forked from lijiext/lammps
add new grid-based examples
This commit is contained in:
Steve Plimpton
parent
7ce4b2eb68
commit
1ba9ff7817
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@ -78,6 +78,7 @@ flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gjf: use of fix langevin Gronbech-Jensen/Farago option
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granregion: use of fix wall/region/gran as boundary on granular particles
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grid use of commands which overlay grids on the simulation domain
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hugoniostat: Hugoniostat shock dynamics
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hyper: global and local hyperdynamics of diffusion on Pt surface
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indent: spherical indenter into a 2d solid
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@ -0,0 +1,23 @@
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These input scripts illustrate the use of several commands that
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overlay grids on the simulation domain.
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fix ave/grid
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compute property/grid
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dump grid
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dump grid/vtk
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The in.grid.2d and in.grid.3d scripts model simple Lennard Jones
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liquids. The in.sph script models SPH water flowing over a dam. All
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the scripts use dynamic load balancing to illustrate that the grid
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cells can be dynamically partitioned across processors similar to how
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particles are.
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To produce output dump files and image files, you will need to
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uncomment the various "dump" commands that produce them. The images
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show processor subdomains as well as the background grid, colored by
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particle counts in each grid cell.
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,52 @@
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# 2d Lennard-Jones melt
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units lj
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atom_style atomic
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dimension 2
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lattice sq 0.5
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region box block 0 50 0 50 -0.5 0.5
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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fix 2 all enforce2d
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# load balancing
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comm_style tiled
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fix 100 all balance 100 0.9 rcb
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# fix ave/grid
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fix ave all ave/grid 10 10 100 10 10 1 vx vy
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# dump grid
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compute ave all property/grid 10 10 1 id ix iy
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#dump ave all grid 100 tmp.dump.2d &
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# c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
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#dump_modify ave sort 1
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#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count
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#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2]
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#dump 10 all image 100 tmp.image.*.2d.png type type &
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# zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 &
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# subbox yes 0.01
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# run
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thermo 100
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run 500
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@ -0,0 +1,50 @@
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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# load balancing
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comm_style tiled
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fix 100 all balance 100 0.9 rcb
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# fix ave/grid
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fix ave all ave/grid 10 10 100 5 5 5 vx vy vz
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# dump grid
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compute ave all property/grid 5 5 5 id ix iy
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#dump ave all grid 100 tmp.dump.3d &
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# c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
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#dump_modify ave sort 1
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#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count
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#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*]
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#dump 10 all image 100 tmp.image.*.3d.png type type &
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# grid f_ave:grid:count view 60 -30 shiny 0.0 &
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# subbox yes 0.01
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# run
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thermo 100
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run 500
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@ -0,0 +1,112 @@
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# SPH water over dam
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atom_style sph
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dimension 2
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newton on
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boundary s s p
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units lj
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read_data data.sph
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# upper limit of timestep based on CFL-like criterion
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# roughly estimate number of timesteps needed for 7.5 seconds
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variable h equal 0.03
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variable c equal 10.0 # soundspeed for Tait's EOS
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variable dt equal 0.1*${h}/${c}
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variable nrun equal 15.0/${dt}
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# assign group name "bc" to boundary particles (type 2)
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# assign group name "water" to water particles (type 1)
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group bc type 2
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group water type 1
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# use hybrid pairstyle which does density summation
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# with cutoff ${h} every timestep (1)
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# use target density of 1000, soundspeed ${c} for Tait's EOS
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pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
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pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h}
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pair_coeff 1 1 sph/rhosum ${h}
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# add gravity. This fix also computes potential energy of mass in gravity field
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fix gfix water gravity -9.81 vector 0 1 0
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fix 2d_fix all enforce2d
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compute rho_peratom all sph/rho/atom
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compute e_peratom all sph/e/atom
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compute esph all reduce sum c_e_peratom
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compute ke all ke
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variable etot equal c_esph+c_ke+f_gfix
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compute ke_peratom all ke/atom
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# adjust nevery | min. allowed dt | max. allowed dt |
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# max. travel distance per dt
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# ${dt} ~= CFL criterion 0.1*h/c
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# remove top atoms
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region cut block INF INF 2.5 INF INF INF
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delete_atoms region cut
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# use a variable timestep
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fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box
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# time-integrate position, velocities,
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# internal energy and density of water particles
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fix integrate_water_fix water sph
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# time-integrate only internal energy and density of boundary particles
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fix integrate_bc_fix bc sph/stationary
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thermo 500
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thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix
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thermo_modify norm no
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# load balancing
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comm_style tiled
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fix 100 all balance 100 0.9 rcb
