.2 | 2.40 +Other | | 0.03432 | | | 9.13 + +Nlocal: 3268.25 ave 4314 max 2222 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1010.75 ave 1101 max 792 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 16694.5 ave 52643 max 0 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 66778 +Ave neighs/atom = 5.1080854 +Neighbor list builds = 5 +Dangerous builds = 0 + +reset_timestep 0 time 0.0 + +velocity mobile create 150.0 54634234 +compute ptemp mobile temp +thermo_modify temp ptemp +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520) + +thermo 1000 + +# dump 1 all atom 1000 race.lammpstrj +run 10000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 3.481 | 3.598 | 3.711 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 150 -2063.91 0 -454.27256 2.8467694 9350000 + 1000 197.01825 -1960.8576 0 153.32871 13.788868 9350000 + 2000 216.32291 -2037.8959 0 283.44712 13.915645 9350000 + 3000 239.06547 -2059.8437 0 505.54782 14.550975 9350000 + 4000 266.60476 -2076.3375 0 784.57583 17.457495 9350000 + 5000 299.6816 -2109.6562 0 1106.202 19.375766 9350000 + 6000 335.17037 -2129.5487 0 1467.1364 24.636144 9350000 + 7000 367.9265 -2101.7855 0 1846.4029 33.591291 9350000 + 8000 404.7304 -2144.8541 0 2198.2739 43.134332 9350000 + 9000 435.7537 -2180.3187 0 2495.7178 53.466393 9350000 + 10000 457.96586 -2194.6411 0 2719.7522 64.522003 9350000 +Loop time of 4.62401 on 4 procs for 10000 steps with 13073 atoms + +Performance: 186.851 ns/day, 0.128 hours/ns, 2162.627 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 | 2.0661 | 2.4819 | 2.9751 | 25.5 | 53.67 +Neigh | 0.18188 | 0.2993 | 0.52875 | 25.5 | 6.47 +Comm | 0.40938 | 1.17 | 1.736 | 51.7 | 25.30 +Output | 0.00028188 | 0.00049757 | 0.0006548 | 0.0 | 0.01 +Modify | 0.22514 | 0.32517 | 0.53165 | 21.2 | 7.03 +Other | | 0.3472 | | | 7.51 + +Nlocal: 3268.25 ave 6890 max 1643 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 1701 ave 2074 max 1456 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 28177.5 ave 34170 max 21435 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 112710 +Ave neighs/atom = 8.6215865 +Neighbor list builds = 129 +Dangerous builds = 0 + +Total wall time: 0:00:05 diff --git a/examples/mesh/log.8May22.mesh_box.g++.1 b/examples/mesh/log.8May22.mesh_box.g++.1 new file mode 100644 index 0000000000..ba8ab1935d --- /dev/null +++ b/examples/mesh/log.8May22.mesh_box.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (4 May 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +units real +atom_style hybrid sphere bond +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130) + +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block 50 250 50 250 50 250 units box +create_box 2 box +Created orthogonal box = (50 50 50) to (250 250 250) + 1 by 1 by 1 MPI processor grid +region particles block 110 190 110 190 110 190 units box +create_atoms 1 region particles +Created 4913 atoms + using lattice units in orthogonal box = (50 50 50) to (250 250 250) + create_atoms CPU = 0.001 seconds +region lid block 100 110 50 250 50 250 units box +group mobile type 1 +4913 atoms in group mobile +set type 1 diameter 7.0 +Setting atom values ... + 4913 settings made for diameter + +create_atoms 2 mesh open_box.stl units box radthresh 4.0 +Reading STL object Open Box from file open_box.stl + read 10 triangles with 512.00 atoms per triangle +Created 5120 atoms + using box units in orthogonal box = (50 50 50) to (250 250 250) + create_atoms CPU = 0.001 seconds +group mesh type 2 +5120 atoms in group mesh + +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 1 2 0.2339 7.008 7.8662140345520858986 +pair_coeff 2 2 0.0 1.0 +mass * 39.95 + +neigh_modify exclude type 2 2 + +timestep 1.0 + +run 0 post no +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 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 = 10.76 + ghost atom cutoff = 10.76 + binsize = 5.38, bins = 38 38 38 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.641 | 5.641 | 5.641 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -1778.6527 0 -1778.6527 -27.271044 +Loop time of 1.544e-06 on 1 procs for 0 steps with 10033 atoms + + +fix dir mobile oneway 10 lid x +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 +fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box + +reset_timestep 0 time 0.0 +velocity mobile create 150.0 54634234 + +compute ptemp mobile temp +thermo_modify temp ptemp +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520) + +thermo 200 +compute ke all ke/atom +#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180 +#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white +#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz + + +run 5000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.157 | 6.157 | 6.157 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 150 -1778.6527 0 417.60814 -14.721534 8000000 + 200 179.71663 -2353.7693 0 277.59468 14.591893 8000000 + 400 181.98778 -2346.3965 0 318.22101 14.694157 8000000 + 600 183.48983 -2373.9255 0 312.68467 15.032091 8000000 + 800 183.99836 -2366.1103 0 327.94574 15.154418 8000000 + 1000 186.19063 -2405.1258 0 321.02886 14.881141 8000000 + 1200 185.74206 -2396.0437 0 323.54307 15.729931 8000000 + 1400 188.03786 -2424.6865 0 328.5147 15.077756 8000000 + 1600 187.4202 -2437.7998 0 306.35792 16.323387 8000000 + 1800 186.98057 -2417.0238 0 320.69695 14.445045 8000000 + 2000 185.81788 -2404.4322 0 316.26462 15.382214 8000000 + 2200 185.60774 -2386.4973 0 331.12284 15.033058 8000000 + 2400 187.14304 -2409.5005 0 330.5991 15.226519 8000000 + 2600 186.63304 -2410.3607 0 322.27162 15.010459 8000000 + 2800 185.96347 -2421.8039 0 301.02465 15.577503 8000000 + 3000 185.22976 -2387.0491 0 325.03669 16.111731 8000000 + 3200 186.32095 -2414.4926 0 313.5702 14.41138 8000000 + 3400 186.75847 -2414.3018 0 320.16692 15.224392 8000000 + 3600 184.82282 -2391.1485 0 314.97889 15.96507 8000000 + 3800 185.71262 -2381.6131 0 337.54256 14.870266 8000000 + 4000 186.58931 -2399.6637 0 332.32827 14.434356 8000000 + 4200 185.27225 -2400.3577 0 312.35024 15.429373 8000000 + 4400 183.90694 -2367.1261 0 325.59133 16.558529 8000000 + 4600 185.84295 -2403.8288 0 317.23517 14.371372 8000000 + 4800 184.58178 -2359.4293 0 343.16897 15.516075 8000000 + 5000 186.15467 -2412.7678 0 312.86031 15.366761 8000000 +Loop time of 9.53365 on 1 procs for 5000 steps with 10033 atoms + +Performance: 45.313 ns/day, 0.530 hours/ns, 524.458 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.3496 | 5.3496 | 5.3496 | 0.0 | 56.11 +Bond | 0.00036644 | 0.00036644 | 0.00036644 | 0.0 | 0.00 +Neigh | 3.1301 | 3.1301 | 3.1301 | 0.0 | 32.83 +Comm | 0.03837 | 0.03837 | 0.03837 | 0.0 | 0.40 +Output | 0.0010388 | 0.0010388 | 0.0010388 | 0.0 | 0.01 +Modify | 0.88529 | 0.88529 | 0.88529 | 0.0 | 9.29 +Other | | 0.1289 | | | 1.35 + +Nlocal: 10033 ave 10033 max 10033 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 98536 ave 98536 max 98536 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 98536 +Ave neighs/atom = 9.8211901 +Ave special neighs/atom = 0 +Neighbor