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refactor DCEL

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This commit is contained in:
James E McClure
2018-09-15 13:39:01 -04:00
parent 5272b7ff47
commit 1619e82db9
7 changed files with 13 additions and 222 deletions
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186
analysis/Minkowski.cpp
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@@ -15,33 +15,12 @@
// Constructor
Minkowski::Minkowski(std::shared_ptr <Domain> dm):
n_obj_pts(0), n_obj_tris(0), kstart(0), kfinish(0), isovalue(0), Volume(0),
LOGFILE(NULL), Dm(dm), vol_n(0), vol_n_global(0)
kstart(0), kfinish(0), isovalue(0), Volume(0),
LOGFILE(NULL), Dm(dm), Vi(0), Vi_global(0)
{
Nx=dm->Nx; Ny=dm->Ny; Nz=dm->Nz;
Volume=double((Nx-2)*(Ny-2)*(Nz-2))*double(Dm->nprocx()*Dm->nprocy()*Dm->nprocz());
TempID = new char[Nx*Ny*Nz];
// Global arrays
PhaseID.resize(Nx,Ny,Nz); PhaseID.fill(0);
SDn.resize(Nx,Ny,Nz); SDn.fill(0);
MeanCurvature.resize(Nx,Ny,Nz); MeanCurvature.fill(0);
GaussCurvature.resize(Nx,Ny,Nz); GaussCurvature.fill(0);
SDn_x.resize(Nx,Ny,Nz); SDn_x.fill(0); // Gradient of the signed distance
SDn_y.resize(Nx,Ny,Nz); SDn_y.fill(0);
SDn_z.resize(Nx,Ny,Nz); SDn_z.fill(0);
//.........................................
// Allocate cube storage space
CubeValues.resize(2,2,2);
obj_tris.resize(3,20);
obj_pts=DTMutableList<Point>(20);
tmp=DTMutableList<Point>(20);
//.........................................
Values.resize(20);
//DistanceValues.resize(20);
NormalVector.resize(60);
if (Dm->rank()==0){
LOGFILE = fopen("minkowski.csv","a+");
if (fseek(LOGFILE,0,SEEK_SET) == fseek(LOGFILE,0,SEEK_CUR))
@@ -60,117 +39,20 @@ Minkowski::~Minkowski()
if ( LOGFILE!=NULL ) { fclose(LOGFILE); }
}
void Minkowski::Initialize()
{
isovalue=0.0;
vol_n = euler = Jn = An = Kn = 0.0;
}
double Minkowski::V(){
return vol_n_global;
return Vi_global;
}
double Minkowski::A(){
return An_global;
return Ai_global;
}
double Minkowski::J(){
return Jn_global;
return Ji_global;
}
double Minkowski::X(){
return euler_global;
}
void Minkowski::UpdateMeshValues()
{
int i,j,k,n;
//...........................................................................
Dm->CommunicateMeshHalo(SDn);
//...........................................................................
// Compute the gradients of the phase indicator and signed distance fields
pmmc_MeshGradient(SDn,SDn_x,SDn_y,SDn_z,Nx,Ny,Nz);
//...........................................................................
// Gradient of the phase indicator field
//...........................................................................
Dm->CommunicateMeshHalo(SDn_x);
//...........................................................................
Dm->CommunicateMeshHalo(SDn_y);
//...........................................................................
Dm->CommunicateMeshHalo(SDn_z);
//...........................................................................
//...........................................................................
// Compute the mesh curvature of the phase indicator field
pmmc_MeshCurvature(SDn, MeanCurvature, GaussCurvature, Nx, Ny, Nz);
//...........................................................................
//...........................................................................
Dm->CommunicateMeshHalo(MeanCurvature);
//...........................................................................
Dm->CommunicateMeshHalo(GaussCurvature);
//...........................................................................