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# fix ave/grid
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fix ave all ave/grid 50 5 250 10 10 1 vx vy
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# dump particles
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#dump dump_id all custom 100 tmp.dump &
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# id type x y z c_ke_peratom
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#dump_modify dump_id first yes
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# dump grid
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#compute ave all property/grid 10 10 1 id ix iy
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#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*]
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#dump_modify ave sort 1
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# dump image
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#compute 1 all property/atom proc
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#variable p atom c_1%10
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#dump 3 all image 500 tmp.*.png c_ke_peratom type &
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# adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 &
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# center d 0.5 0.5 0.5 size 1024 768 box no 0.0 &
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# grid f_ave:grid:count
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#variable colors string &
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# "min blue 0.25 green 0.5 orange 0.75 yellow max red"
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#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors}
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# run
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neigh_modify every 5 delay 0 check no
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variable skin equal 0.3*${h}
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neighbor ${skin} bin
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run 6000
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@ -0,0 +1,104 @@
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LAMMPS (3 Nov 2022)
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# 2d Lennard-Jones melt
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units lj
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atom_style atomic
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dimension 2
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lattice sq 0.5
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Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
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region box block 0 50 0 50 -0.5 0.5
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create_box 1 box
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Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 2500 atoms
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using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
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create_atoms CPU = 0.001 seconds
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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fix 2 all enforce2d
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# load balancing
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comm_style tiled
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fix 100 all balance 100 0.9 rcb
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# fix ave/grid
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fix ave all ave/grid 10 10 100 10 10 1 vx vy
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# dump grid
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compute ave all property/grid 10 10 1 id ix iy
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#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
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#dump_modify ave sort 1
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#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count
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#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2]
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#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01
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# run
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thermo 100
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run 500
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 51 51 2
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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/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.6 | 2.6 | 2.6 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1.44 -0.99804688 0 0.44137713 -0.58692862 5000
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100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000
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200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000
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300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000
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400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000
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500 1.6163874 -1.184699 0 0.43104185 1.346977 5000
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Loop time of 0.0605938 on 1 procs for 500 steps with 2500 atoms
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Performance: 3564723.496 tau/day, 8251.675 timesteps/s, 20.629 Matom-step/s
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100.0% CPU use with 1 MPI tasks x no 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 | 0.042252 | 0.042252 | 0.042252 | 0.0 | 69.73
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Neigh | 0.0080564 | 0.0080564 | 0.0080564 | 0.0 | 13.30
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Comm | 0.00092699 | 0.00092699 | 0.00092699 | 0.0 | 1.53
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Output | 5.6077e-05 | 5.6077e-05 | 5.6077e-05 | 0.0 | 0.09
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Modify | 0.0087579 | 0.0087579 | 0.0087579 | 0.0 | 14.45
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Other | | 0.000544 | | | 0.90
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Nlocal: 2500 ave 2500 max 2500 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 405 ave 405 max 405 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 14487 ave 14487 max 14487 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 14487
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Ave neighs/atom = 5.7948
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Neighbor list builds = 25
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -0,0 +1,105 @@
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LAMMPS (3 Nov 2022)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
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# 2d Lennard-Jones melt
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units lj
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atom_style atomic
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dimension 2
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lattice sq 0.5
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Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
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region box block 0 50 0 50 -0.5 0.5
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create_box 1 box
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Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
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4 by 3 by 1 MPI processor grid
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create_atoms 1 box
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Created 2500 atoms
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using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
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create_atoms CPU = 0.000 seconds
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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fix 2 all enforce2d
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# load balancing
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comm_style tiled
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fix 100 all balance 100 0.9 rcb
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# fix ave/grid
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fix ave all ave/grid 10 10 100 10 10 1 vx vy
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# dump grid
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compute ave all property/grid 10 10 1 id ix iy
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#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
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#dump_modify ave sort 1
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#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count
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#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2]
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#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01
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# run
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thermo 100
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run 500
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Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 20 steps, delay = 0 steps, check = no
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 51 51 2
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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/2d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.546 | 2.573 | 2.595 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 1.44 -0.99804687 0 0.44137713 -0.58692863 5000
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100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000
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200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000
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300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000
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400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000
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500 1.6163874 -1.184699 0 0.43104185 1.346977 5000
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Loop time of 0.0234746 on 12 procs for 500 steps with 2500 atoms
