add examples import one image to manual
This commit is contained in:
Axel Kohlmeyer
@ -126,6 +126,11 @@ the specified coordinates. This can be useful for debugging purposes
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or to create a tiny system with a handful of particles at specified
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positions.
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.. figure:: img/marble_race.jpg
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:figwidth: 33%
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:align: right
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:target: _images/marble_race.jpg
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For the *mesh* style, a file with a triangle mesh in `ASCII STL format
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<https://en.wikipedia.org/wiki/STL_(file_format)#ASCII_STL>`_ is read
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and one or more particles are placed into the area of each triangle.
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BIN
doc/src/img/marble_race.jpg
Normal file
BIN
doc/src/img/marble_race.jpg
Normal file
Binary file not shown.
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After Width: | Height: | Size: 39 KiB |
@ -86,6 +86,7 @@ mc: MC package models: GCMC, Widom, fix mol/swap
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mdi: use of the MDI package and MolSSI MDI code coupling library
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meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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mesh: create_atoms mesh command
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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min: energy minimization of 2d LJ melt
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mliap: examples for using several bundled MLIAP potentials
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43
examples/mesh/in.marble_race
Normal file
43
examples/mesh/in.marble_race
Normal file
@ -0,0 +1,43 @@
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units real
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lattice sc 5.0
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region box block -110 60 -30 220 -90 130 units box
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create_box 2 box
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region particles cylinder y 0 -30 47 130 190 units box
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create_atoms 1 region particles
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region lid cylinder y 0 -30 47 190 200 units box
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group mobile type 1
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create_atoms 2 mesh race_track.stl units box
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group mesh type 2
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mass * 39.95
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pair_style lj/cut 8.76
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pair_coeff 1 1 0.2339 3.504
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pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
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pair_coeff 2 2 0.0 1.0
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balance 1.1 shift xyz 10 1.01
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neigh_modify exclude type 2 2
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timestep 1.0
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fix track mesh setforce 0.0 0.0 0.0
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fix pull mobile addforce 0.0 -0.05 0.0 region particles
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fix dir mobile oneway 10 lid -y
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fix move mobile nve
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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
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minimize 0.0 0.0 1000 1000
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reset_timestep 0 time 0.0
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velocity mobile create 150.0 54634234
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compute ptemp mobile temp
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thermo_modify temp ptemp
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thermo 1000
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# dump 1 all atom 1000 race.lammpstrj
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run 10000
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48
examples/mesh/in.mesh_box
Normal file
48
examples/mesh/in.mesh_box
Normal file
@ -0,0 +1,48 @@
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units real
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atom_style hybrid sphere bond
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lattice sc 5.0
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region box block 50 250 50 250 50 250 units box
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create_box 2 box
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region particles block 110 190 110 190 110 190 units box
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create_atoms 1 region particles
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region lid block 100 110 50 250 50 250 units box
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group mobile type 1
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set type 1 diameter 7.0
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create_atoms 2 mesh open_box.stl units box radthresh 4.0
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group mesh type 2
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pair_style lj/cut 8.76
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pair_coeff 1 1 0.2339 3.504
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pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
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pair_coeff 2 2 0.0 1.0
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mass * 39.95
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neigh_modify exclude type 2 2
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timestep 1.0
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run 0 post no
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fix dir mobile oneway 10 lid x
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fix move mobile nve
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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
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fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
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reset_timestep 0 time 0.0
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velocity mobile create 150.0 54634234
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compute ptemp mobile temp
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thermo_modify temp ptemp
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thermo 200
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compute ke all ke/atom
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#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
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#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
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#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
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run 5000
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156
examples/mesh/log.8May22.marble_race.g++.1
Normal file
156
examples/mesh/log.8May22.marble_race.g++.1
Normal file
@ -0,0 +1,156 @@
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LAMMPS (4 May 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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units real
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block -110 60 -30 220 -90 130 units box
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create_box 2 box
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Created orthogonal box = (-110 -30 -90) to (60 220 130)
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1 by 1 by 1 MPI processor grid
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region particles cylinder y 0 -30 47 130 190 units box
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create_atoms 1 region particles
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Created 3601 atoms
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using lattice units in orthogonal box = (-110 -30 -90) to (60 220 130)
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create_atoms CPU = 0.001 seconds
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region lid cylinder y 0 -30 47 190 200 units box
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group mobile type 1
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3601 atoms in group mobile
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create_atoms 2 mesh race_track.stl units box
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Reading STL object Georgs Murmelbahn from file race_track.stl
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read 9472 triangles with 1.00 atoms per triangle
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Created 9472 atoms
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using box units in orthogonal box = (-110 -30 -90) to (60 220 130)
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create_atoms CPU = 0.040 seconds
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group mesh type 2
