refactor sphere stuff

This commit is contained in:
James E McClure 2018-05-16 10:16:11 -04:00
parent f30bc31d39
commit 74b6a40925
5 changed files with 304 additions and 489 deletions

252
common/SpherePack.cpp Normal file
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@ -0,0 +1,252 @@
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <math.h>
#include <time.h>
#include <exception>
#include <stdexcept>
#include "common/Array.h"
#include "common/Utilities.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
#include "common/Database.h"
#include "common/SpherePack.h"
void WriteLocalSolidID(char *FILENAME, char *ID, int N)
{
char value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = ID[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void WriteLocalSolidDistance(char *FILENAME, double *Distance, int N)
{
double value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = Distance[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void ReadSpherePacking(int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad)
{
// Read in the full sphere pack
//...... READ IN THE SPHERES...................................
cout << "Reading the packing file..." << endl;
FILE *fid = fopen("pack.out","rb");
INSIST(fid!=NULL,"Error opening pack.out");
//.........Trash the header lines..........
char line[100];
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
//........read the spheres..................
// We will read until a blank like or end-of-file is reached
int count = 0;
while ( !feof(fid) && fgets(line,100,fid)!=NULL ) {
char* line2 = line;
List_cx[count] = strtod(line2,&line2);
List_cy[count] = strtod(line2,&line2);
List_cz[count] = strtod(line2,&line2);
List_rad[count] = strtod(line2,&line2);
count++;
}
cout << "Number of spheres extracted is: " << count << endl;
INSIST( count==nspheres, "Specified number of spheres is probably incorrect!" );
// .............................................................
}
void AssignLocalSolidID(char *ID, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
char value;
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
// double max_x,max_y,max_z;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/(Nx*nprocx-1);
hy = Ly/(Ny*nprocy-1);
hz = Lz/(Nz*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*Nx-1)*hx;
min_y = double(jproc*Ny-1)*hy;
min_z = double(kproc*Nz-1)*hz;
// max_x = ((iproc+1)*Nx+1)*hx;
// max_y = ((jproc+1)*Ny+1)*hy;
// max_z = ((kproc+1)*Nz+1)*hz;
//............................................
//............................................
// Pre-initialize local ID
for (n=0;n<N;n++){
ID[n]=1;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-r)/hx)-1;
imax = int ((cx+r)/hx)+1;
jmin = int ((cy-r)/hy)-1;
jmax = int ((cy+r)/hy)+1;
kmin = int ((cz-r)/hz)-1;
kmax = int ((cz+r)/hz)+1;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// Initialize ID value to 'fluid (=1)'
x = i*hx;
y = j*hy;
z = k*hz;
value = 1;
// if inside sphere, set to zero
if ( (cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z) < r*r){
value=0;
}
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
if ( ID[n] != 0 ){
ID[n] = value;
}
}
}
}
}
}
void SignedDistance(double *Distance, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
double distance;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/((Nx-2)*nprocx-1);
hy = Ly/((Ny-2)*nprocy-1);
hz = Lz/((Nz-2)*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*(Nx-2)-1)*hx;
min_y = double(jproc*(Ny-2)-1)*hy;
min_z = double(kproc*(Nz-2)-1)*hz;
//............................................
//............................................