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Performance: 9201451.891 tau/day, 21299.657 timesteps/s, 53.249 Matom-step/s
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99.2% CPU use with 12 MPI tasks x no 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 | 0.0037768 | 0.006317 | 0.0074702 | 1.7 | 26.91
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Neigh | 0.0010967 | 0.0013082 | 0.0014397 | 0.3 | 5.57
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Comm | 0.0096964 | 0.011159 | 0.0145 | 1.7 | 47.54
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Output | 9.5604e-05 | 0.00012067 | 0.00016341 | 0.0 | 0.51
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Modify | 0.0034389 | 0.0039338 | 0.0041602 | 0.4 | 16.76
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Other | | 0.0006358 | | | 2.71
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Nlocal: 208.333 ave 210 max 207 min
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Histogram: 2 0 0 6 0 0 2 0 0 2
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Nghost: 137.333 ave 155 max 121 min
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Histogram: 1 1 2 1 3 1 0 0 1 2
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Neighs: 1207.25 ave 1253 max 1169 min
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Histogram: 2 1 2 0 3 1 0 0 1 2
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Total # of neighbors = 14487
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Ave neighs/atom = 5.7948
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Neighbor list builds = 25
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Dangerous builds not checked
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Total wall time: 0:00:00
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@ -0,0 +1,105 @@
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LAMMPS (3 Nov 2022)
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WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
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# 2d Lennard-Jones melt
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units lj
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atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.5
|
||||
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||
region box block 0 50 0 50 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 2500 atoms
|
||||
using lattice units in orthogonal box = (0 0 -0.70710678) to (70.710678 70.710678 0.70710678)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 10 10 100 10 10 1 vx vy
|
||||
|
||||
# dump grid
|
||||
|
||||
compute ave all property/grid 10 10 1 id ix iy
|
||||
#dump ave all grid 100 tmp.dump.2d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
#dump vtk1 all grid/vtk 100 tmp.dump1.2d.*.vtr f_ave:grid:count
|
||||
|
||||
#dump vtk2 all grid/vtk 100 tmp.dump2.2d.*.vtr f_ave:grid:data[2]
|
||||
|
||||
#dump 10 all image 100 tmp.image.*.2d.png type type # zoom 1.6 grid f_ave:grid:count adiam 0.6 shiny 0.0 # subbox yes 0.01
|
||||
|
||||
# run
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 51 51 2
|
||||
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/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.555 | 2.556 | 2.557 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 -0.99804687 0 0.44137712 -0.58692863 5000
|
||||
100 1.5598149 -1.1263538 0 0.43283708 1.5290994 5000
|
||||
200 1.6032951 -1.1706712 0 0.43198254 1.3417115 5000
|
||||
300 1.6027535 -1.1702899 0 0.43182248 1.3590294 5000
|
||||
400 1.6099053 -1.1774853 0 0.43177606 1.3305193 5000
|
||||
500 1.6163874 -1.184699 0 0.43104185 1.346977 5000
|
||||
Loop time of 0.031365 on 4 procs for 500 steps with 2500 atoms
|
||||
|
||||
Performance: 6886659.462 tau/day, 15941.341 timesteps/s, 39.853 Matom-step/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0098202 | 0.01197 | 0.018294 | 3.3 | 38.16
|
||||
Neigh | 0.0023502 | 0.0025479 | 0.0030895 | 0.6 | 8.12
|
||||
Comm | 0.0046956 | 0.012744 | 0.015481 | 4.1 | 40.63
|
||||
Output | 5.6153e-05 | 6.3163e-05 | 7.3849e-05 | 0.0 | 0.20
|
||||
Modify | 0.0032687 | 0.0036046 | 0.0046066 | 1.0 | 11.49
|
||||
Other | | 0.0004358 | | | 1.39
|
||||
|
||||
Nlocal: 625 ave 627 max 623 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 212 ave 216 max 207 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Neighs: 3621.75 ave 3673 max 3585 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14487
|
||||
Ave neighs/atom = 5.7948
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,102 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 10 10 100 5 5 5 vx vy vz
|
||||
|
||||
# dump grid
|
||||
|
||||
compute ave all property/grid 5 5 5 id ix iy
|
||||
#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count
|
||||
|
||||
#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*]
|
||||
|
||||
#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01
|
||||
|
||||
# run
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
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) = 3.072 | 3.072 | 3.072 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137
|
||||
100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137
|
||||
200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137
|
||||
300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137
|
||||
400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137
|
||||
500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137
|
||||
Loop time of 0.531792 on 1 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 406174.160 tau/day, 940.218 timesteps/s, 3.761 Matom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.42996 | 0.42996 | 0.42996 | 0.0 | 80.85
|
||||
Neigh | 0.082407 | 0.082407 | 0.082407 | 0.0 | 15.50
|
||||
Comm | 0.007947 | 0.007947 | 0.007947 | 0.0 | 1.49
|
||||
Output | 8.9375e-05 | 8.9375e-05 | 8.9375e-05 | 0.0 | 0.02
|
||||
Modify | 0.009507 | 0.009507 | 0.009507 | 0.0 | 1.79
|
||||
Other | | 0.001879 | | | 0.35
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5657 ave 5657 max 5657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 149883 ave 149883 max 149883 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 149883
|
||||
Ave neighs/atom = 37.47075
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,103 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
1 by 2 by 5 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 10 10 100 5 5 5 vx vy vz
|
||||
|
||||
# dump grid
|
||||
|
||||
compute ave all property/grid 5 5 5 id ix iy
|
||||
#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count
|
||||
|
||||
#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*]
|
||||
|
||||
#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01
|
||||
|
||||
# run
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
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) = 2.613 | 2.651 | 2.686 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137
|
||||
100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137
|
||||
200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137
|
||||
300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137
|
||||
400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137
|
||||
500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137
|
||||
Loop time of 0.192284 on 10 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 1123340.176 tau/day, 2600.324 timesteps/s, 10.401 Matom-step/s
|
||||
94.0% CPU use with 10 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.059331 | 0.090145 | 0.11296 | 7.8 | 46.88
|
||||
Neigh | 0.0129 | 0.016371 | 0.019414 | 2.1 | 8.51
|
||||
Comm | 0.048952 | 0.07696 | 0.1131 | 9.9 | 40.02
|
||||
Output | 0.00012204 | 0.00013855 | 0.00019358 | 0.0 | 0.07
|
||||
Modify | 0.0053527 | 0.0062584 | 0.0070699 | 0.9 | 3.25
|
||||
Other | | 0.00241 | | | 1.25
|
||||
|
||||
Nlocal: 400 ave 402 max 398 min
|
||||
Histogram: 2 0 1 0 0 3 0 3 0 1
|
||||
Nghost: 1709.1 ave 1774 max 1663 min
|
||||
Histogram: 1 2 4 0 0 0 0 0 1 2
|
||||
Neighs: 14988.3 ave 15609 max 14496 min
|
||||
Histogram: 3 1 0 0 1 1 1 2 0 1
|
||||
|
||||
Total # of neighbors = 149883
|
||||
Ave neighs/atom = 37.47075
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,103 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 10 10 100 5 5 5 vx vy vz
|
||||
|
||||
# dump grid
|
||||
|
||||
compute ave all property/grid 5 5 5 id ix iy
|
||||
#dump ave all grid 100 tmp.dump.3d # c_ave:grid:data[*] f_ave:grid:count f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
#dump vtk1 all grid/vtk 100 tmp.dump1.3d.*.vtr f_ave:grid:count
|
||||
|
||||
#dump vtk2 all grid/vtk 100 tmp.dump2.3d.*.vtr f_ave:grid:data[*]
|
||||
|
||||
#dump 10 all image 100 tmp.image.*.3d.png type type # grid f_ave:grid:count view 60 -30 shiny 0.0 # subbox yes 0.01
|
||||
|
||||
# run
|
||||
|
||||
thermo 100
|
||||
|
||||
run 500
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 20 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 12 12 12
|
||||
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) = 2.748 | 2.797 | 2.844 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 -6.7733681 0 -4.6139081 -5.0199732 4738.2137
|
||||
100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 4738.2137
|
||||
200 0.75139921 -5.7500924 0 -4.6232753 0.25362795 4738.2137
|
||||
300 0.73979146 -5.7326964 0 -4.6232866 0.37781798 4738.2137
|
||||
400 0.73834687 -5.7300319 0 -4.6227884 0.41282909 4738.2137
|
||||
500 0.72941121 -5.7153612 0 -4.6215179 0.49793402 4738.2137
|
||||
Loop time of 0.198482 on 4 procs for 500 steps with 4000 atoms
|
||||
|
||||
Performance: 1088259.442 tau/day, 2519.119 timesteps/s, 10.076 Matom-step/s
|
||||
96.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.13322 | 0.13586 | 0.13838 | 0.5 | 68.45
|
||||
Neigh | 0.027201 | 0.027464 | 0.027811 | 0.1 | 13.84
|
||||
Comm | 0.025899 | 0.028681 | 0.031618 | 1.4 | 14.45
|
||||
Output | 7.6799e-05 | 8.8378e-05 | 0.00011635 | 0.0 | 0.04
|
||||
Modify | 0.0050217 | 0.0051246 | 0.0053789 | 0.2 | 2.58
|
||||
Other | | 0.001269 | | | 0.64
|
||||
|
||||
Nlocal: 1000 ave 1002 max 998 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 2797.75 ave 2810 max 2790 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 37470.8 ave 38366 max 36995 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 149883
|
||||
Ave neighs/atom = 37.47075
|
||||
Neighbor list builds = 25
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,193 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
# SPH water over dam
|
||||
|
||||
atom_style sph
|
||||
dimension 2
|
||||
newton on
|
||||
boundary s s p
|
||||
units lj
|
||||
|
||||
read_data data.sph
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15702 atoms
|
||||
reading velocities ...
