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7b731e327be8989fe1983e21d813627272ea05eb
LBPM/common/Domain.cpp
James McClure 7b731e327b update pseudo-reflection
2020-05-04 15:26:41 -04:00

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// Created by James McClure
// Copyright 2008-2013
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <math.h>
#include <time.h>
#include <exception> // std::exception
#include <stdexcept>
#include "common/Domain.h"
#include "common/Array.h"
#include "common/Utilities.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
// Inline function to read line without a return argument
static inline void fgetl( char * str, int num, FILE * stream )
{
char* ptr = fgets( str, num, stream );
if ( 0 ) {char *temp = (char *)&ptr; temp++;}
}
/********************************************************
* Constructors/Destructor *
********************************************************/
Domain::Domain( int nx, int ny, int nz, int rnk, int npx, int npy, int npz,
double lx, double ly, double lz, int BC):
database(NULL), Nx(0), Ny(0), Nz(0),
Lx(0), Ly(0), Lz(0), Volume(0), BoundaryCondition(0), voxel_length(1),
Comm(MPI_COMM_WORLD),
inlet_layers_x(0), inlet_layers_y(0), inlet_layers_z(0),
inlet_layers_phase(1),outlet_layers_phase(2),
sendCount_x(0), sendCount_y(0), sendCount_z(0), sendCount_X(0), sendCount_Y(0), sendCount_Z(0),
sendCount_xy(0), sendCount_yz(0), sendCount_xz(0), sendCount_Xy(0), sendCount_Yz(0), sendCount_xZ(0),
sendCount_xY(0), sendCount_yZ(0), sendCount_Xz(0), sendCount_XY(0), sendCount_YZ(0), sendCount_XZ(0),
sendList_x(NULL), sendList_y(NULL), sendList_z(NULL), sendList_X(NULL), sendList_Y(NULL), sendList_Z(NULL),
sendList_xy(NULL), sendList_yz(NULL), sendList_xz(NULL), sendList_Xy(NULL), sendList_Yz(NULL), sendList_xZ(NULL),
sendList_xY(NULL), sendList_yZ(NULL), sendList_Xz(NULL), sendList_XY(NULL), sendList_YZ(NULL), sendList_XZ(NULL),
sendBuf_x(NULL), sendBuf_y(NULL), sendBuf_z(NULL), sendBuf_X(NULL), sendBuf_Y(NULL), sendBuf_Z(NULL),
sendBuf_xy(NULL), sendBuf_yz(NULL), sendBuf_xz(NULL), sendBuf_Xy(NULL), sendBuf_Yz(NULL), sendBuf_xZ(NULL),
sendBuf_xY(NULL), sendBuf_yZ(NULL), sendBuf_Xz(NULL), sendBuf_XY(NULL), sendBuf_YZ(NULL), sendBuf_XZ(NULL),
recvCount_x(0), recvCount_y(0), recvCount_z(0), recvCount_X(0), recvCount_Y(0), recvCount_Z(0),
recvCount_xy(0), recvCount_yz(0), recvCount_xz(0), recvCount_Xy(0), recvCount_Yz(0), recvCount_xZ(0),
recvCount_xY(0), recvCount_yZ(0), recvCount_Xz(0), recvCount_XY(0), recvCount_YZ(0), recvCount_XZ(0),
recvList_x(NULL), recvList_y(NULL), recvList_z(NULL), recvList_X(NULL), recvList_Y(NULL), recvList_Z(NULL),
recvList_xy(NULL), recvList_yz(NULL), recvList_xz(NULL), recvList_Xy(NULL), recvList_Yz(NULL), recvList_xZ(NULL),
recvList_xY(NULL), recvList_yZ(NULL), recvList_Xz(NULL), recvList_XY(NULL), recvList_YZ(NULL), recvList_XZ(NULL),
recvBuf_x(NULL), recvBuf_y(NULL), recvBuf_z(NULL), recvBuf_X(NULL), recvBuf_Y(NULL), recvBuf_Z(NULL),
recvBuf_xy(NULL), recvBuf_yz(NULL), recvBuf_xz(NULL), recvBuf_Xy(NULL), recvBuf_Yz(NULL), recvBuf_xZ(NULL),
recvBuf_xY(NULL), recvBuf_yZ(NULL), recvBuf_Xz(NULL), recvBuf_XY(NULL), recvBuf_YZ(NULL), recvBuf_XZ(NULL),
sendData_x(NULL), sendData_y(NULL), sendData_z(NULL), sendData_X(NULL), sendData_Y(NULL), sendData_Z(NULL),
sendData_xy(NULL), sendData_yz(NULL), sendData_xz(NULL), sendData_Xy(NULL), sendData_Yz(NULL), sendData_xZ(NULL),
sendData_xY(NULL), sendData_yZ(NULL), sendData_Xz(NULL), sendData_XY(NULL), sendData_YZ(NULL), sendData_XZ(NULL),
recvData_x(NULL), recvData_y(NULL), recvData_z(NULL), recvData_X(NULL), recvData_Y(NULL), recvData_Z(NULL),
recvData_xy(NULL), recvData_yz(NULL), recvData_xz(NULL), recvData_Xy(NULL), recvData_Yz(NULL), recvData_xZ(NULL),
recvData_xY(NULL), recvData_yZ(NULL), recvData_Xz(NULL), recvData_XY(NULL), recvData_YZ(NULL), recvData_XZ(NULL),
id(NULL)
{
NULL_USE( rnk );
NULL_USE( npy );
NULL_USE( npz );
// set up the neighbor ranks
int myrank;
MPI_Comm_rank( Comm, &myrank );
rank_info = RankInfoStruct( myrank, rank_info.nx, rank_info.ny, rank_info.nz );
MPI_Barrier(Comm);
auto db = std::make_shared<Database>( );
db->putScalar<int>( "BC", BC );
db->putVector<int>( "nproc", { npx, npx, npx } );
db->putVector<int>( "n", { nx, ny, nz } );
db->putScalar<int>( "nspheres", 0 );
db->putVector<double>( "L", { lx, ly, lz } );
initialize( db );
}
Domain::Domain( std::shared_ptr<Database> db, MPI_Comm Communicator):