list builds = 374 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/mesh/log.8May22.mesh_box.g++.4 b/examples/mesh/log.8May22.mesh_box.g++.4 new file mode 100644 index 0000000000..a255fdd55c --- /dev/null +++ b/examples/mesh/log.8May22.mesh_box.g++.4 @@ -0,0 +1,146 @@ +LAMMPS (4 May 2022) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task + +units real +atom_style hybrid sphere bond +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130) + +lattice sc 5.0 +Lattice spacing in x,y,z = 5 5 5 +region box block 50 250 50 250 50 250 units box +create_box 2 box +Created orthogonal box = (50 50 50) to (250 250 250) + 1 by 2 by 2 MPI processor grid +region particles block 110 190 110 190 110 190 units box +create_atoms 1 region particles +Created 4913 atoms + using lattice units in orthogonal box = (50 50 50) to (250 250 250) + create_atoms CPU = 0.001 seconds +region lid block 100 110 50 250 50 250 units box +group mobile type 1 +4913 atoms in group mobile +set type 1 diameter 7.0 +Setting atom values ... + 4913 settings made for diameter + +create_atoms 2 mesh open_box.stl units box radthresh 4.0 +Reading STL object Open Box from file open_box.stl + read 10 triangles with 512.00 atoms per triangle +Created 5120 atoms + using box units in orthogonal box = (50 50 50) to (250 250 250) + create_atoms CPU = 0.000 seconds +group mesh type 2 +5120 atoms in group mesh + +pair_style lj/cut 8.76 +pair_coeff 1 1 0.2339 3.504 +pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0)) +pair_coeff 1 2 0.2339 7.008 7.8662140345520858986 +pair_coeff 2 2 0.0 1.0 +mass * 39.95 + +neigh_modify exclude type 2 2 + +timestep 1.0 + +run 0 post no +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 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 = 10.76 + ghost atom cutoff = 10.76 + binsize = 5.38, bins = 38 38 38 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.457 | 5.476 | 5.493 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 -1778.6527 0 -1778.6527 -27.271044 +Loop time of 3.34625e-06 on 4 procs for 0 steps with 10033 atoms + + +fix dir mobile oneway 10 lid x +fix move mobile nve +fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0 +fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box + +reset_timestep 0 time 0.0 +velocity mobile create 150.0 54634234 + +compute ptemp mobile temp +thermo_modify temp ptemp +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520) + +thermo 200 +compute ke all ke/atom +#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180 +#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white +#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz + + +run 5000 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 5.998 | 6.028 | 6.059 Mbytes + Step Temp E_pair E_mol TotEng Press Volume + 0 150 -1778.6527 0 417.60814 -14.721534 8000000 + 200 178.85669 -2312.6876 0 306.08541 15.832907 8000000 + 400 182.01107 -2334.4183 0 330.54024 14.457841 8000000 + 600 183.04428 -2348.8534 0 331.23317 15.166984 8000000 + 800 185.68203 -2396.0112 0 322.69659 14.155191 8000000 + 1000 185.58372 -2376.7148 0 340.55362 14.125122 8000000 + 1200 184.96212 -2401.9634 0 306.20372 14.791738 8000000 + 1400 186.67578 -2392.327 0 340.93097 14.859731 8000000 + 1600 186.98761 -2418.1463 0 319.67739 15.173567 8000000 + 1800 188.23692 -2431.082 0 325.03382 15.02044 8000000 + 2000 184.29434 -2378.8865 0 319.50307 16.504785 8000000 + 2200 187.1493 -2395.48 0 344.71119 14.464979 8000000 + 2400 186.60933 -2409.0279 0 323.25719 15.165523 8000000 + 2600 