|
||||
15702 velocities
|
||||
read_data CPU = 0.037 seconds
|
||||
|
||||
# upper limit of timestep based on CFL-like criterion
|
||||
# roughly estimate number of timesteps needed for 7.5 seconds
|
||||
|
||||
variable h equal 0.03
|
||||
variable c equal 10.0 # soundspeed for Tait's EOS
|
||||
variable dt equal 0.1*${h}/${c}
|
||||
variable dt equal 0.1*0.03/${c}
|
||||
variable dt equal 0.1*0.03/10
|
||||
variable nrun equal 15.0/${dt}
|
||||
variable nrun equal 15.0/0.0003
|
||||
|
||||
# assign group name "bc" to boundary particles (type 2)
|
||||
# assign group name "water" to water particles (type 1)
|
||||
|
||||
group bc type 2
|
||||
6000 atoms in group bc
|
||||
group water type 1
|
||||
9702 atoms in group water
|
||||
|
||||
# use hybrid pairstyle which does density summation
|
||||
# with cutoff ${h} every timestep (1)
|
||||
# use target density of 1000, soundspeed ${c} for Tait's EOS
|
||||
|
||||
pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
|
||||
pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03
|
||||
pair_coeff 1 1 sph/rhosum ${h}
|
||||
pair_coeff 1 1 sph/rhosum 0.03
|
||||
|
||||
# add gravity. This fix also computes potential energy of mass in gravity field
|
||||
|
||||
fix gfix water gravity -9.81 vector 0 1 0
|
||||
fix 2d_fix all enforce2d
|
||||
|
||||
compute rho_peratom all sph/rho/atom
|
||||
compute e_peratom all sph/e/atom
|
||||
compute esph all reduce sum c_e_peratom
|
||||
compute ke all ke
|
||||
variable etot equal c_esph+c_ke+f_gfix
|
||||
compute ke_peratom all ke/atom
|
||||
|
||||
# adjust nevery | min. allowed dt | max. allowed dt |
|
||||
# max. travel distance per dt
|
||||
# ${dt} ~= CFL criterion 0.1*h/c
|
||||
|
||||
# remove top atoms
|
||||
|
||||
region cut block INF INF 2.5 INF INF INF
|
||||
delete_atoms region cut
|
||||
Deleted 3174 atoms, new total = 12528
|
||||
|
||||
# use a variable timestep
|
||||
|
||||
fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box
|
||||
fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box
|
||||
|
||||
# time-integrate position, velocities,
|
||||
# internal energy and density of water particles
|
||||
|
||||
fix integrate_water_fix water sph
|
||||
|
||||
# time-integrate only internal energy and density of boundary particles
|
||||
|
||||
fix integrate_bc_fix bc sph/stationary
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix
|
||||
thermo_modify norm no
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 50 5 250 10 10 1 vx vy
|
||||
|
||||
# dump particles
|
||||
|
||||
#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom
|
||||
#dump_modify dump_id first yes
|
||||
|
||||
# dump grid
|
||||
|
||||
#compute ave all property/grid 10 10 1 id ix iy
|
||||
#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
# dump image
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
|
||||
#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count
|
||||
#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red"
|
||||
#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors}
|
||||
|
||||
# run
|
||||
|
||||
neigh_modify every 5 delay 0 check no
|
||||
variable skin equal 0.3*${h}
|
||||
variable skin equal 0.3*0.03
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.009 bin
|
||||
|
||||
run 6000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.039
|
||||
ghost atom cutoff = 0.039
|
||||
binsize = 0.0195, bins = 205 411 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair sph/rhosum, perpetual, skip from (3)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair sph/taitwater, perpetual, half/full from (3)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.755 | 6.755 | 6.755 Mbytes
|
||||
Step KinEng c_esph v_etot f_gfix Press Time f_dtfix
|
||||
0 0 0 19320.854 19320.854 -3.624517 0 0
|
||||
500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500
|
||||
1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000
|
||||
1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500
|
||||
2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000
|
||||
2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500
|
||||
3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000
|
||||
3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500
|
||||
4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000
|
||||
4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500
|
||||
5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000
|
||||
5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500
|
||||
6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000
|
||||
Loop time of 22.4589 on 1 procs for 6000 steps with 12528 atoms
|
||||
|
||||
Performance: 1919.324 tau/day, 267.155 timesteps/s, 3.347 Matom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.365 | 15.365 | 15.365 | 0.0 | 68.41
|
||||
Neigh | 5.2774 | 5.2774 | 5.2774 | 0.0 | 23.50
|
||||
Comm | 0.021675 | 0.021675 | 0.021675 | 0.0 | 0.10
|
||||
Output | 0.0011944 | 0.0011944 | 0.0011944 | 0.0 | 0.01
|
||||
Modify | 1.6991 | 1.6991 | 1.6991 | 0.0 | 7.57
|
||||
Other | | 0.09478 | | | 0.42
|
||||
|
||||
Nlocal: 12528 ave 12528 max 12528 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: 153317 ave 153317 max 153317 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 153317
|
||||
Ave neighs/atom = 12.237947
|
||||
Neighbor list builds = 1200
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:22
|
||||
|
|
@ -0,0 +1,194 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
|
||||
# SPH water over dam
|
||||
|
||||
atom_style sph
|
||||
dimension 2
|
||||
newton on
|
||||
boundary s s p
|
||||
units lj
|
||||
|
||||
read_data data.sph
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001)
|
||||
3 by 4 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15702 atoms
|
||||
reading velocities ...