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9472 atoms in group mesh
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mass * 39.95
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pair_style lj/cut 8.76
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pair_coeff 1 1 0.2339 3.504
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pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
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pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
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pair_coeff 2 2 0.0 1.0
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balance 1.1 shift xyz 10 1.01
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Balancing ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.76
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ghost atom cutoff = 10.76
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binsize = 5.38, bins = 32 47 41
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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neigh_modify exclude type 2 2
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timestep 1.0
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fix track mesh setforce 0.0 0.0 0.0
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fix pull mobile addforce 0.0 -0.05 0.0 region particles
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fix dir mobile oneway 10 lid -y
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fix move mobile nve
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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
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minimize 0.0 0.0 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.803 | 4.803 | 4.803 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0 737062.81 0 737062.81 21986.781 9350000
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67 0 -2063.91 0 -2063.91 -5.0227698 9350000
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Loop time of 0.518872 on 1 procs for 67 steps with 13073 atoms
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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737062.806250078 -2063.90998808136 -2063.90998808136
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Force two-norm initial, final = 689296.27 22.226599
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Force max component initial, final = 336546.89 0.90593277
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Final line search alpha, max atom move = 1.2850327e-11 1.1641532e-11
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Iterations, force evaluations = 67 393
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.38371 | 0.38371 | 0.38371 | 0.0 | 73.95
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Neigh | 0.038019 | 0.038019 | 0.038019 | 0.0 | 7.33
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Comm | 0.001586 | 0.001586 | 0.001586 | 0.0 | 0.31
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0.033492 | 0.033492 | 0.033492 | 0.0 | 6.45
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Other | | 0.06206 | | | 11.96
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Nlocal: 13073 ave 13073 max 13073 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 590 ave 590 max 590 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 66778 ave 66778 max 66778 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 66778
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Ave neighs/atom = 5.1080854
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Neighbor list builds = 5
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Dangerous builds = 0
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reset_timestep 0 time 0.0
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velocity mobile create 150.0 54634234
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compute ptemp mobile temp
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thermo_modify temp ptemp
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
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thermo 1000
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# dump 1 all atom 1000 race.lammpstrj
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run 10000
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 3.678 | 3.678 | 3.678 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 150 -2063.91 0 -454.27256 2.8467694 9350000
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1000 197.01825 -1960.8576 0 153.32871 13.788868 9350000
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2000 216.32291 -2037.8959 0 283.44712 13.915645 9350000
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3000 239.06547 -2059.8437 0 505.54782 14.550975 9350000
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4000 266.60476 -2076.3375 0 784.57583 17.457495 9350000
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5000 299.6816 -2109.6562 0 1106.202 19.375766 9350000
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6000 335.17037 -2129.5487 0 1467.1364 24.636144 9350000
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7000 367.9265 -2101.7855 0 1846.4029 33.591291 9350000
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8000 404.7304 -2144.8541 0 2198.2739 43.134333 9350000
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9000 435.75368 -2180.3183 0 2495.7179 53.466409 9350000
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10000 457.96804 -2194.6681 0 2719.7486 64.521177 9350000
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Loop time of 12.1468 on 1 procs for 10000 steps with 13073 atoms
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Performance: 71.130 ns/day, 0.337 hours/ns, 823.265 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 9.4112 | 9.4112 | 9.4112 | 0.0 | 77.48
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Neigh | 1.1197 | 1.1197 | 1.1197 | 0.0 | 9.22
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Comm | 0.042153 | 0.042153 | 0.042153 | 0.0 | 0.35
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Output | 0.00041578 | 0.00041578 | 0.00041578 | 0.0 | 0.00
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Modify | 1.2618 | 1.2618 | 1.2618 | 0.0 | 10.39
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Other | | 0.3115 | | | 2.56
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Nlocal: 13073 ave 13073 max 13073 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 590 ave 590 max 590 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 112709 ave 112709 max 112709 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 112709
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Ave neighs/atom = 8.62151
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Neighbor list builds = 129
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Dangerous builds = 0
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Total wall time: 0:00:12
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163
examples/mesh/log.8May22.marble_race.g++.4
Normal file
163
examples/mesh/log.8May22.marble_race.g++.4
Normal file
@ -0,0 +1,163 @@
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LAMMPS (4 May 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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units real
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block -110 60 -30 220 -90 130 units box
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create_box 2 box
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Created orthogonal box = (-110 -30 -90) to (60 220 130)
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1 by 2 by 2 MPI processor grid
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region particles cylinder y 0 -30 47 130 190 units box
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create_atoms 1 region particles
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Created 3601 atoms
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using lattice units in orthogonal box = (-110 -30 -90) to (60 220 130)
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create_atoms CPU = 0.001 seconds
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region lid cylinder y 0 -30 47 190 200 units box
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group mobile type 1
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3601 atoms in group mobile
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create_atoms 2 mesh race_track.stl units box
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Reading STL object Georgs Murmelbahn from file race_track.stl
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read 9472 triangles with 1.00 atoms per triangle
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Created 9472 atoms
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using box units in orthogonal box = (-110 -30 -90) to (60 220 130)
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create_atoms CPU = 0.069 seconds
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group mesh type 2
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9472 atoms in group mesh
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mass * 39.95
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pair_style lj/cut 8.76
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pair_coeff 1 1 0.2339 3.504
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pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
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pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
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pair_coeff 2 2 0.0 1.0
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balance 1.1 shift xyz 10 1.01
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Balancing ...