database(db), Nx(0), Ny(0), Nz(0),
Lx(0), Ly(0), Lz(0), Volume(0), BoundaryCondition(0),
Comm(MPI_COMM_NULL),
inlet_layers_x(0), inlet_layers_y(0), inlet_layers_z(0),
outlet_layers_x(0), outlet_layers_y(0), outlet_layers_z(0),
inlet_layers_phase(1),outlet_layers_phase(2),
sendCount_x(0), sendCount_y(0), sendCount_z(0), sendCount_X(0), sendCount_Y(0), sendCount_Z(0),
sendCount_xy(0), sendCount_yz(0), sendCount_xz(0), sendCount_Xy(0), sendCount_Yz(0), sendCount_xZ(0),
sendCount_xY(0), sendCount_yZ(0), sendCount_Xz(0), sendCount_XY(0), sendCount_YZ(0), sendCount_XZ(0),
sendList_x(NULL), sendList_y(NULL), sendList_z(NULL), sendList_X(NULL), sendList_Y(NULL), sendList_Z(NULL),
sendList_xy(NULL), sendList_yz(NULL), sendList_xz(NULL), sendList_Xy(NULL), sendList_Yz(NULL), sendList_xZ(NULL),
sendList_xY(NULL), sendList_yZ(NULL), sendList_Xz(NULL), sendList_XY(NULL), sendList_YZ(NULL), sendList_XZ(NULL),
sendBuf_x(NULL), sendBuf_y(NULL), sendBuf_z(NULL), sendBuf_X(NULL), sendBuf_Y(NULL), sendBuf_Z(NULL),
sendBuf_xy(NULL), sendBuf_yz(NULL), sendBuf_xz(NULL), sendBuf_Xy(NULL), sendBuf_Yz(NULL), sendBuf_xZ(NULL),
sendBuf_xY(NULL), sendBuf_yZ(NULL), sendBuf_Xz(NULL), sendBuf_XY(NULL), sendBuf_YZ(NULL), sendBuf_XZ(NULL),
recvCount_x(0), recvCount_y(0), recvCount_z(0), recvCount_X(0), recvCount_Y(0), recvCount_Z(0),
recvCount_xy(0), recvCount_yz(0), recvCount_xz(0), recvCount_Xy(0), recvCount_Yz(0), recvCount_xZ(0),
recvCount_xY(0), recvCount_yZ(0), recvCount_Xz(0), recvCount_XY(0), recvCount_YZ(0), recvCount_XZ(0),
recvList_x(NULL), recvList_y(NULL), recvList_z(NULL), recvList_X(NULL), recvList_Y(NULL), recvList_Z(NULL),
recvList_xy(NULL), recvList_yz(NULL), recvList_xz(NULL), recvList_Xy(NULL), recvList_Yz(NULL), recvList_xZ(NULL),
recvList_xY(NULL), recvList_yZ(NULL), recvList_Xz(NULL), recvList_XY(NULL), recvList_YZ(NULL), recvList_XZ(NULL),
recvBuf_x(NULL), recvBuf_y(NULL), recvBuf_z(NULL), recvBuf_X(NULL), recvBuf_Y(NULL), recvBuf_Z(NULL),
recvBuf_xy(NULL), recvBuf_yz(NULL), recvBuf_xz(NULL), recvBuf_Xy(NULL), recvBuf_Yz(NULL), recvBuf_xZ(NULL),
recvBuf_xY(NULL), recvBuf_yZ(NULL), recvBuf_Xz(NULL), recvBuf_XY(NULL), recvBuf_YZ(NULL), recvBuf_XZ(NULL),
sendData_x(NULL), sendData_y(NULL), sendData_z(NULL), sendData_X(NULL), sendData_Y(NULL), sendData_Z(NULL),
sendData_xy(NULL), sendData_yz(NULL), sendData_xz(NULL), sendData_Xy(NULL), sendData_Yz(NULL), sendData_xZ(NULL),
sendData_xY(NULL), sendData_yZ(NULL), sendData_Xz(NULL), sendData_XY(NULL), sendData_YZ(NULL), sendData_XZ(NULL),
recvData_x(NULL), recvData_y(NULL), recvData_z(NULL), recvData_X(NULL), recvData_Y(NULL), recvData_Z(NULL),
recvData_xy(NULL), recvData_yz(NULL), recvData_xz(NULL), recvData_Xy(NULL), recvData_Yz(NULL), recvData_xZ(NULL),
recvData_xY(NULL), recvData_yZ(NULL), recvData_Xz(NULL), recvData_XY(NULL), recvData_YZ(NULL), recvData_XZ(NULL),
id(NULL)
{
MPI_Comm_dup(Communicator,&Comm);
// set up the neighbor ranks
int myrank;
MPI_Comm_rank( Comm, &myrank );
initialize( db );
rank_info = RankInfoStruct( myrank, rank_info.nx, rank_info.ny, rank_info.nz );
MPI_Barrier(Comm);
}
Domain::~Domain()
{
// Free sendList
delete [] sendList_x; delete [] sendList_y; delete [] sendList_z;
delete [] sendList_X; delete [] sendList_Y; delete [] sendList_Z;
delete [] sendList_xy; delete [] sendList_yz; delete [] sendList_xz;
delete [] sendList_Xy; delete [] sendList_Yz; delete [] sendList_xZ;
delete [] sendList_xY; delete [] sendList_yZ; delete [] sendList_Xz;
delete [] sendList_XY; delete [] sendList_YZ; delete [] sendList_XZ;
// Free sendBuf
delete [] sendBuf_x; delete [] sendBuf_y; delete [] sendBuf_z;
delete [] sendBuf_X; delete [] sendBuf_Y; delete [] sendBuf_Z;
delete [] sendBuf_xy; delete [] sendBuf_yz; delete [] sendBuf_xz;
delete [] sendBuf_Xy; delete [] sendBuf_Yz; delete [] sendBuf_xZ;
delete [] sendBuf_xY; delete [] sendBuf_yZ; delete [] sendBuf_Xz;
delete [] sendBuf_XY; delete [] sendBuf_YZ; delete [] sendBuf_XZ;
// Free recvList
delete [] recvList_x; delete [] recvList_y; delete [] recvList_z;
delete [] recvList_X; delete [] recvList_Y; delete [] recvList_Z;
delete [] recvList_xy; delete [] recvList_yz; delete [] recvList_xz;
delete [] recvList_Xy; delete [] recvList_Yz; delete [] recvList_xZ;
delete [] recvList_xY; delete [] recvList_yZ; delete [] recvList_Xz;
delete [] recvList_XY; delete [] recvList_YZ; delete [] recvList_XZ;
// Free recvBuf
delete [] recvBuf_x; delete [] recvBuf_y; delete [] recvBuf_z;