|
||||
15702 velocities
|
||||
read_data CPU = 0.075 seconds
|
||||
|
||||
# upper limit of timestep based on CFL-like criterion
|
||||
# roughly estimate number of timesteps needed for 7.5 seconds
|
||||
|
||||
variable h equal 0.03
|
||||
variable c equal 10.0 # soundspeed for Tait's EOS
|
||||
variable dt equal 0.1*${h}/${c}
|
||||
variable dt equal 0.1*0.03/${c}
|
||||
variable dt equal 0.1*0.03/10
|
||||
variable nrun equal 15.0/${dt}
|
||||
variable nrun equal 15.0/0.0003
|
||||
|
||||
# assign group name "bc" to boundary particles (type 2)
|
||||
# assign group name "water" to water particles (type 1)
|
||||
|
||||
group bc type 2
|
||||
6000 atoms in group bc
|
||||
group water type 1
|
||||
9702 atoms in group water
|
||||
|
||||
# use hybrid pairstyle which does density summation
|
||||
# with cutoff ${h} every timestep (1)
|
||||
# use target density of 1000, soundspeed ${c} for Tait's EOS
|
||||
|
||||
pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
|
||||
pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03
|
||||
pair_coeff 1 1 sph/rhosum ${h}
|
||||
pair_coeff 1 1 sph/rhosum 0.03
|
||||
|
||||
# add gravity. This fix also computes potential energy of mass in gravity field
|
||||
|
||||
fix gfix water gravity -9.81 vector 0 1 0
|
||||
fix 2d_fix all enforce2d
|
||||
|
||||
compute rho_peratom all sph/rho/atom
|
||||
compute e_peratom all sph/e/atom
|
||||
compute esph all reduce sum c_e_peratom
|
||||
compute ke all ke
|
||||
variable etot equal c_esph+c_ke+f_gfix
|
||||
compute ke_peratom all ke/atom
|
||||
|
||||
# adjust nevery | min. allowed dt | max. allowed dt |
|
||||
# max. travel distance per dt
|
||||
# ${dt} ~= CFL criterion 0.1*h/c
|
||||
|
||||
# remove top atoms
|
||||
|
||||
region cut block INF INF 2.5 INF INF INF
|
||||
delete_atoms region cut
|
||||
Deleted 3174 atoms, new total = 12528
|
||||
|
||||
# use a variable timestep
|
||||
|
||||
fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box
|
||||
fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box
|
||||
|
||||
# time-integrate position, velocities,
|
||||
# internal energy and density of water particles
|
||||
|
||||
fix integrate_water_fix water sph
|
||||
|
||||
# time-integrate only internal energy and density of boundary particles
|
||||
|
||||
fix integrate_bc_fix bc sph/stationary
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix
|
||||
thermo_modify norm no
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 50 5 250 10 10 1 vx vy
|
||||
|
||||
# dump particles
|
||||
|
||||
#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom
|
||||
#dump_modify dump_id first yes
|
||||
|
||||
# dump grid
|
||||
|
||||
#compute ave all property/grid 10 10 1 id ix iy
|
||||
#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
# dump image
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
|
||||
#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count
|
||||
#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red"
|
||||
#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors}
|
||||
|
||||
# run
|
||||
|
||||
neigh_modify every 5 delay 0 check no
|
||||
variable skin equal 0.3*${h}
|
||||
variable skin equal 0.3*0.03
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.009 bin
|
||||
|
||||
run 6000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.039
|
||||
ghost atom cutoff = 0.039
|
||||
binsize = 0.0195, bins = 205 411 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair sph/rhosum, perpetual, skip from (3)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair sph/taitwater, perpetual, half/full from (3)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.06 | 5.302 | 6.72 Mbytes
|
||||
Step KinEng c_esph v_etot f_gfix Press Time f_dtfix
|
||||
0 0 0 19320.854 19320.854 -3.624517 0 0
|
||||
500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500
|
||||
1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000
|
||||
1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500
|
||||
2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000
|
||||
2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500
|
||||
3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000
|
||||
3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500
|
||||
4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000
|
||||
4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500
|
||||
5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000
|
||||
5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500
|
||||
6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000
|
||||
Loop time of 5.47224 on 12 procs for 6000 steps with 12528 atoms
|
||||
|
||||
Performance: 7877.181 tau/day, 1096.443 timesteps/s, 13.736 Matom-step/s
|
||||
99.2% CPU use with 12 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.8469 | 3.1632 | 3.4316 | 11.3 | 57.80
|
||||
Neigh | 0.56431 | 0.78494 | 0.95346 | 14.2 | 14.34
|
||||
Comm | 0.4559 | 0.89439 | 1.4747 | 35.4 | 16.34
|
||||
Output | 0.0005864 | 0.00060563 | 0.00074071 | 0.0 | 0.01
|
||||
Modify | 0.51006 | 0.57563 | 0.65636 | 4.9 | 10.52
|
||||
Other | | 0.05352 | | | 0.98
|
||||
|
||||
Nlocal: 1044 ave 1046 max 1043 min
|
||||
Histogram: 2 0 0 9 0 0 0 0 0 1
|
||||
Nghost: 244.75 ave 320 max 120 min
|
||||
Histogram: 2 1 0 1 0 0 1 1 1 5
|
||||
Neighs: 12776.4 ave 16885 max 9467 min
|
||||
Histogram: 1 1 1 2 3 1 0 2 0 1
|
||||
|
||||
Total # of neighbors = 153317
|
||||
Ave neighs/atom = 12.237947
|
||||
Neighbor list builds = 1200
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:05
|
||||
|
|
@ -0,0 +1,194 @@
|
|||
LAMMPS (3 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
|
||||
# SPH water over dam
|
||||
|
||||
atom_style sph
|
||||
dimension 2
|
||||
newton on
|
||||
boundary s s p
|
||||
units lj
|
||||
|
||||
read_data data.sph
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -0.001) to (4.001 8.001 0.001)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15702 atoms
|
||||
reading velocities ...
