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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6836 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-08-27 20:08:16 +00:00
parent 3179014485
commit 91f4940250
11 changed files with 32261 additions and 0 deletions
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1
examples/USER/sph/README Normal file
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see the USER-SPH user's guide for a detailed explanation of these examples.

63
examples/USER/sph/cavity_flow/cavity_flow.lmp Normal file
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dimension 2
units si
atom_style meso
# create simulation box
region box block -0.050e-3 1.044e-3 -0.05e-3 1.044e-3 -1.0e-6 1.0e-6 units box
create_box 3 box
# create fluid particles
region fluid block 0.0001e-3 0.999e-3 0.0001e-3 0.999e-3 EDGE EDGE side in units box
lattice sq 0.025e-3
create_atoms 1 region fluid
# create bottom, left, and right wall
region walls block 0.0001e-3 0.999e-3 0.0001e-3 EDGE EDGE EDGE side out units box
lattice sq2 0.025e-3
create_atoms 2 region walls
# create a driver strip of particles, which exerts shear forces on the fluid
region driver block EDGE EDGE 0.999e-3 EDGE EDGE EDGE side in units box
create_atoms 3 region driver
group fluid type 1
group walls type 2
group driver type 3
group integrate_full union fluid driver
mass 3 2.0e-7
mass 2 2.0e-7
mass 1 4.0e-7
set group all meso_rho 1000.0
# use Tait's EOS in combination with Morris' laminar viscosity.
# We set rho_0 = 1000 kg/m^3, c = 0.1 m/s, h = 6.5e-5 m.
# The dynamic viscosity is set to 1.0e-3 Pa s, corresponding to a kinematic viscosity of 1.0e-6 m^2/s
pair_style hybrid sph/taitwater/morris
pair_coeff * * sph/taitwater/morris 1000 0.1 1.0e-3 6.5e-5
pair_coeff 2 3 none # exclude interaction between walls and shear driver
compute rho_peratom all meso_rho/atom
compute e_peratom all meso_e/atom
compute ke_peratom all ke/atom
compute esph all reduce sum c_e_peratom
compute ke all ke
variable etot equal c_ke+c_esph
# assign a constant velocity to shear driver
velocity driver set 0.001 0.0 0.0 units box
fix freeze_fix driver setforce 0.0 0.0 0.0
# do full time integration for shear driver and fluid, but keep walls stationary
fix integrate_fix_full integrate_full meso
fix integrate_fix_stationary walls meso/stationary
dump dump_id all custom 100 dump.lammpstrj id type xs ys zs vx vy c_rho_peratom c_e_peratom
dump_modify dump_id first yes
thermo 100
thermo_style custom step c_esph v_etot
thermo_modify norm no
neighbor 3.0e-6 bin
timestep 5.0e-5
run 4000

24
examples/USER/sph/heatconduction/compare_analytic.gpl Executable file
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#!/usr/bin/gnuplot
# compare sph/heatconduction output with analytic solution to diffusion equation
alpha = 1.0e-4
time = 4.0
analytic_profile(x) = 1.5 + 0.5*erf((x-49.5e-2)/sqrt(4.0*alpha*time))
set ylabel "internal energy per particle"
set xlabel "x position [m]"
plot [][0.5:2.5]'dump.last' u 3:6 ti "SPH simulation", analytic_profile(x) ti "analytic solution"
pause -1
#set terminal postscript color enhanced lw 2
#set out "heat_profile.ps"
set table "simu.dat"
plot [0:1][0.5:2.5]'dump.last' u 3:6
set table "analytic.dat"
set samples 1000
plot [0:1][0.5:2.5] analytic_profile(x)
#replot

51
examples/USER/sph/heatconduction/sph_heat_conduction_2d.lmp Normal file
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# mesoscopic heat conduction
# heat flow from hot right region to cold left region
# compare the temperature profile at the end opf the simulation,
# contained in file dump.last, to analytic solution.
#
#
dimension 2
units si
atom_style meso
boundary f p p
lattice sq 0.01
region box block 0 100 0 10 0 0.1
create_box 1 box
create_atoms 1 box
mass 1 1.0e-5
region left block EDGE 49.9 EDGE EDGE EDGE EDGE
region right block 50 EDGE EDGE EDGE EDGE EDGE
set region left meso_e 1.0 # internal energies
set region right meso_e 2.0
set group all meso_rho 0.1 # mesoscopic density is also needed for this pair style
# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
pair_style sph/heatconduction
# i j diffusion coeff. cutoff
pair_coeff 1 1 1.0e-4 2.0e-2
compute ie_atom all meso_e/atom
compute ie all reduce sum c_ie_atom
thermo 10
thermo_style custom step temp c_ie
timestep 0.25e-1
neighbor 0.2e-2 bin
fix integrate_fix all meso/stationary
dump dump_fix all custom 10 dump.heat id type x y z c_ie_atom
dump_modify dump_fix first yes
run 160
undump dump_fix
dump dump_fix all custom 10 dump.last id type x y z c_ie_atom
dump_modify dump_fix first yes
run 0
undump dump_fix
dump dump_fix all custom 10 dump.last.xs id type xs ys zs c_ie_atom
dump_modify dump_fix first yes
run 0
undump dump_fix