delete [] recvBuf_X; delete [] recvBuf_Y; delete [] recvBuf_Z;
delete [] recvBuf_xy; delete [] recvBuf_yz; delete [] recvBuf_xz;
delete [] recvBuf_Xy; delete [] recvBuf_Yz; delete [] recvBuf_xZ;
delete [] recvBuf_xY; delete [] recvBuf_yZ; delete [] recvBuf_Xz;
delete [] recvBuf_XY; delete [] recvBuf_YZ; delete [] recvBuf_XZ;
// Free sendData
delete [] sendData_x; delete [] sendData_y; delete [] sendData_z;
delete [] sendData_X; delete [] sendData_Y; delete [] sendData_Z;
delete [] sendData_xy; delete [] sendData_xY; delete [] sendData_Xy;
delete [] sendData_XY; delete [] sendData_xz; delete [] sendData_xZ;
delete [] sendData_Xz; delete [] sendData_XZ; delete [] sendData_yz;
delete [] sendData_yZ; delete [] sendData_Yz; delete [] sendData_YZ;
// Free recvData
delete [] recvData_x; delete [] recvData_y; delete [] recvData_z;
delete [] recvData_X; delete [] recvData_Y; delete [] recvData_Z;
delete [] recvData_xy; delete [] recvData_xY; delete [] recvData_Xy;
delete [] recvData_XY; delete [] recvData_xz; delete [] recvData_xZ;
delete [] recvData_Xz; delete [] recvData_XZ; delete [] recvData_yz;
delete [] recvData_yZ; delete [] recvData_Yz; delete [] recvData_YZ;
// Free id
delete [] id;
// Free the communicator
if ( Comm != MPI_COMM_WORLD && Comm != MPI_COMM_NULL ) {
MPI_Comm_free(&Comm);
}
}
void Domain::initialize( std::shared_ptr<Database> db )
{
d_db = db;
auto nproc = d_db->getVector<int>("nproc");
auto n = d_db->getVector<int>("n");
ASSERT( n.size() == 3u );
ASSERT( nproc.size() == 3u );
int nx = n[0];
int ny = n[1];
int nz = n[2];
if (d_db->keyExists( "InletLayers" )){
auto InletCount = d_db->getVector<int>( "InletLayers" );
inlet_layers_x = InletCount[0];
inlet_layers_y = InletCount[1];
inlet_layers_z = InletCount[2];
}
if (d_db->keyExists( "OutletLayers" )){
auto OutletCount = d_db->getVector<int>( "OutletLayers" );
outlet_layers_x = OutletCount[0];
outlet_layers_y = OutletCount[1];
outlet_layers_z = OutletCount[2];
}
if (d_db->keyExists( "InletLayersPhase" )){
inlet_layers_phase = d_db->getScalar<int>( "InletLayersPhase" );
}
if (d_db->keyExists( "OutletLayersPhase" )){
outlet_layers_phase = d_db->getScalar<int>( "OutletLayersPhase" );
}
voxel_length = 1.0;
if (d_db->keyExists( "voxel_length" )){
voxel_length = d_db->getScalar<double>("voxel_length");
}
else if (d_db->keyExists( "L" )){
auto Length = d_db->getVector<double>("L");
Lx = Length[0];
Ly = Length[1];
Lz = Length[2];
voxel_length = Lx/(nx*nproc[0]);
}
Lx = nx*nproc[0]*voxel_length;
Ly = ny*nproc[1]*voxel_length;
Lz = nz*nproc[2]*voxel_length;
Nx = nx+2;
Ny = ny+2;
Nz = nz+2;
// Initialize ranks
int myrank;
MPI_Comm_rank( Comm, &myrank );
rank_info = RankInfoStruct(myrank,nproc[0],nproc[1],nproc[2]);
// inlet layers only apply to lower part of domain
if (rank_info.ix > 0) inlet_layers_x = 0;
if (rank_info.jy > 0) inlet_layers_y = 0;
if (rank_info.kz > 0) inlet_layers_z = 0;
// outlet layers only apply to top part of domain
if (rank_info.ix < nproc[0]-1 ) outlet_layers_x = 0;
if (rank_info.jy < nproc[1]-1) outlet_layers_y = 0;
if (rank_info.kz < nproc[2]-1) outlet_layers_z = 0;
// Fill remaining variables
N = Nx*Ny*Nz;
Volume = nx*ny*nx*nproc[0]*nproc[1]*nproc[2]*1.0;
if (myrank==0) printf("voxel length = %f micron \n", voxel_length);
id = new signed char[N];
memset(id,0,N);
BoundaryCondition = d_db->getScalar<int>("BC");
int nprocs;
MPI_Comm_size( Comm, &nprocs );
INSIST(nprocs == nproc[0]*nproc[1]*nproc[2],"Fatal error in processor count!");
}
void Domain::Decomp( const std::string& Filename )
{
//.......................................................................
// Reading the domain information file
//.......................................................................
int rank_offset = 0;
int RANK = rank();
int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
int64_t global_Nx,global_Ny,global_Nz;
int64_t i,j,k,n;
int64_t xStart,yStart,zStart;
int checkerSize;
bool USE_CHECKER = false;
//int inlet_layers_x, inlet_layers_y, inlet_layers_z;
//int outlet_layers_x, outlet_layers_y, outlet_layers_z;
xStart=yStart=zStart=0;
inlet_layers_x = 0;
inlet_layers_y = 0;
inlet_layers_z = 0;
outlet_layers_x = 0;
outlet_layers_y = 0;
outlet_layers_z = 0;
inlet_layers_phase=1;
outlet_layers_phase=2;
checkerSize = 32;
// Read domain parameters
//auto Filename = database->getScalar<std::string>( "Filename" );
//auto L = database->getVector<double>( "L" );
auto size = database->getVector<int>( "n" );