// Pre-initialize Distance
for (n=0;n<N;n++){
Distance[n]=100.0;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-2*r)/hx);
imax = int ((cx+2*r)/hx)+2;
jmin = int ((cy-2*r)/hy);
jmax = int ((cy+2*r)/hy)+2;
kmin = int ((cz-2*r)/hz);
kmax = int ((cz+2*r)/hz)+2;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// x,y,z is distance in physical units
x = i*hx;
y = j*hy;
z = k*hz;
// if inside sphere, set to zero
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
// Compute the distance
distance = sqrt((cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z)) - r;
// Assign the minimum distance
if (distance < Distance[n]) Distance[n] = distance;
}
}
}
}
// Map the distance to lattice units
for (n=0; n<N; n++) Distance[n] = Distance[n]/hx;
}

35
common/SpherePack.h Normal file
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#ifndef SpherePack_INC
#define SpherePack_INC
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <math.h>
#include <time.h>
#include <exception>
#include <stdexcept>
#include "common/Array.h"
#include "common/Utilities.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
#include "common/Database.h"
/*
Simple tools to work with sphere packs
*/
void WriteLocalSolidID(char *FILENAME, char *ID, int N);
void WriteLocalSolidDistance(char *FILENAME, double *Distance, int N);
void ReadSpherePacking(int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad);
void AssignLocalSolidID(char *ID, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz);
void SignedDistance(double *Distance, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz);

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@ -8,6 +8,7 @@
//#include "common/pmmc.h"
#include "common/Domain.h"
#include "common/SpherePack.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
@ -19,265 +20,27 @@
using namespace std;
void WriteLocalSolidID(char *FILENAME, char *ID, int N)
{
char value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = ID[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void WriteLocalSolidDistance(char *FILENAME, double *Distance, int N)
{
double value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = Distance[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void ReadSpherePacking(int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad)
{
// Read in the full sphere pack
//...... READ IN THE SPHERES...................................
cout << "Reading the packing file..." << endl;
FILE *fid = fopen("pack.out","rb");
INSIST(fid!=NULL,"Error opening pack.out");
//.........Trash the header lines..........
char line[100];
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
//........read the spheres..................
// We will read until a blank like or end-of-file is reached
int count = 0;
while ( !feof(fid) && fgets(line,100,fid)!=NULL ) {
char* line2 = line;
List_cx[count] = strtod(line2,&line2);
List_cy[count] = strtod(line2,&line2);
List_cz[count] = strtod(line2,&line2);
List_rad[count] = strtod(line2,&line2);
count++;
}
cout << "Number of spheres extracted is: " << count << endl;
INSIST( count==nspheres, "Specified number of spheres is probably incorrect!" );
// .............................................................
}
void AssignLocalSolidID(char *ID, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
char value;
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
// double max_x,max_y,max_z;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/(Nx*nprocx-1);
hy = Ly/(Ny*nprocy-1);
hz = Lz/(Nz*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*Nx-1)*hx;
min_y = double(jproc*Ny-1)*hy;
min_z = double(kproc*Nz-1)*hz;
// max_x = ((iproc+1)*Nx+1)*hx;
// max_y = ((jproc+1)*Ny+1)*hy;
// max_z = ((kproc+1)*Nz+1)*hz;
//............................................
//............................................
// Pre-initialize local ID
for (n=0;n<N;n++){
ID[n]=1;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-r)/hx)-1;
imax = int ((cx+r)/hx)+1;
jmin = int ((cy-r)/hy)-1;
jmax = int ((cy+r)/hy)+1;
kmin = int ((cz-r)/hz)-1;
kmax = int ((cz+r)/hz)+1;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// Initialize ID value to 'fluid (=1)'
x = i*hx;
y = j*hy;
z = k*hz;
value = 1;
// if inside sphere, set to zero
if ( (cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z) < r*r){
value=0;
}
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
if ( ID[n] != 0 ){
ID[n] = value;
}
}
}
}
}
}
void SignedDistance(double *Distance, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
double distance;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/((Nx-2)*nprocx-1);
hy = Ly/((Ny-2)*nprocy-1);
hz = Lz/((Nz-2)*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*(Nx-2)-1)*hx;
min_y = double(jproc*(Ny-2)-1)*hy;
min_z = double(kproc*(Nz-2)-1)*hz;
//............................................
//............................................