49
examples/USER/sph/heatconduction/sph_heat_conduction_3d.lmp Normal file
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# mesoscopic heat conduction
# heat flow from hot right region to cold left region
# compare the temperature profile at the end opf the simulation,
# contained in file dump.last, to analytic solution.
#
#
units si
atom_style meso
newton on
boundary f p p
lattice sc 0.01
region box block 0 100 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0e-5
region left block EDGE 49.9 EDGE EDGE EDGE EDGE
region right block 50 EDGE EDGE EDGE EDGE EDGE
set region left meso_e 1.0 # internal energies
set region right meso_e 2.0
set group all meso_rho 10.0 # mesoscopic density is also needed for this pair style
# For correct temperature profiles, mescoscopic density and mass * number density must coincide!
pair_style sph/heatconduction
# i j diffusion coeff. cutoff
pair_coeff 1 1 1.0e-4 2.0e-2
neighbor 0.2e-2 bin
neigh_modify every 20 delay 0 check no
compute ie_atom all meso_e/atom
compute ie all reduce sum c_ie_atom
thermo_style custom step temp c_ie
thermo_modify norm no
fix integrate_fix all meso/stationary
thermo 10
timestep 0.25e-1
dump dump_fix all custom 10 dump.heat id type x y z c_ie_atom
dump_modify dump_fix first yes
run 160
undump dump_fix
dump dump_fix all custom 10 dump.last id type x y z c_ie_atom
dump_modify dump_fix first yes
run 0

6
examples/USER/sph/shock_tube/compare_exact.gpl Executable file
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#!/usr/bin/gnuplot
# compare SPH shock output with exact solution
plot 'dump.3d.last' u 3:6, "exact_solution.dat" w l
pause -1

501
examples/USER/sph/shock_tube/exact_solution.dat Executable file
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3.880000E+01 2.500000E-01 0.000000E+00 2.500000E-01
3.900000E+01 2.500000E-01 0.000000E+00 2.500000E-01
3.920000E+01 2.500000E-01 0.000000E+00 2.500000E-01
3.940000E+01 2.500000E-01 0.000000E+00 2.500000E-01
3.960000E+01 2.500000E-01 0.000000E+00 2.500000E-01
3.980000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.000000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.020000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.040000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.060000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.080000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.100000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.120000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.140000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.160000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.180000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.200000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.220000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.240000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.260000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.280000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.300000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.320000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.340000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.360000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.380000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.400000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.420000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.440000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.460000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.480000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.500000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.520000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.540000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.560000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.580000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.600000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.620000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.640000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.660000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.680000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.700000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.720000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.740000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.760000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.780000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.800000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.820000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.840000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.860000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.880000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.900000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.920000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.940000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.960000E+01 2.500000E-01 0.000000E+00 2.500000E-01
4.980000E+01 2.500000E-01 0.000000E+00 2.500000E-01
5.000000E+01 2.500000E-01 0.000000E+00 2.500000E-01

45
examples/USER/sph/shock_tube/shock2d.lmp Executable file
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atom_style meso
dimension 2
boundary s p p
region box block -100 150 -4 4 -0.1 0.1 units box
create_box 2 box
lattice sq 1.0
create_atoms 1 box
region left block EDGE 0.0 EDGE EDGE EDGE EDGE units box
region right block 1 EDGE EDGE EDGE EDGE EDGE units box
set region right type 2
mass 1 1
mass 2 0.25
set type 1 meso_e 2.5 # internal energy corresponding to p=1, rho=1
set type 2 meso_e 0.625 # internal energy corresponding to p=0.25, rho=0.25
set type 1 meso_rho 1.0
set type 2 meso_rho 0.25
pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
pair_coeff * * sph/rhosum 4.0
pair_coeff * * sph/idealgas 0.75 4.0
compute rhoatom all meso_rho/atom
compute ieatom all meso_e/atom
compute emeso all reduce sum c_ieatom # total internal energy
compute ke all ke
variable etot equal c_ke+c_emeso # total energy
# dump positions and local density
dump dump_id all custom 100 dump.2d id type x z y c_rhoatom
dump_modify dump_id first yes
neighbor 0.5 bin
neigh_modify every 5 delay 0 check yes
thermo 10
thermo_style custom step c_ke c_emeso v_etot
thermo_modify norm no
fix integration_fix all meso
fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
timestep 0.05
log log.2d
run 400 # run for t=20