// Initializing the blob ID
for (k=0; k<Nz; k++){
for (j=0; j<Ny; j++){
for (i=0; i<Nx; i++){
n = k*Nx*Ny+j*Nx+i;
if (Dm->id[n] == 0){
// Solid phase
PhaseID(i,j,k) = 0;
}
else {
// non-wetting phase
PhaseID(i,j,k) = 1;
}
}
}
}
}
void Minkowski::ComputeLocal()
{
int i,j,k,kmin,kmax;
int cube[8][3] = {{0,0,0},{1,0,0},{0,1,0},{1,1,0},{0,0,1},{1,0,1},{0,1,1},{1,1,1}};
// If external boundary conditions are set, do not average over the inlet
kmin=1; kmax=Nz-1;
if (Dm->BoundaryCondition > 0 && Dm->kproc() == 0) kmin=4;
if (Dm->BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;
vol_n = euler = Jn = An = Kn = 0.0;
for (k=kmin; k<kmax; k++){
for (j=1; j<Ny-1; j++){
for (i=1; i<Nx-1; i++){
//...........................................................................
n_obj_pts=0;
n_obj_tris=0;
//...........................................................................
// Compute volume averages
for (int p=0;p<8;p++){
//n = i+cube[p][0] + (j+cube[p][1])*Nx + (k+cube[p][2])*Nx*Ny;
// 1-D index for this cube corner
if ( SDn(i+cube[p][0],j+cube[p][1],k+cube[p][2]) < 0 ){
vol_n += 0.125;
}
}
n_obj_pts=n_obj_tris=0;
// Compute the non-wetting phase surface and associated area
An += geomavg_MarchingCubes(SDn,isovalue,i,j,k,obj_pts,n_obj_pts,obj_tris,n_obj_tris);
Jn += pmmc_CubeSurfaceInterpValue(CubeValues,MeanCurvature,obj_pts,obj_tris,Values,
i,j,k,n_obj_pts,n_obj_tris);
// Compute Euler characteristic from integral of gaussian curvature
Kn += pmmc_CubeSurfaceInterpValue(CubeValues,GaussCurvature,obj_pts,obj_tris,Values,
i,j,k,n_obj_pts,n_obj_tris);
euler += geomavg_EulerCharacteristic(obj_pts,obj_tris,n_obj_pts,n_obj_tris,i,j,k);
}
}
}
return Xi_global;
}
void Minkowski::ComputeScalar(const DoubleArray Field, const double isovalue)
@@ -243,64 +125,10 @@ void Minkowski::ComputeScalar(const DoubleArray Field, const double isovalue)
}
/*
void Minkowski::AssignComponentLabels()
{
int LabelNWP=1;
int LabelWP=2;
// NOTE: labeling the wetting phase components is tricky! One sandstone media had over 800,000 components
// NumberComponents_WP = ComputeGlobalPhaseComponent(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,PhaseID,LabelWP,Label_WP);
// treat all wetting phase is connected
NumberComponents_WP=1;
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
Label_WP(i,j,k) = 0;
//if (SDs(i,j,k) > 0.0) PhaseID(i,j,k) = 0;
//else if (Phase(i,j,k) > 0.0) PhaseID(i,j,k) = LabelNWP;
//else PhaseID(i,j,k) = LabelWP;
}
}
}
// Fewer non-wetting phase features are present
//NumberComponents_NWP = ComputeGlobalPhaseComponent(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,PhaseID,LabelNWP,Label_NWP);
NumberComponents_NWP = ComputeGlobalBlobIDs(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,SDs,SDn,solid_isovalue,isovalue,Label_NWP,Dm->Comm);
}
*/
void Minkowski::Reduce()
{
//...........................................................................
