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Dam example, generalizing non-quintic kernels

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This commit is contained in:
jtclemm
2024-06-03 15:04:24 -06:00
parent 8d25c510c1
commit fc0b155de9
12 changed files with 129 additions and 40 deletions
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4
doc/src/Howto_rheo.rst
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@ -17,6 +17,10 @@ these calculations. Additional numerical details can be found in
:ref:`(Palermo) <howto_rheo_palermo>` and
:ref:`(Clemmer) <howto_rheo_clemmer>`.
Note, if you simply want to run a traditional SPH simulation, the SPH package
is likely better suited for your application. It has fewer advanced features
and therefore benefits from improved performance.
----------
At the core of the package is :doc:`fix rheo <fix_rheo>` which integrates

1
examples/rheo/balloon/in.rheo.balloon
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@ -60,6 +60,7 @@ fix 1 all rheo ${cut} quintic 0 &
fix 2 all rheo/viscosity * constant ${eta}
fix 3 all rheo/pressure * linear
fix 4 all wall/harmonic ylo EDGE 2.0 1.0 1.0
fix 5 all enforce2d
compute rho all rheo/property/atom rho
compute phase all rheo/property/atom phase

45
examples/rheo/dam-break/in.rheo.dam.break
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@ -3,24 +3,24 @@
dimension 2
units lj
atom_style rheo
boundary f f p
boundary f s p
comm_modify vel yes
newton off
# ------ Create simulation box ------ #
variable n equal 1.0
variable cut equal 3.0
variable dx equal 4.0
variable cut equal 2.2
variable dx equal 3.0
region box block -1 200 -1 80 -0.1 0.1 units box
#region box block -1 100 -1 40 -0.1 0.1 units box
region box block -1 150 -1 80 -0.1 0.1 units box
create_box 2 box
lattice hex ${n}
region fluid block $(xlo+v_dx) $(xlo+44.0) $(ylo+v_dx) $(yhi-16.0) EDGE EDGE units box
#region fluid block $(xlo+v_dx) $(xlo+20.0) $(ylo+v_dx) $(yhi-10.0) EDGE EDGE units box
region walls block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE units box side out
region fluid block $(xlo+v_dx+1.0) $(xlo+40.0) $(ylo+v_dx+1.0) $(yhi-20.0) EDGE EDGE units box
region walls1 block $(xlo+v_dx) $(xhi-v_dx) $(ylo+v_dx) $(yhi-v_dx) EDGE EDGE side out units box
region walls2 block EDGE EDGE EDGE $(yhi-v_dx) EDGE EDGE side in units box
region walls intersect 2 walls1 walls2
create_atoms 1 region fluid
create_atoms 2 region walls
@ -33,12 +33,13 @@ group rig type 2
variable rho0 equal 1.0
variable mp equal ${rho0}/${n}
variable cs equal 1.0
variable zeta equal 0.05
variable zeta equal 0.1
variable dt_max equal 0.1*${cut}/${cs}/3
variable eta equal 0.05
variable Dr equal 0.05
variable eta equal 0.1
variable Dr equal 0.1
mass * ${mp}
mass 1 ${mp}
mass 2 $(2*v_mp)
set group all rheo/rho ${rho0}
set group all rheo/status 0
@ -46,36 +47,30 @@ set group rig rheo/status 1
timestep ${dt_max}
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
pair_style rheo ${cut} artificial/visc ${zeta} #rho/damp ${Dr}
pair_coeff * *
# ------ Fixes & computes ------ #
fix 1 all rheo ${cut} quintic 10 &
shift &
surface/detection coordination 22 8 &
interface/reconstruct
#fix 1 all rheo ${cut} RK1 10 surface/detection coordination 36 10 interface/reconstruct shift
rho/sum
fix 2 all rheo/viscosity * constant ${eta}
fix 3 all rheo/pressure * linear
fix 4 all gravity 5e-4 vector 0 -1 0
fix 4 all gravity 1e-3 vector 0 -1 0
fix 5 rig setforce 0.0 0.0 0.0
fix 6 all enforce2d
compute rho all rheo/property/atom rho
compute phase all rheo/property/atom phase
compute p all rheo/property/atom pressure
compute surf all rheo/property/atom surface
compute sn all rheo/property/atom surface/n/x surface/n/y
compute vshift all rheo/property/atom shift/v/x shift/v/y
# ------ Output & Run ------ #
thermo 100
thermo 20
thermo_style custom step time ke press
dump 1 all custom 20 atomDump id type x y vx vy fx fy c_rho c_phase c_surf c_p c_vshift[*] c_sn[*]
#dump 1 all custom 200 atomDump id type x y vx vy fx fy c_rho c_surf c_p c_sn[*]
#thermo 1
run 300000 # 400000
run 30000