185.29773 -2391.0001 0 322.08084 15.967212 8000000 + 2800 185.05884 -2376.7398 0 332.84337 14.263097 8000000 + 3000 185.03409 -2385.6071 0 323.61377 15.053931 8000000 + 3200 185.37823 -2400.0415 0 314.21823 16.076039 8000000 + 3400 187.03675 -2424.3537 0 314.18955 14.596162 8000000 + 3600 185.55628 -2397.9284 0 318.93826 14.036493 8000000 + 3800 187.10605 -2408.018 0 331.54002 14.527143 8000000 + 4000 186.2403 -2410.4382 0 316.44375 15.342402 8000000 + 4200 187.32974 -2389.1104 0 353.72276 13.931896 8000000 + 4400 189.27742 -2435.0111 0 336.33944 14.316321 8000000 + 4600 189.26108 -2453.7231 0 317.38821 15.615617 8000000 + 4800 187.9187 -2429.9397 0 321.51688 15.226135 8000000 + 5000 186.91414 -2428.2233 0 308.52478 15.780318 8000000 +Loop time of 3.39374 on 4 procs for 5000 steps with 10033 atoms + +Performance: 127.293 ns/day, 0.189 hours/ns, 1473.303 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 | 1.0734 | 1.4274 | 1.7321 | 24.7 | 42.06 +Bond | 0.00031015 | 0.00032026 | 0.00033017 | 0.0 | 0.01 +Neigh | 0.65409 | 0.83138 | 1.0016 | 17.4 | 24.50 +Comm | 0.33062 | 0.82642 | 1.379 | 52.2 | 24.35 +Output | 0.00070506 | 0.00086089 | 0.0010669 | 0.0 | 0.03 +Modify | 0.21589 | 0.24797 | 0.28078 | 5.5 | 7.31 +Other | | 0.05935 | | | 1.75 + +Nlocal: 2508.25 ave 2930 max 2111 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 1038.5 ave 1110 max 985 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 24668.2 ave 32893 max 17327 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 98673 +Ave neighs/atom = 9.834845 +Ave special neighs/atom = 0 +Neighbor list builds = 371 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/mesh/open_box.stl b/examples/mesh/open_box.stl new file mode 100644 index 0000000000..f9ef56d64a --- /dev/null +++ b/examples/mesh/open_box.stl @@ -0,0 +1,72 @@ +solid Open Box + facet normal 0.0 0.0 1.0 + outer loop + vertex 100.0 100.0 100.0 + vertex 200.0 100.0 100.0 + vertex 200.0 200.0 100.0 + endloop + endfacet + facet normal 0.0 0.0 1.0 + outer loop + vertex 100.0 100.0 100.0 + vertex 100.0 200.0 100.0 + vertex 200.0 200.0 100.0 + endloop + endfacet + facet normal 0.0 0.0 -1.0 + outer loop + vertex 100.0 100.0 200.0 + vertex 200.0 100.0 200.0 + vertex 200.0 200.0 200.0 + endloop + endfacet + facet normal 0.0 0.0 -1.0 + outer loop + vertex 100.0 100.0 200.0 + vertex 100.0 200.0 200.0 + vertex 200.0 200.0 200.0 + endloop + endfacet + facet normal 0.0 1.0 0.0 + outer loop + vertex 100.0 100.0 100.0 + vertex 200.0 100.0 100.0 + vertex 200.0 100.0 200.0 + endloop + endfacet + facet normal 0.0 1.0 0.0 + outer loop + vertex 100.0 100.0 100.0 + vertex 100.0 100.0 200.0 + vertex 200.0 100.0 200.0 + endloop + endfacet + facet normal 0.0 -1.0 0.0 + outer loop + vertex 100.0 200.0 100.0 + vertex 200.0 200.0 100.0 + vertex 200.0 200.0 200.0 + endloop + endfacet + facet normal 0.0 -1.0 0.0 + outer loop + vertex 100.0 200.0 100.0 + vertex 100.0 200.0 200.0 + vertex 200.0 200.0 200.0 + endloop + endfacet + facet normal -1.0 0.0 0.0 + outer loop + vertex 200.0 100.0 100.0 + vertex 200.0 200.0 100.0 + vertex 200.0 200.0 200.0 + endloop + endfacet + facet normal -1.0 0.0 0.0 + outer loop + vertex 200.0 100.0 100.0 + vertex 200.0 100.0 200.0 + vertex 200.0 200.0 200.0 + endloop + endfacet +endsolid diff --git a/examples/mesh/race_track.stl b/examples/mesh/race_track.stl new file mode 120000 index 0000000000..e05acc5019 --- /dev/null +++ b/examples/mesh/race_track.stl @@ -0,0 +1 @@ +../PACKAGES/machdyn/funnel_flow/boundary.stl \ No newline at end of file