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 10.76
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ghost atom cutoff = 10.76
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binsize = 5.38, bins = 32 47 41
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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rebalancing time: 0.001 seconds
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iteration count = 17
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initial/final maximal load/proc = 6175 4316
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initial/final imbalance factor = 1.8893903 1.3205844
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x cuts: 0 1
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y cuts: 0 0.5859375 1
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z cuts: 0 0.36376953 1
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neigh_modify exclude type 2 2
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timestep 1.0
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|
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fix track mesh setforce 0.0 0.0 0.0
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fix pull mobile addforce 0.0 -0.05 0.0 region particles
|
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fix dir mobile oneway 10 lid -y
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fix move mobile nve
|
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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
|
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minimize 0.0 0.0 1000 1000
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WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.54 | 4.57 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0 737062.81 0 737062.81 21986.781 9350000
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67 0 -2063.91 0 -2063.91 -5.0227698 9350000
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Loop time of 0.375696 on 4 procs for 67 steps with 13073 atoms
|
||||
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99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
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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
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Iterations, force evaluations = 67 393
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MPI task timing breakdown:
|
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Section | min time | avg time | max time |%varavg| %total
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||||
---------------------------------------------------------------
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Pair | 0.0026793 | 0.10176 | 0.30773 | 39.0 | 27.09
|
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Neigh | 0.0083945 | 0.011206 | 0.01705 | 3.3 | 2.98
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Comm | 0.0076602 | 0.21941 | 0.32088 | 27.2 | 58.40
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0.0035482 | 0.0090038 | 0.018889 | 6.2 | 2.40
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Other | | 0.03432 | | | 9.13
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Nlocal: 3268.25 ave 4314 max 2222 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
|
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Nghost: 1010.75 ave 1101 max 792 min
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||||
Histogram: 1 0 0 0 0 0 0 0 1 2
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Neighs: 16694.5 ave 52643 max 0 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Total # of neighbors = 66778
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Ave neighs/atom = 5.1080854
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Neighbor list builds = 5
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Dangerous builds = 0
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|
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reset_timestep 0 time 0.0
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|
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velocity mobile create 150.0 54634234
|
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compute ptemp mobile temp
|
||||
thermo_modify temp ptemp
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
|
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|
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thermo 1000
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|
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# dump 1 all atom 1000 race.lammpstrj
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run 10000
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||||
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
|
||||
146
examples/mesh/log.8May22.mesh_box.g++.1
Normal file
146
examples/mesh/log.8May22.mesh_box.g++.1
Normal file
@ -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
|
||||
146
examples/mesh/log.8May22.mesh_box.g++.4
Normal file
146
examples/mesh/log.8May22.mesh_box.g++.4
Normal file
@ -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
|
||||
72
examples/mesh/open_box.stl
Normal file
72
examples/mesh/open_box.stl
Normal file
@ -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
|
||||
1
examples/mesh/race_track.stl
Symbolic link
1
examples/mesh/race_track.stl
Symbolic link
@ -0,0 +1 @@
|
||||
../PACKAGES/machdyn/funnel_flow/boundary.stl
|
||||
Reference in New Issue
Block a user