// Pre-initialize Distance
for (n=0;n<N;n++){
Distance[n]=100.0;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-2*r)/hx);
imax = int ((cx+2*r)/hx)+2;
jmin = int ((cy-2*r)/hy);
jmax = int ((cy+2*r)/hy)+2;
kmin = int ((cz-2*r)/hz);
kmax = int ((cz+2*r)/hz)+2;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// x,y,z is distance in physical units
x = i*hx;
y = j*hy;
z = k*hz;
// if inside sphere, set to zero
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
// Compute the distance
distance = sqrt((cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z)) - r;
// Assign the minimum distance
if (distance < Distance[n]) Distance[n] = distance;
}
}
}
}
// Map the distance to lattice units
for (n=0; n<N; n++) Distance[n] = Distance[n]/hx;
}
inline void PackID(int *list, int count, char *sendbuf, char *ID){
// Fill in the phase ID values from neighboring processors
// This packs up the values that need to be sent from one processor to another
int idx,n;
// Fill in the phase ID values from neighboring processors
// This packs up the values that need to be sent from one processor to another
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
sendbuf[idx] = ID[n];
}
for (idx=0; idx<count; idx++){
n = list[idx];
sendbuf[idx] = ID[n];
}
}
//***************************************************************************************
inline void UnpackID(int *list, int count, char *recvbuf, char *ID){
// Fill in the phase ID values from neighboring processors
// This unpacks the values once they have been recieved from neighbors
int idx,n;
// Fill in the phase ID values from neighboring processors
// This unpacks the values once they have been recieved from neighbors
int idx,n;
for (idx=0; idx<count; idx++){
n = list[idx];
ID[n] = recvbuf[idx];
}
for (idx=0; idx<count; idx++){
n = list[idx];
ID[n] = recvbuf[idx];
}
}

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@ -2,6 +2,7 @@
#include <math.h>
#include "analysis/pmmc.h"
#include "common/Domain.h"
#include "common/SpherePack.h"
using namespace std;

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@ -8,6 +8,7 @@
#include "analysis/pmmc.h"
#include "common/Domain.h"
#include "common/SpherePack.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
@ -19,243 +20,6 @@
using namespace std;
void WriteLocalSolidID(char *FILENAME, char *ID, int N)
{
char value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = ID[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void WriteLocalSolidDistance(char *FILENAME, double *Distance, int N)
{
double value;
ofstream File(FILENAME,ios::binary);
for (int n=0; n<N; n++){
value = Distance[n];
File.write((char*) &value, sizeof(value));
}
File.close();
}
void ReadSpherePacking(int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad)
{
// Read in the full sphere pack
//...... READ IN THE SPHERES...................................
cout << "Reading the packing file..." << endl;
FILE *fid = fopen("pack.out","rb");
INSIST(fid!=NULL,"Error opening pack.out");
//.........Trash the header lines..........
char line[100];
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
fgetl(line, 100, fid);
//........read the spheres..................
// We will read until a blank like or end-of-file is reached
int count = 0;
while ( !feof(fid) && fgets(line,100,fid)!=NULL ) {
char* line2 = line;
List_cx[count] = strtod(line2,&line2);
List_cy[count] = strtod(line2,&line2);
List_cz[count] = strtod(line2,&line2);
List_rad[count] = strtod(line2,&line2);
count++;
}
cout << "Number of spheres extracted is: " << count << endl;
INSIST( count==nspheres, "Specified number of spheres is probably incorrect!" );
// .............................................................
}
void AssignLocalSolidID(char *ID, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
char value;
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
// double max_x,max_y,max_z;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/(Nx*nprocx-1);
hy = Ly/(Ny*nprocy-1);
hz = Lz/(Nz*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*Nx-1)*hx;
min_y = double(jproc*Ny-1)*hy;
min_z = double(kproc*Nz-1)*hz;
// max_x = ((iproc+1)*Nx+1)*hx;
// max_y = ((jproc+1)*Ny+1)*hy;
// max_z = ((kproc+1)*Nz+1)*hz;
//............................................
//............................................