auto SIZE = database->getVector<int>( "N" );
auto nproc = database->getVector<int>( "nproc" );
if (database->keyExists( "offset" )){
auto offset = database->getVector<int>( "offset" );
xStart = offset[0];
yStart = offset[1];
zStart = offset[2];
}
if (database->keyExists( "InletLayers" )){
auto InletCount = database->getVector<int>( "InletLayers" );
inlet_layers_x = InletCount[0];
inlet_layers_y = InletCount[1];
inlet_layers_z = InletCount[2];
}
if (database->keyExists( "OutletLayers" )){
auto OutletCount = database->getVector<int>( "OutletLayers" );
outlet_layers_x = OutletCount[0];
outlet_layers_y = OutletCount[1];
outlet_layers_z = OutletCount[2];
}
if (database->keyExists( "checkerSize" )){
checkerSize = database->getScalar<int>( "checkerSize" );
USE_CHECKER = true;
}
else {
checkerSize = SIZE[0];
}
if (database->keyExists( "InletLayersPhase" )){
inlet_layers_phase = database->getScalar<int>( "InletLayersPhase" );
}
if (database->keyExists( "OutletLayersPhase" )){
outlet_layers_phase = database->getScalar<int>( "OutletLayersPhase" );
}
auto ReadValues = database->getVector<int>( "ReadValues" );
auto WriteValues = database->getVector<int>( "WriteValues" );
auto ReadType = database->getScalar<std::string>( "ReadType" );
if (ReadType == "8bit"){
}
else if (ReadType == "16bit"){
}
else{
//printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
ReadType = "8bit";
}
nx = size[0];
ny = size[1];
nz = size[2];
nprocx = nproc[0];
nprocy = nproc[1];
nprocz = nproc[2];
global_Nx = SIZE[0];
global_Ny = SIZE[1];
global_Nz = SIZE[2];
nprocs=nprocx*nprocy*nprocz;
char *SegData = NULL;
if (RANK==0){
printf("Input media: %s\n",Filename.c_str());
printf("Relabeling %lu values\n",ReadValues.size());
for (size_t idx=0; idx<ReadValues.size(); idx++){
int oldvalue=ReadValues[idx];
int newvalue=WriteValues[idx];
printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
}
// Rank=0 reads the entire segmented data and distributes to worker processes
printf("Dimensions of segmented image: %ld x %ld x %ld \n",global_Nx,global_Ny,global_Nz);
int64_t SIZE = global_Nx*global_Ny*global_Nz;
SegData = new char[SIZE];
if (ReadType == "8bit"){
printf("Reading 8-bit input data \n");
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
size_t ReadSeg;
ReadSeg=fread(SegData,1,SIZE,SEGDAT);
if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
fclose(SEGDAT);
}
else if (ReadType == "16bit"){
printf("Reading 16-bit input data \n");
short int *InputData;
InputData = new short int[SIZE];
FILE *SEGDAT = fopen(Filename.c_str(),"rb");
if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading segmented data");
size_t ReadSeg;
ReadSeg=fread(InputData,2,SIZE,SEGDAT);
if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading segmented data \n");
fclose(SEGDAT);
for (int n=0; n<SIZE; n++){
SegData[n] = char(InputData[n]);
}
}
printf("Read segmented data from %s \n",Filename.c_str());
// relabel the data
std::vector<long int> LabelCount(ReadValues.size(),0);
for (int k = 0; k<global_Nz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
n = k*global_Nx*global_Ny+j*global_Nx+i;
//char locval = loc_id[n];
char locval = SegData[n];
for (size_t idx=0; idx<ReadValues.size(); idx++){
signed char oldvalue=ReadValues[idx];
signed char newvalue=WriteValues[idx];
if (locval == oldvalue){
SegData[n] = newvalue;
LabelCount[idx]++;
idx = ReadValues.size();
}
}
}
}
}
for (size_t idx=0; idx<ReadValues.size(); idx++){
long int label=ReadValues[idx];
long int count=LabelCount[idx];
printf("Label=%ld, Count=%ld \n",label,count);
}
if (USE_CHECKER) {
if (inlet_layers_x > 0){
// use checkerboard pattern
printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
for (int k = 0; k<global_Nz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = xStart; i < xStart+inlet_layers_x; i++){
if ( (j/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (inlet_layers_y > 0){
printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
// use checkerboard pattern
for (int k = 0; k<global_Nz; k++){
for (int j = yStart; j < yStart+inlet_layers_y; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (inlet_layers_z > 0){
printf("Checkerboard pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
// use checkerboard pattern
for (int k = zStart; k < zStart+inlet_layers_z; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize+j/checkerSize)%2 == 0){
// void checkers