|
||||
15702 velocities
|
||||
read_data CPU = 0.043 seconds
|
||||
|
||||
# upper limit of timestep based on CFL-like criterion
|
||||
# roughly estimate number of timesteps needed for 7.5 seconds
|
||||
|
||||
variable h equal 0.03
|
||||
variable c equal 10.0 # soundspeed for Tait's EOS
|
||||
variable dt equal 0.1*${h}/${c}
|
||||
variable dt equal 0.1*0.03/${c}
|
||||
variable dt equal 0.1*0.03/10
|
||||
variable nrun equal 15.0/${dt}
|
||||
variable nrun equal 15.0/0.0003
|
||||
|
||||
# assign group name "bc" to boundary particles (type 2)
|
||||
# assign group name "water" to water particles (type 1)
|
||||
|
||||
group bc type 2
|
||||
6000 atoms in group bc
|
||||
group water type 1
|
||||
9702 atoms in group water
|
||||
|
||||
# use hybrid pairstyle which does density summation
|
||||
# with cutoff ${h} every timestep (1)
|
||||
# use target density of 1000, soundspeed ${c} for Tait's EOS
|
||||
|
||||
pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
|
||||
pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 ${h}
|
||||
pair_coeff * * sph/taitwater 1000.0 10 1.0 0.03
|
||||
pair_coeff 1 1 sph/rhosum ${h}
|
||||
pair_coeff 1 1 sph/rhosum 0.03
|
||||
|
||||
# add gravity. This fix also computes potential energy of mass in gravity field
|
||||
|
||||
fix gfix water gravity -9.81 vector 0 1 0
|
||||
fix 2d_fix all enforce2d
|
||||
|
||||
compute rho_peratom all sph/rho/atom
|
||||
compute e_peratom all sph/e/atom
|
||||
compute esph all reduce sum c_e_peratom
|
||||
compute ke all ke
|
||||
variable etot equal c_esph+c_ke+f_gfix
|
||||
compute ke_peratom all ke/atom
|
||||
|
||||
# adjust nevery | min. allowed dt | max. allowed dt |
|
||||
# max. travel distance per dt
|
||||
# ${dt} ~= CFL criterion 0.1*h/c
|
||||
|
||||
# remove top atoms
|
||||
|
||||
region cut block INF INF 2.5 INF INF INF
|
||||
delete_atoms region cut
|
||||
Deleted 3174 atoms, new total = 12528
|
||||
|
||||
# use a variable timestep
|
||||
|
||||
fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box
|
||||
fix dtfix all dt/reset 1 NULL 0.0003 0.0005 units box
|
||||
|
||||
# time-integrate position, velocities,
|
||||
# internal energy and density of water particles
|
||||
|
||||
fix integrate_water_fix water sph
|
||||
|
||||
# time-integrate only internal energy and density of boundary particles
|
||||
|
||||
fix integrate_bc_fix bc sph/stationary
|
||||
|
||||
thermo 500
|
||||
thermo_style custom step ke c_esph v_etot f_gfix press time f_dtfix
|
||||
thermo_modify norm no
|
||||
|
||||
# load balancing
|
||||
|
||||
comm_style tiled
|
||||
fix 100 all balance 100 0.9 rcb
|
||||
|
||||
# fix ave/grid
|
||||
|
||||
fix ave all ave/grid 50 5 250 10 10 1 vx vy
|
||||
|
||||
# dump particles
|
||||
|
||||
#dump dump_id all custom 100 tmp.dump # id type x y z c_ke_peratom
|
||||
#dump_modify dump_id first yes
|
||||
|
||||
# dump grid
|
||||
|
||||
#compute ave all property/grid 10 10 1 id ix iy
|
||||
#dump ave all grid 250 tmp.grid c_ave:grid:data[*] f_ave:grid:data[*]
|
||||
#dump_modify ave sort 1
|
||||
|
||||
# dump image
|
||||
|
||||
#compute 1 all property/atom proc
|
||||
#variable p atom c_1%10
|
||||
|
||||
#dump 3 all image 500 tmp.*.png c_ke_peratom type # adiam 0.015 view 0 0 zoom 2.5 subbox yes 0.01 # center d 0.5 0.5 0.5 size 1024 768 box no 0.0 # grid f_ave:grid:count
|
||||
#variable colors string # "min blue 0.25 green 0.5 orange 0.75 yellow max red"
|
||||
#dump_modify 3 pad 5 amap 0 1.5 cf 1 5 ${colors}
|
||||
|
||||
# run
|
||||
|
||||
neigh_modify every 5 delay 0 check no
|
||||
variable skin equal 0.3*${h}
|
||||
variable skin equal 0.3*0.03
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.009 bin
|
||||
|
||||
run 6000
|
||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 5 steps, delay = 0 steps, check = no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.039
|
||||
ghost atom cutoff = 0.039
|
||||
binsize = 0.0195, bins = 205 411 1
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair sph/rhosum, perpetual, skip from (3)
|
||||
attributes: full, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(2) pair sph/taitwater, perpetual, half/full from (3)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) neighbor class addition, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/2d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.607 | 5.957 | 6.474 Mbytes