// Pre-initialize local ID
for (n=0;n<N;n++){
ID[n]=1;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-r)/hx)-1;
imax = int ((cx+r)/hx)+1;
jmin = int ((cy-r)/hy)-1;
jmax = int ((cy+r)/hy)+1;
kmin = int ((cz-r)/hz)-1;
kmax = int ((cz+r)/hz)+1;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// Initialize ID value to 'fluid (=1)'
x = i*hx;
y = j*hy;
z = k*hz;
value = 1;
// if inside sphere, set to zero
if ( (cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z) < r*r){
value=0;
}
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
if ( ID[n] != 0 ){
ID[n] = value;
}
}
}
}
}
}
void SignedDistance(double *Distance, int nspheres, double *List_cx, double *List_cy, double *List_cz, double *List_rad,
double Lx, double Ly, double Lz, int Nx, int Ny, int Nz,
int iproc, int jproc, int kproc, int nprocx, int nprocy, int nprocz)
{
// Use sphere lists to determine which nodes are in porespace
// Write out binary file for nodes
int N = Nx*Ny*Nz; // Domain size, including the halo
double hx,hy,hz;
double x,y,z;
double cx,cy,cz,r;
int imin,imax,jmin,jmax,kmin,kmax;
int p,i,j,k,n;
//............................................
double min_x,min_y,min_z;
double distance;
//............................................
// Lattice spacing for the entire domain
// It should generally be true that hx=hy=hz
// Otherwise, you will end up with ellipsoids
hx = Lx/((Nx-2)*nprocx-1);
hy = Ly/((Ny-2)*nprocy-1);
hz = Lz/((Nz-2)*nprocz-1);
//............................................
// Get maximum and minimum for this domain
// Halo is included !
min_x = double(iproc*(Nx-2)-1)*hx;
min_y = double(jproc*(Ny-2)-1)*hy;
min_z = double(kproc*(Nz-2)-1)*hz;
//............................................
//............................................
// Pre-initialize Distance
for (n=0;n<N;n++){
Distance[n]=100.0;
}
//............................................
//............................................
// .........Loop over the spheres.............
for (p=0;p<nspheres;p++){
// Get the sphere from the list, map to local min
cx = List_cx[p] - min_x;
cy = List_cy[p] - min_y;
cz = List_cz[p] - min_z;
r = List_rad[p];
// Check if
// Range for this sphere in global indexing
imin = int ((cx-2*r)/hx);
imax = int ((cx+2*r)/hx)+2;
jmin = int ((cy-2*r)/hy);
jmax = int ((cy+2*r)/hy)+2;
kmin = int ((cz-2*r)/hz);
kmax = int ((cz+2*r)/hz)+2;
// Obviously we have to do something at the edges
if (imin<0) imin = 0;
if (imin>Nx) imin = Nx;
if (imax<0) imax = 0;
if (imax>Nx) imax = Nx;
if (jmin<0) jmin = 0;
if (jmin>Ny) jmin = Ny;
if (jmax<0) jmax = 0;
if (jmax>Ny) jmax = Ny;
if (kmin<0) kmin = 0;
if (kmin>Nz) kmin = Nz;
if (kmax<0) kmax = 0;
if (kmax>Nz) kmax = Nz;
// Loop over the domain for this sphere (may be null)
for (i=imin;i<imax;i++){
for (j=jmin;j<jmax;j++){
for (k=kmin;k<kmax;k++){
// x,y,z is distance in physical units
x = i*hx;
y = j*hy;
z = k*hz;
// if inside sphere, set to zero
// get the position in the list
n = k*Nx*Ny+j*Nx+i;
// Compute the distance
distance = sqrt((cx-x)*(cx-x)+(cy-y)*(cy-y)+(cz-z)*(cz-z)) - r;
// Assign the minimum distance
if (distance < Distance[n]) Distance[n] = distance;
}
}
}
}
// Map the distance to lattice units
for (n=0; n<N; n++) Distance[n] = Distance[n]/hx;
}
int main(int argc, char **argv)
{
//*****************************************