//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = inlet_layers_phase;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_x > 0){
// use checkerboard pattern
printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
for (int k = 0; k<global_Nz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = xStart + nx*nprocx - outlet_layers_x; i < xStart + nx*nprocx; i++){
if ( (j/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_y > 0){
printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
// use checkerboard pattern
for (int k = 0; k<global_Nz; k++){
for (int j = yStart + ny*nprocy - outlet_layers_y; j < yStart + ny*nprocy; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize + k/checkerSize)%2 == 0){
// void checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
if (outlet_layers_z > 0){
printf("Checkerboard pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
// use checkerboard pattern
for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
if ( (i/checkerSize+j/checkerSize)%2 == 0){
// void checkers
//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = outlet_layers_phase;
}
else{
// solid checkers
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
}
}
}
}
}
}
else {
if (inlet_layers_z > 0){
printf("Mixed reflection pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
for (int k = zStart; k < zStart+inlet_layers_z; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
signed char local_id = SegData[k*global_Nx*global_Ny+j*global_Nx+i];
signed char reflection_id = SegData[(zStart + nz*nprocz - 1)*global_Nx*global_Ny+j*global_Nx+i];
if ( local_id < 1 && reflection_id > 0){
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = reflection_id;
}
}
}
}
}
if (outlet_layers_z > 0){
printf("Mixed reflection pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
for (int j = 0; j<global_Ny; j++){
for (int i = 0; i<global_Nx; i++){
signed char local_id = SegData[k*global_Nx*global_Ny+j*global_Nx+i];
signed char reflection_id = SegData[zStart*global_Nx*global_Ny+j*global_Nx+i];
if ( local_id < 1 && reflection_id > 0){
SegData[k*global_Nx*global_Ny+j*global_Nx+i] = reflection_id;
}
}
}
}
}
}
}
// Get the rank info
int64_t N = (nx+2)*(ny+2)*(nz+2);
// number of sites to use for periodic boundary condition transition zone
int64_t z_transition_size = (nprocz*nz - (global_Nz - zStart))/2;
if (z_transition_size < 0) z_transition_size=0;
char LocalRankFilename[40];
char *loc_id;
loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
// Set up the sub-domains
if (RANK==0){
printf("Distributing subdomains across %i processors \n",nprocs);
printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
printf("Size of transition region: %ld \n", z_transition_size);
for (int kp=0; kp<nprocz; kp++){
for (int jp=0; jp<nprocy; jp++){
for (int ip=0; ip<nprocx; ip++){
// rank of the process that gets this subdomain
int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
// Pack and send the subdomain for rnk
for (k=0;k<nz+2;k++){
for (j=0;j<ny+2;j++){
for (i=0;i<nx+2;i++){
int64_t x = xStart + ip*nx + i-1;
int64_t y = yStart + jp*ny + j-1;
// int64_t z = zStart + kp*nz + k-1;
int64_t z = zStart + kp*nz + k-1 - z_transition_size;
if (x<xStart) x=xStart;
if (!(x<global_Nx)) x=global_Nx-1;
if (y<yStart) y=yStart;
if (!(y<global_Ny)) y=global_Ny-1;
if (z<zStart) z=zStart;
if (!(z<global_Nz)) z=global_Nz-1;
int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
int64_t nglobal = z*global_Nx*global_Ny+y*global_Nx+x;
loc_id[nlocal] = SegData[nglobal];
}
}
}
if (rnk==0){
for (k=0;k<nz+2;k++){
for (j=0;j<ny+2;j++){
for (i=0;i<nx+2;i++){
int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
id[nlocal] = loc_id[nlocal];
}
}
}
}
else{
//printf("Sending data to process %i \n", rnk);
MPI_Send(loc_id,N,MPI_CHAR,rnk,15,Comm);
}
// Write the data for this rank data
sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
FILE *ID = fopen(LocalRankFilename,"wb");
fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
fclose(ID);
}
}
}
}
else{
// Recieve the subdomain from rank = 0
//printf("Ready to recieve data %i at process %i \n", N,rank);
MPI_Recv(id,N,MPI_CHAR,0,15,Comm,MPI_STATUS_IGNORE);
}
//Comm.barrier();
MPI_Barrier(Comm);
// Compute the porosity
double sum;
double sum_local=0.0;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
if (BoundaryCondition > 0 && BoundaryCondition !=5) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
//.........................................................