48
examples/USER/sph/shock_tube/shock3d.lmp Normal file
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atom_style meso
boundary s p p
region box block -100 150 -4 4 -4 4 units box
create_box 2 box
lattice sc 1.0
create_atoms 1 box
region left block EDGE 0.0 EDGE EDGE EDGE EDGE units box
region right block 1 EDGE EDGE EDGE EDGE EDGE units box
set region right type 2
mass 1 1
mass 2 0.25
set type 1 meso_e 2.5 # internal energy corresponding to p=1, rho=1
set type 2 meso_e 0.625 # internal energy corresponding to p=0.25, rho=0.25
set type 1 meso_rho 1.0
set type 2 meso_rho 0.25
pair_style hybrid/overlay sph/rhosum 1 sph/idealgas
pair_coeff * * sph/rhosum 4.0
pair_coeff * * sph/idealgas 0.75 4.0
compute rhoatom all meso_rho/atom
compute ieatom all meso_e/atom
compute emeso all reduce sum c_ieatom # total internal energy
compute ke all ke
variable etot equal c_ke+c_emeso # total energy
# dump positions and local density
dump dump_id all custom 100 dump.3d id type x z y c_rhoatom
dump_modify dump_id first yes
neighbor 0.5 bin
neigh_modify every 5 delay 0 check yes
thermo 10
thermo_style custom step c_ke c_emeso v_etot
thermo_modify norm no
fix integration_fix all meso
fix 1 all setforce NULL 0.0 0.0 # treat as a quasi 1d problem
timestep 0.05
log log.3d
run 400 # run for t=20
undump dump_id
dump dump_id all custom 100 dump.3d.last id type x z y c_rhoatom
run 0

31424
examples/USER/sph/water_collapse/data.initial Normal file
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49
examples/USER/sph/water_collapse/water_collapse.lmp Normal file
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processors 4 1 1 # manually assign processors to spatial regions
atom_style meso
dimension 2
newton on
boundary f f p
units lj
read_data data.initial
variable h equal 0.03
variable c equal 10.0 # soundspeed for Tait's EOS
variable dt equal 0.1*${h}/${c} # upper limit of timestep based on CFL-like criterion
variable nrun equal 15.0/${dt} # roughly estimate number of timesteps needed for 7.5 seconds
group bc type 2 # assign group name "bc" to boundary particles (type 2)
group water type 1 # assign group name "water" to water particles (type 1)
# use hybrid pairstyle which does density summation with cutoff ${h} every timestep (1)
pair_style hybrid/overlay sph/rhosum 1 sph/taitwater
pair_coeff * * sph/taitwater 1000.0 ${c} 1.0 ${h} # use target density of 1000, soundspeed ${c} for Tait's EOS
pair_coeff 1 1 sph/rhosum ${h}
fix gfix water gravity -9.81 vector 0 1 0 # add gravity. This fix also computes potential energy of mass in gravity field.
fix 2d_fix all enforce2d
compute rho_peratom all meso_rho/atom
compute e_peratom all meso_e/atom
compute esph all reduce sum c_e_peratom
compute ke all ke
variable etot equal c_esph+c_ke+f_gfix
# adjust nevery | min. allowed dt | max. allowed dt | max. travel distance per dt # // ${dt} ~= CFL criterion 0.1*h/c
fix dtfix all dt/reset 1 NULL ${dt} 0.0005 units box # use a variable timestep
# time-integrate position, velocities, internal energy and density of water particles
fix integrate_water_fix water meso
# time-integrate only internal energy and density of boundary particles
fix integrate_bc_fix bc meso/stationary
dump dump_id all custom 100 dump.lammpstrj id type xs ys zs c_rho_peratom c_e_peratom fx fy
dump_modify dump_id first yes
thermo 10
thermo_style custom step ke c_esph v_etot f_gfix press f_dtfix[1] f_dtfix
thermo_modify norm no
neigh_modify every 5 delay 0 check no
variable skin equal 0.3*${h}
neighbor ${skin} bin # set Verlet list skin distance
run ${nrun}