1
examples/rheo/ice-cubes/in.rheo.ice.cubes
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@ -64,6 +64,7 @@ fix 4 all rheo/thermal conductivity * constant ${kappa} &
fix 5 all wall/region wall harmonic 1.0 1.0 1.0
fix 6 all gravity 5e-4 vector 0 -1 0
fix 7 all deposit 8 0 1000 37241459 mol my_mol region drop near 2.0 vy -0.02 -0.02
fix 8 all enforce2d
compute rho all rheo/property/atom rho
compute phase all rheo/property/atom phase

2
examples/rheo/oxidation/in.rheo.oxidation
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@ -10,7 +10,6 @@ newton off
region box block -60 60 0 80 -0.01 0.01 units box
create_box 3 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
region lbar block -15 0 3 80 EDGE EDGE units box
region rbar block 0 15 3 80 EDGE EDGE units box
region bar union 2 lbar rbar
@ -83,6 +82,7 @@ fix 7 all gravity 5e-5 vector 0 -1 0
fix 8 floor setforce 0.0 0.0 0.0
fix 9 surf add/heat linear 1.1 0.05
fix 10 floor add/heat constant 0 overwrite yes # fix the temperature of the floor
fix 11 all enforce2d
compute surf all rheo/property/atom surface
compute rho all rheo/property/atom rho

4
examples/rheo/poiseuille/in.rheo.poiseuille
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@ -6,7 +6,6 @@ atom_style rheo
boundary p p p
comm_modify vel yes
# ------ Create simulation box ------ #
variable n equal 1.0
@ -53,7 +52,6 @@ timestep ${dt_max}
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
pair_coeff * *
# ------ Fixes & computes ------ #
fix 1 all rheo ${cut} quintic 0 shift
@ -62,10 +60,10 @@ fix 2 all rheo/viscosity * constant ${eta}
fix 3 all rheo/pressure * linear
fix 4 rig setforce 0.0 0.0 0.0
fix 5 fluid addforce ${fext} 0.0 0.0
fix 6 all enforce2d
compute rho all rheo/property/atom rho
# ------ Output & Run ------ #
thermo 200

3
examples/rheo/taylor-green/in.rheo.taylor.green
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@ -7,7 +7,6 @@ boundary p p p
comm_modify vel yes
newton off
# ------ Create simulation box ------ #
variable n equal 1.0
@ -47,12 +46,12 @@ timestep ${dt_max}
pair_style rheo ${cut} artificial/visc ${zeta} rho/damp ${Dr}
pair_coeff * *
# ------ Fixes & computes ------ #
fix 1 all rheo ${cut} RK1 8 shift
fix 2 all rheo/viscosity * constant ${eta}
fix 3 all rheo/pressure * linear
fix 4 all enforce2d
compute rho all rheo/property/atom rho