// If external boundary conditions are applied remove solid
if (BoundaryCondition > 0 && BoundaryCondition !=5 && kproc() == 0){
if (inlet_layers_z < 4){
inlet_layers_z=4;
if(RANK==0){
printf("NOTE:Non-periodic BC is applied, but the number of Z-inlet layers is not specified (or is smaller than 3 voxels) \n the number of Z-inlet layer is reset to %i voxels, saturated with phase label=%i \n",inlet_layers_z-1,inlet_layers_phase);
}
}
for (int k=0; k<inlet_layers_z; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = inlet_layers_phase;
}
}
}
}
if (BoundaryCondition > 0 && BoundaryCondition !=5 && kproc() == nprocz-1){
if (outlet_layers_z < 4){
outlet_layers_z=4;
if(RANK==nprocs-1){
printf("NOTE:Non-periodic BC is applied, but the number of Z-outlet layers is not specified (or is smaller than 3 voxels) \n the number of Z-outlet layer is reset to %i voxels, saturated with phase label=%i \n",outlet_layers_z-1,outlet_layers_phase);
}
}
for (int k=Nz-outlet_layers_z; k<Nz; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = outlet_layers_phase;
}
}
}
}
for (int k=inlet_layers_z+1; k<Nz-outlet_layers_z-1;k++){
for (int j=1;j<Ny-1;j++){
for (int i=1;i<Nx-1;i++){
int n = k*Nx*Ny+j*Nx+i;
if (id[n] > 0){
sum_local+=1.0;
}
}
}
}
MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,Comm);
//sum = Comm.sumReduce(sum_local);
porosity = sum*iVol_global;
if (rank()==0) printf("Media porosity = %f \n",porosity);
//.........................................................
}
void Domain::AggregateLabels( const std::string& filename ){
int nx = Nx;
int ny = Ny;
int nz = Nz;
int npx = nprocx();
int npy = nprocy();
int npz = nprocz();
int ipx = iproc();
int ipy = jproc();
int ipz = kproc();
int nprocs = nprocx()*nprocy()*nprocz();
int full_nx = npx*(nx-2);
int full_ny = npy*(ny-2);
int full_nz = npz*(nz-2);
int local_size = (nx-2)*(ny-2)*(nz-2);
long int full_size = long(full_nx)*long(full_ny)*long(full_nz);
signed char *LocalID;
LocalID = new signed char [local_size];
//printf("aggregate labels: local size=%i, global size = %i",local_size, full_size);
// assign the ID for the local sub-region
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
for (int i=1; i<nx-1; i++){
int n = k*nx*ny+j*nx+i;
signed char local_id_val = id[n];
LocalID[(k-1)*(nx-2)*(ny-2) + (j-1)*(nx-2) + i-1] = local_id_val;
}
}
}
MPI_Barrier(Comm);
// populate the FullID
if (rank() == 0){
signed char *FullID;
FullID = new signed char [full_size];
// first handle local ID for rank 0
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
for (int i=1; i<nx-1; i++){
int x = i-1;
int y = j-1;
int z = k-1;
int n_local = (k-1)*(nx-2)*(ny-2) + (j-1)*(nx-2) + i-1;
int n_full = z*full_nx*full_ny + y*full_nx + x;
FullID[n_full] = LocalID[n_local];
}
}
}
// next get the local ID from the other ranks
for (int rnk = 1; rnk<nprocs; rnk++){
ipz = rnk / (npx*npy);
ipy = (rnk - ipz*npx*npy) / npx;
ipx = (rnk - ipz*npx*npy - ipy*npx);
//printf("ipx=%i ipy=%i ipz=%i\n", ipx, ipy, ipz);
int tag = 15+rnk;
MPI_Recv(LocalID,local_size,MPI_CHAR,rnk,tag,Comm,MPI_STATUS_IGNORE);
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
for (int i=1; i<nx-1; i++){
int x = i-1 + ipx*(nx-2);
int y = j-1 + ipy*(ny-2);
int z = k-1 + ipz*(nz-2);
int n_local = (k-1)*(nx-2)*(ny-2) + (j-1)*(nx-2) + i-1;
int n_full = z*full_nx*full_ny + y*full_nx + x;
FullID[n_full] = LocalID[n_local];
}
}
}
}
// write the output
FILE *OUTFILE = fopen(filename.c_str(),"wb");
fwrite(FullID,1,full_size,OUTFILE);
fclose(OUTFILE);
}
else{
// send LocalID to rank=0
int tag = 15+ rank();
int dstrank = 0;
MPI_Send(LocalID,local_size,MPI_CHAR,dstrank,tag,Comm);
}
MPI_Barrier(Comm);
}
/********************************************************
* Initialize communication *
********************************************************/
void Domain::CommInit()
{
int i,j,k,n;
int sendtag = 21;
int recvtag = 21;
//......................................................................................