MPI_Barrier(Dm->Comm);
// Phase averages
MPI_Allreduce(&vol_n,&vol_n_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
MPI_Allreduce(&euler,&euler_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
MPI_Allreduce(&An,&An_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
MPI_Allreduce(&Jn,&Jn_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
MPI_Barrier(Dm->Comm);
// normalize to per unit volume basis
vol_n_global /=Volume;
An_global /=Volume;
Jn_global /=Volume;
euler_global /=Volume;
euler_global /= (2*PI);
}
void Minkowski::NonDimensionalize(double D)
{
An_global *= D;
Jn_global *= D*D;
euler_global *= D*D*D;
}
void Minkowski::PrintAll()
{
if (Dm->rank()==0){
fprintf(LOGFILE,"%.5g %.5g %.5g %.5g\n",vol_n_global, An_global, Jn_global, euler_global); // minkowski measures
fprintf(LOGFILE,"%.5g %.5g %.5g %.5g\n",Vi_global, Ai_global, Ji_global, Xi_global); // minkowski measures
fflush(LOGFILE);
}
}

45
analysis/Minkowski.h
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@@ -4,7 +4,7 @@
#include <vector>
#include "analysis/decl.h"
#include "analysis/dcel.h"
#include "common/Domain.h"
#include "common/Communication.h"
#include "analysis/analysis.h"
@@ -18,31 +18,11 @@
class Minkowski{
//...........................................................................
int n_obj_pts;
int n_obj_tris;
//...........................................................................
int nc;
int kstart,kfinish;
double isovalue;
double Volume;
// initialize lists for vertices for surfaces, common line
DTMutableList<Point> obj_pts;
DTMutableList<Point> tmp;
// initialize triangle lists for surfaces
IntArray obj_tris;
// Temporary storage arrays
DoubleArray CubeValues;
DoubleArray Values;
DoubleArray NormalVector;
DoubleArray RecvBuffer;
char *TempID;
// CSV / text file where time history of averages is saved
FILE *LOGFILE;
@@ -54,24 +34,12 @@ public:
// Averaging variables
//...........................................................................
// local averages (to each MPI process)
double vol_n; // volumes the exclude the interfacial region
// Global averages (all processes)
double vol_n_global; // volumes the exclude the interfacial region
double euler,Kn,Jn,An;
double euler_global,Kn_global,Jn_global,An_global;
double Ai,Ji,Xi,Vi;
// Global averages (all processes)
double Ai_global,Ji_global,Xi_global,Vi_global;
//...........................................................................
int Nx,Ny,Nz;
IntArray PhaseID; // Phase ID array (solid=0, non-wetting=1, wetting=2)
DoubleArray SDn;
DoubleArray MeanCurvature;
DoubleArray GaussCurvature;
DoubleArray SDn_x; // Gradient of the signed distance
DoubleArray SDn_y;
DoubleArray SDn_z;
double V();
double A();
double J();
@@ -80,14 +48,9 @@ public:
//...........................................................................
Minkowski(std::shared_ptr <Domain> Dm);
~Minkowski();
void Initialize();
void UpdateMeshValues();
void ComputeLocal();
void Reduce();
void NonDimensionalize(double D);
void PrintAll();
int GetCubeLabel(int i, int j, int k, IntArray &BlobLabel);
void ComputeScalar(const DoubleArray Field, const double isovalue);
void PrintAll();
};
#endif

0
analysis/decl.cpp → analysis/dcel.cpp
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0
analysis/decl.h → analysis/dcel.h
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4
tests/CMakeLists.txt
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@@ -54,8 +54,8 @@ ADD_LBPM_TEST( TestForceMoments ../example/Piston/input.db)
ADD_LBPM_TEST( TestForceD3Q19 )
ADD_LBPM_TEST( TestMomentsD3Q19 )
ADD_LBPM_TEST( TestInterfaceSpeed ../example/Bubble/input.db)
ADD_LBPM_TEST( TestSphereCurvature )
ADD_LBPM_TEST( TestTriNormal )
ADD_LBPM_TEST( Test_dcel_Minkowski )
ADD_LBPM_TEST( Test_dcel_TriNormal )
#ADD_LBPM_TEST_1_2_4( TestTwoPhase )
ADD_LBPM_TEST_1_2_4( TestBlobIdentify )
#ADD_LBPM_TEST_PARALLEL( TestTwoPhase 8 )

0
tests/TestSphereCurvature.cpp → tests/Test_dcel_Minkowski.cpp
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0
tests/TestTriNormal.cpp → tests/Test_dcel_TriNormal.cpp
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