94
src/RHEO/compute_rheo_kernel.cpp
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@ -25,6 +25,7 @@
#include "error.h"
#include "fix_rheo.h"
#include "force.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
@ -43,6 +44,7 @@
using namespace LAMMPS_NS;
using namespace RHEO_NS;
using namespace MathConst;
using namespace MathExtra;
static constexpr int DELTA = 2000;
@ -57,8 +59,7 @@ ComputeRHEOKernel::ComputeRHEOKernel(LAMMPS *lmp, int narg, char **arg) :
kernel_style = utils::inumeric(FLERR,arg[3],false,lmp);
if (kernel_style == QUINTIC) {
if (kernel_style == QUINTIC || kernel_style == WENDLANDC4) {
correction_order = -1;
} else if (kernel_style == RK0) {
correction_order = 0;
@ -115,13 +116,23 @@ void ComputeRHEOKernel::init()
hsqinv = hinv * hinv;
if (kernel_style != WENDLANDC4) {
if (dim == 3) {
pre_w = 0.002652582384864922 * 27.0 * hsqinv * hinv;
pre_w = 1.0 / (120.0 * MY_PI) * 27.0 * hsqinv * hinv;
pre_wp = pre_w * 3.0 * hinv;
} else {
pre_w = 0.004661441847879780 * 9 * hsqinv;
pre_w = 7.0 / (478.0 * MY_PI) * 9 * hsqinv;
pre_wp = pre_w * 3.0 * hinv;
}
} else {
if (dim == 3) {
pre_w = 495.0 / (32.0 * MY_PI * hsq * h);
pre_wp = pre_w * hinv;
} else {
pre_w = 9.0 / (MY_PI * hsq);
pre_wp = pre_w * hinv;
}
}
nmax_store = atom->nmax;
memory->create(coordination, nmax_store, "rheo:coordination");
@ -163,11 +174,27 @@ int ComputeRHEOKernel::check_corrections(int i)
/* ---------------------------------------------------------------------- */
double ComputeRHEOKernel::calc_w_self(int i, int j)
{
double w;
if (kernel_style == WENDLANDC4)
w = calc_w_wendlandc4(i, j, 0.0, 0.0, 0.0, 0.0);
else
w = calc_w_quintic(i, j, 0.0, 0.0, 0.0, 0.0);
return w;
}
/* ---------------------------------------------------------------------- */
double ComputeRHEOKernel::calc_w(int i, int j, double delx, double dely, double delz, double r)
{
double w;
int corrections_i, corrections_j, corrections;
if (kernel_style == WENDLANDC4)
return calc_w_wendlandc4(i,j,delx,dely,delz,r);
if (kernel_style != QUINTIC) {
corrections_i = check_corrections(i);
corrections_j = check_corrections(j);
@ -191,6 +218,9 @@ double ComputeRHEOKernel::calc_dw(int i, int j, double delx, double dely, double
double wp;
int corrections_i, corrections_j;
if (kernel_style == WENDLANDC4)
return calc_dw_wendlandc4(i,j,delx,dely,delz,r,dWij,dWji);
if (kernel_style != QUINTIC) {
corrections_i = check_corrections(i);
corrections_j = check_corrections(j);
@ -288,6 +318,62 @@ double ComputeRHEOKernel::calc_dw_quintic(int i, int j, double delx, double dely
return wp;
}
/* ---------------------------------------------------------------------- */
double ComputeRHEOKernel::calc_w_wendlandc4(int i, int j, double delx, double dely, double delz, double r)
{
double w, tmp6, s;
s = r * hinv;
if (s > 1.0) {
w = 0.0;
} else {
tmp6 = (1.0 - s) * (1.0 - s);
tmp6 *= tmp6 * tmp6;
w = tmp6 * (1.0 + 6.0 * s + 35.0 * THIRD * s * s);
}
w *= pre_w;
Wij = w;
Wji = w;
return w;
}
/* ---------------------------------------------------------------------- */
double ComputeRHEOKernel::calc_dw_wendlandc4(int i, int j, double delx, double dely, double delz, double r, double *dW1, double *dW2)
{
double wp, tmp1, tmp5, tmp6, s, wprinv;
double *mass = atom->mass;
int *type = atom->type;
s = r * hinv;
if (s > 1.0) {
wp = 0.0;
} else {
tmp1 = 1.0 - s;
tmp5 = tmp1 * tmp1;
tmp5 = tmp5 * tmp5 * tmp1;
tmp6 = tmp5 * tmp1;
wp = tmp6 * (6.0 + 70.0 * THIRD * s);
wp -= 6 * tmp5 * (1.0 + 6.0 * s + 35.0 * THIRD * s * s);
}
wp *= pre_wp;
wprinv = wp / r;
dW1[0] = delx * wprinv;
dW1[1] = dely * wprinv;
dW1[2] = delz * wprinv;
dW2[0] = -delx * wprinv;
dW2[1] = -dely * wprinv;
dW2[2] = -delz * wprinv;
return wp;
}
/* ---------------------------------------------------------------------- */

3
src/RHEO/compute_rheo_kernel.h
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@ -36,10 +36,13 @@ class ComputeRHEOKernel : public Compute {
void unpack_forward_comm(int, int, double *) override;
double memory_usage() override;
void compute_coordination();
double calc_w_self(int,int);
double calc_w(int,int,double,double,double,double);
double calc_dw(int,int,double,double,double,double);
double calc_w_quintic(int,int,double,double,double,double);
double calc_dw_quintic(int,int,double,double,double,double,double *,double *);
double calc_w_wendlandc4(int,int,double,double,double,double);
double calc_dw_wendlandc4(int,int,double,double,double,double,double *,double *);
void grow_arrays(int);
double dWij[3], dWji[3], Wij, Wji;

2
src/RHEO/compute_rheo_rho_sum.cpp
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@ -94,7 +94,7 @@ void ComputeRHEORhoSum::compute_peratom()
// initialize arrays, local with quintic self-contribution, ghosts are zeroed
for (i = 0; i < nlocal; i++) {
w = compute_kernel->calc_w_quintic(i, i, 0.0, 0.0, 0.0, 0.0);
w = compute_kernel->calc_w_self(i, i);
rho[i] = w * mass[type[i]];
}

2
src/RHEO/fix_rheo.cpp
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@ -90,6 +90,8 @@ FixRHEO::FixRHEO(LAMMPS *lmp, int narg, char **arg) :
cut = h;
if (strcmp(arg[4], "quintic") == 0) {
kernel_style = QUINTIC;
} else if (strcmp(arg[4], "wendland/c4") == 0) {
kernel_style = WENDLANDC4;
} else if (strcmp(arg[4], "RK0") == 0) {
kernel_style = RK0;
} else if (strcmp(arg[4], "RK1") == 0) {

2
src/RHEO/fix_rheo.h
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@ -72,7 +72,7 @@ class FixRHEO : public Fix {
namespace RHEO_NS {
enum {QUINTIC, RK0, RK1, RK2};
enum {QUINTIC, WENDLANDC4, RK0, RK1, RK2};
enum {COORDINATION, DIVR};
// Status variables