sendCount_x = sendCount_y = sendCount_z = sendCount_X = sendCount_Y = sendCount_Z = 0;
sendCount_xy = sendCount_yz = sendCount_xz = sendCount_Xy = sendCount_Yz = sendCount_xZ = 0;
sendCount_xY = sendCount_yZ = sendCount_Xz = sendCount_XY = sendCount_YZ = sendCount_XZ = 0;
//......................................................................................
for (k=1; k<Nz-1; k++){
for (j=1; j<Ny-1; j++){
for (i=1; i<Nx-1; i++){
// Check the phase ID
if (id[k*Nx*Ny+j*Nx+i] > 0){
// Counts for the six faces
if (i==1) sendCount_x++;
if (j==1) sendCount_y++;
if (k==1) sendCount_z++;
if (i==Nx-2) sendCount_X++;
if (j==Ny-2) sendCount_Y++;
if (k==Nz-2) sendCount_Z++;
// Counts for the twelve edges
if (i==1 && j==1) sendCount_xy++;
if (i==1 && j==Ny-2) sendCount_xY++;
if (i==Nx-2 && j==1) sendCount_Xy++;
if (i==Nx-2 && j==Ny-2) sendCount_XY++;
if (i==1 && k==1) sendCount_xz++;
if (i==1 && k==Nz-2) sendCount_xZ++;
if (i==Nx-2 && k==1) sendCount_Xz++;
if (i==Nx-2 && k==Nz-2) sendCount_XZ++;
if (j==1 && k==1) sendCount_yz++;
if (j==1 && k==Nz-2) sendCount_yZ++;
if (j==Ny-2 && k==1) sendCount_Yz++;
if (j==Ny-2 && k==Nz-2) sendCount_YZ++;
}
}
}
}
// allocate send lists
sendList_x = new int [sendCount_x];
sendList_y = new int [sendCount_y];
sendList_z = new int [sendCount_z];
sendList_X = new int [sendCount_X];
sendList_Y = new int [sendCount_Y];
sendList_Z = new int [sendCount_Z];
sendList_xy = new int [sendCount_xy];
sendList_yz = new int [sendCount_yz];
sendList_xz = new int [sendCount_xz];
sendList_Xy = new int [sendCount_Xy];
sendList_Yz = new int [sendCount_Yz];
sendList_xZ = new int [sendCount_xZ];
sendList_xY = new int [sendCount_xY];
sendList_yZ = new int [sendCount_yZ];
sendList_Xz = new int [sendCount_Xz];
sendList_XY = new int [sendCount_XY];
sendList_YZ = new int [sendCount_YZ];
sendList_XZ = new int [sendCount_XZ];
// Populate the send list
sendCount_x = sendCount_y = sendCount_z = sendCount_X = sendCount_Y = sendCount_Z = 0;
sendCount_xy = sendCount_yz = sendCount_xz = sendCount_Xy = sendCount_Yz = sendCount_xZ = 0;
sendCount_xY = sendCount_yZ = sendCount_Xz = sendCount_XY = sendCount_YZ = sendCount_XZ = 0;
for (k=1; k<Nz-1; k++){
for (j=1; j<Ny-1; j++){
for (i=1; i<Nx-1; i++){
// Local value to send
n = k*Nx*Ny+j*Nx+i;
if (id[n] > 0){
// Counts for the six faces
if (i==1) sendList_x[sendCount_x++]=n;
if (j==1) sendList_y[sendCount_y++]=n;
if (k==1) sendList_z[sendCount_z++]=n;
if (i==Nx-2) sendList_X[sendCount_X++]=n;
if (j==Ny-2) sendList_Y[sendCount_Y++]=n;
if (k==Nz-2) sendList_Z[sendCount_Z++]=n;
// Counts for the twelve edges
if (i==1 && j==1) sendList_xy[sendCount_xy++]=n;
if (i==1 && j==Ny-2) sendList_xY[sendCount_xY++]=n;
if (i==Nx-2 && j==1) sendList_Xy[sendCount_Xy++]=n;
if (i==Nx-2 && j==Ny-2) sendList_XY[sendCount_XY++]=n;
if (i==1 && k==1) sendList_xz[sendCount_xz++]=n;
if (i==1 && k==Nz-2) sendList_xZ[sendCount_xZ++]=n;
if (i==Nx-2 && k==1) sendList_Xz[sendCount_Xz++]=n;
if (i==Nx-2 && k==Nz-2) sendList_XZ[sendCount_XZ++]=n;
if (j==1 && k==1) sendList_yz[sendCount_yz++]=n;
if (j==1 && k==Nz-2) sendList_yZ[sendCount_yZ++]=n;
if (j==Ny-2 && k==1) sendList_Yz[sendCount_Yz++]=n;
if (j==Ny-2 && k==Nz-2) sendList_YZ[sendCount_YZ++]=n;
}
}
}
}
// allocate send buffers
sendBuf_x = new int [sendCount_x];
sendBuf_y = new int [sendCount_y];
sendBuf_z = new int [sendCount_z];
sendBuf_X = new int [sendCount_X];
sendBuf_Y = new int [sendCount_Y];
sendBuf_Z = new int [sendCount_Z];
sendBuf_xy = new int [sendCount_xy];
sendBuf_yz = new int [sendCount_yz];
sendBuf_xz = new int [sendCount_xz];
sendBuf_Xy = new int [sendCount_Xy];
sendBuf_Yz = new int [sendCount_Yz];
sendBuf_xZ = new int [sendCount_xZ];
sendBuf_xY = new int [sendCount_xY];
sendBuf_yZ = new int [sendCount_yZ];
sendBuf_Xz = new int [sendCount_Xz];
sendBuf_XY = new int [sendCount_XY];
sendBuf_YZ = new int [sendCount_YZ];
sendBuf_XZ = new int [sendCount_XZ];
//......................................................................................