|
||||
Step KinEng c_esph v_etot f_gfix Press Time f_dtfix
|
||||
0 0 0 19320.854 19320.854 -3.624517 0 0
|
||||
500 1274.8192 226.44643 19320.367 17819.101 754.35811 0.14057754 500
|
||||
1000 2793.9358 410.18897 19320.367 16116.242 1184.8364 0.21912692 1000
|
||||
1500 4227.2566 547.60309 19320.367 14545.508 1290.9567 0.27943572 1500
|
||||
2000 5515.6545 763.42902 19320.367 13041.284 1468.5449 0.33279685 2000
|
||||
2500 6595.5906 1087.0212 19320.368 11637.756 1878.9882 0.38198106 2500
|
||||
3000 7053.147 1574.0538 19320.369 10693.168 2250.759 0.41605101 3000
|
||||
3500 7396.4079 2058.4224 19320.369 9865.539 2517.1665 0.45034972 3500
|
||||
4000 7690.0468 2419.389 19320.369 9210.9336 2615.8142 0.48685712 4000
|
||||
4500 7986.5331 2529.7094 19320.369 8804.1268 2453.9595 0.52464306 4500
|
||||
5000 8206.3658 2497.1242 19320.369 8616.879 1998.6296 0.56308208 5000
|
||||
5500 8264.0602 2487.5778 19320.369 8568.7309 1614.3683 0.60225589 5500
|
||||
6000 8185.7128 2570.3178 19320.369 8564.3383 1463.8307 0.64295437 6000
|
||||
Loop time of 8.44486 on 4 procs for 6000 steps with 12528 atoms
|
||||
|
||||
Performance: 5104.390 tau/day, 710.492 timesteps/s, 8.901 Matom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.3618 | 5.4752 | 5.5857 | 3.5 | 64.83
|
||||
Neigh | 1.607 | 1.7333 | 1.8496 | 6.6 | 20.53
|
||||
Comm | 0.36438 | 0.60163 | 0.70886 | 18.0 | 7.12
|
||||
Output | 0.00062026 | 0.00064412 | 0.00071499 | 0.0 | 0.01
|
||||
Modify | 0.57676 | 0.59785 | 0.60941 | 1.6 | 7.08
|
||||
Other | | 0.03618 | | | 0.43
|
||||
|
||||
Nlocal: 3132 ave 3134 max 3131 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Nghost: 248.25 ave 333 max 165 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 38329.2 ave 41127 max 35425 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 153317
|
||||
Ave neighs/atom = 12.237947
|
||||
Neighbor list builds = 1200
|
||||
Dangerous builds not checked
|
||||
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -40,10 +40,22 @@ thermo 100
|
|||
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
|
||||
thermo_modify format float "%20.16g"
|
||||
|
||||
compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
|
||||
dump ave all grid 500 tmp.dump.ave &
|
||||
c_10:grid:data[*] f_ave:grid:data
|
||||
dump_modify ave sort 1
|
||||
# dump output
|
||||
|
||||
#compute 1 all property/grid 10 10 10 id ix iy iz
|
||||
#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
|
||||
#dump_modify 1 sort 1
|
||||
|
||||
#compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
|
||||
|
||||
#dump ave all grid 100 tmp.dump.ave &
|
||||
# c_10:grid:data[*] f_ave:grid:data
|
||||
#dump_modify ave sort id
|
||||
|
||||
#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
|
||||
#dump_modify vtk sort id buffer no
|
||||
|
||||
# run simulation
|
||||
|
||||
run 1000
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (3 Aug 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
units metal
|
||||
atom_style atomic
|
||||
boundary p p p
|
||||
|
|
@ -34,7 +34,7 @@ region atom_box block -10 10 -10 10 -10 10 units lattice
|
|||
create_atoms 1 region atom_box
|
||||
Created 16000 atoms
|
||||
using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7)
|
||||
create_atoms CPU = 0.004 seconds
|
||||
create_atoms CPU = 0.002 seconds
|
||||
|
||||
mass 1 55.845
|
||||
|
||||
|
|
@ -58,9 +58,22 @@ thermo 100
|
|||
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
|
||||
thermo_modify format float "%20.16g"
|
||||
|
||||
compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
|
||||
dump ave all grid 500 tmp.dump.ave c_10:grid:data[*] f_ave:grid:data
|
||||
# dump output
|
||||
|
||||
#compute 1 all property/grid 10 10 10 id ix iy iz
|
||||
#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
|
||||
#dump_modify 1 sort 1
|
||||
|
||||
#compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
|
||||
|
||||
#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data
|
||||
#dump_modify ave sort id
|
||||
|
||||
#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
|
||||
#dump_modify vtk sort id buffer no
|
||||
|
||||
# run simulation
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
|
|
@ -75,7 +88,7 @@ Neighbor list info ...
|
|||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.99 | 10.99 | 10.99 Mbytes
|
||||
Step Temp TotEng f_twotemp[1] f_twotemp[2]
|
||||
0 0 -68483.52254543516 371.9188105082105 0
|
||||
100 17.01353086098387 -68446.50228930202 334.6217068813629 0.3763710887774046
|
||||
|
|
@ -88,20 +101,20 @@ Per MPI rank memory allocation (min/avg/max) = 12.09 | 12.09 | 12.09 Mbytes
|
|||
800 50.4375018189932 -68272.72651051797 160.995046695269 0.1708386295858845
|
||||
900 52.17011714635106 -68257.85059865142 146.1567281868867 0.1032829304640776
|
||||
1000 53.49296457217382 -68244.38715993936 132.7166474251702 0.06428993394665769
|
||||
Loop time of 15.6373 on 1 procs for 1000 steps with 16000 atoms
|
||||
Loop time of 5.99191 on 1 procs for 1000 steps with 16000 atoms
|
||||
|
||||
Performance: 0.553 ns/day, 43.437 hours/ns, 63.950 timesteps/s
|
||||
Performance: 1.442 ns/day, 16.644 hours/ns, 166.892 timesteps/s, 2.670 Matom-step/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.493 | 14.493 | 14.493 | 0.0 | 92.68
|
||||
Pair | 5.3136 | 5.3136 | 5.3136 | 0.0 | 88.68
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.088097 | 0.088097 | 0.088097 | 0.0 | 0.56
|
||||
Output | 0.0044447 | 0.0044447 | 0.0044447 | 0.0 | 0.03
|
||||
Modify | 1.0075 | 1.0075 | 1.0075 | 0.0 | 6.44
|
||||
Other | | 0.04433 | | | 0.28
|
||||
Comm | 0.035738 | 0.035738 | 0.035738 | 0.0 | 0.60
|
||||
Output | 0.00049119 | 0.00049119 | 0.00049119 | 0.0 | 0.01
|
||||
Modify | 0.62365 | 0.62365 | 0.62365 | 0.0 | 10.41
|
||||
Other | | 0.01844 | | | 0.31
|
||||
|
||||
Nlocal: 16000 ave 16000 max 16000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -114,4 +127,4 @@ Total # of neighbors = 896000
|
|||
Ave neighs/atom = 56
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:15
|
||||
Total wall time: 0:00:06
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
LAMMPS (3 Aug 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:524)
|
||||
LAMMPS (3 Nov 2022)
|
||||
WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:528)
|
||||
units metal
|
||||
atom_style atomic
|
||||
boundary p p p
|
||||
|
|
@ -35,7 +35,7 @@ region atom_box block -10 10 -10 10 -10 10 units lattice
|
|||
create_atoms 1 region atom_box
|
||||
Created 16000 atoms
|
||||
using lattice units in orthogonal box = (-28.7 -28.7 -28.7) to (28.7 28.7 28.7)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass 1 55.845
|
||||
|
||||
|
|
@ -59,10 +59,22 @@ thermo 100
|
|||
thermo_style custom step temp etotal f_twotemp[1] f_twotemp[2]
|
||||
thermo_modify format float "%20.16g"
|
||||
|
||||
compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
fix ave all ave/grid 100 5 500 10 10 10 f_twotemp:grid:data
|
||||
dump ave all grid 500 tmp.dump.ave c_10:grid:data[*] f_ave:grid:data
|
||||
dump_modify ave sort 1
|
||||
# dump output
|
||||
|
||||
#compute 1 all property/grid 10 10 10 id ix iy iz
|
||||
#dump 1 all grid 100 tmp.dump c_1:grid:data[*] f_twotemp:grid:data
|
||||
#dump_modify 1 sort 1
|
||||
|
||||
#compute 10 all property/grid 10 10 10 id xc yc zc
|
||||
#fix ave all ave/grid 10 10 100 10 10 10 f_twotemp:grid:data
|
||||
|
||||
#dump ave all grid 100 tmp.dump.ave # c_10:grid:data[*] f_ave:grid:data
|
||||
#dump_modify ave sort id
|
||||
|
||||
#dump vtk all grid/vtk 100 tmp.dump.*.vtk f_ave:grid:data
|
||||
#dump_modify vtk sort id buffer no
|
||||
|
||||
# run simulation
|
||||
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
|
|
@ -77,7 +89,7 @@ Neighbor list info ...
|
|||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.903 | 5.904 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.843 | 4.843 | 4.843 Mbytes
|
||||
Step Temp TotEng f_twotemp[1] f_twotemp[2]
|
||||
0 0 -68483.52254530673 371.9188105082186 0
|
||||
100 16.95536995775684 -68446.64765713879 334.7745598327931 0.3602932995006087
|
||||
|
|
@ -90,20 +102,20 @@ Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.903 | 5.904 Mbytes
|
|||
800 49.66707856481075 -68274.98092841901 163.2540575286425 0.1600890300738265
|
||||
900 52.17692450487317 -68259.8031091165 148.1017576370548 0.1177316234407941
|
||||
1000 54.24228199265479 -68245.58589458198 133.8816957314364 0.1314999893461343
|
||||
Loop time of 4.78682 on 4 procs for 1000 steps with 16000 atoms
|
||||
Loop time of 2.16917 on 4 procs for 1000 steps with 16000 atoms
|
||||
|
||||
Performance: 1.805 ns/day, 13.297 hours/ns, 208.907 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 3.983 ns/day, 6.025 hours/ns, 461.006 timesteps/s, 7.376 Matom-step/s
|
||||
97.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1562 | 4.2154 | 4.2851 | 2.7 | 88.06
|
||||
Pair | 1.8638 | 1.8826 | 1.9014 | 1.0 | 86.79
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.16658 | 0.23631 | 0.29566 | 11.5 | 4.94
|
||||
Output | 0.0016285 | 0.0016618 | 0.0017414 | 0.1 | 0.03
|
||||
Modify | 0.31425 | 0.31577 | 0.31755 | 0.2 | 6.60
|
||||
Other | | 0.01766 | | | 0.37
|
||||
Comm | 0.057938 | 0.076258 | 0.094755 | 4.8 | 3.52
|
||||
Output | 0.00020722 | 0.00022911 | 0.00029186 | 0.0 | 0.01
|
||||
Modify | 0.20222 | 0.20238 | 0.20256 | 0.0 | 9.33
|
||||
Other | | 0.007738 | | | 0.36
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -116,4 +128,4 @@ Total # of neighbors = 896000
|
|||
Ave neighs/atom = 56
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:04
|
||||
Total wall time: 0:00:02
|
||||
Loading…
Reference in New Issue