MPI_Isend(&sendCount_x, 1,MPI_INT,rank_x(),sendtag+0,Comm,&req1[0]);
MPI_Irecv(&recvCount_X, 1,MPI_INT,rank_X(),recvtag+0,Comm,&req2[0]);
MPI_Isend(&sendCount_X, 1,MPI_INT,rank_X(),sendtag+1,Comm,&req1[1]);
MPI_Irecv(&recvCount_x, 1,MPI_INT,rank_x(),recvtag+1,Comm,&req2[1]);
MPI_Isend(&sendCount_y, 1,MPI_INT,rank_y(),sendtag+2,Comm,&req1[2]);
MPI_Irecv(&recvCount_Y, 1,MPI_INT,rank_Y(),recvtag+2,Comm,&req2[2]);
MPI_Isend(&sendCount_Y, 1,MPI_INT,rank_Y(),sendtag+3,Comm,&req1[3]);
MPI_Irecv(&recvCount_y, 1,MPI_INT,rank_y(),recvtag+3,Comm,&req2[3]);
MPI_Isend(&sendCount_z, 1,MPI_INT,rank_z(),sendtag+4,Comm,&req1[4]);
MPI_Irecv(&recvCount_Z, 1,MPI_INT,rank_Z(),recvtag+4,Comm,&req2[4]);
MPI_Isend(&sendCount_Z, 1,MPI_INT,rank_Z(),sendtag+5,Comm,&req1[5]);
MPI_Irecv(&recvCount_z, 1,MPI_INT,rank_z(),recvtag+5,Comm,&req2[5]);
MPI_Isend(&sendCount_xy, 1,MPI_INT,rank_xy(),sendtag+6,Comm,&req1[6]);
MPI_Irecv(&recvCount_XY, 1,MPI_INT,rank_XY(),recvtag+6,Comm,&req2[6]);
MPI_Isend(&sendCount_XY, 1,MPI_INT,rank_XY(),sendtag+7,Comm,&req1[7]);
MPI_Irecv(&recvCount_xy, 1,MPI_INT,rank_xy(),recvtag+7,Comm,&req2[7]);
MPI_Isend(&sendCount_Xy, 1,MPI_INT,rank_Xy(),sendtag+8,Comm,&req1[8]);
MPI_Irecv(&recvCount_xY, 1,MPI_INT,rank_xY(),recvtag+8,Comm,&req2[8]);
MPI_Isend(&sendCount_xY, 1,MPI_INT,rank_xY(),sendtag+9,Comm,&req1[9]);
MPI_Irecv(&recvCount_Xy, 1,MPI_INT,rank_Xy(),recvtag+9,Comm,&req2[9]);
MPI_Isend(&sendCount_xz, 1,MPI_INT,rank_xz(),sendtag+10,Comm,&req1[10]);
MPI_Irecv(&recvCount_XZ, 1,MPI_INT,rank_XZ(),recvtag+10,Comm,&req2[10]);
MPI_Isend(&sendCount_XZ, 1,MPI_INT,rank_XZ(),sendtag+11,Comm,&req1[11]);
MPI_Irecv(&recvCount_xz, 1,MPI_INT,rank_xz(),recvtag+11,Comm,&req2[11]);
MPI_Isend(&sendCount_Xz, 1,MPI_INT,rank_Xz(),sendtag+12,Comm,&req1[12]);
MPI_Irecv(&recvCount_xZ, 1,MPI_INT,rank_xZ(),recvtag+12,Comm,&req2[12]);
MPI_Isend(&sendCount_xZ, 1,MPI_INT,rank_xZ(),sendtag+13,Comm,&req1[13]);
MPI_Irecv(&recvCount_Xz, 1,MPI_INT,rank_Xz(),recvtag+13,Comm,&req2[13]);
MPI_Isend(&sendCount_yz, 1,MPI_INT,rank_yz(),sendtag+14,Comm,&req1[14]);
MPI_Irecv(&recvCount_YZ, 1,MPI_INT,rank_YZ(),recvtag+14,Comm,&req2[14]);
MPI_Isend(&sendCount_YZ, 1,MPI_INT,rank_YZ(),sendtag+15,Comm,&req1[15]);
MPI_Irecv(&recvCount_yz, 1,MPI_INT,rank_yz(),recvtag+15,Comm,&req2[15]);
MPI_Isend(&sendCount_Yz, 1,MPI_INT,rank_Yz(),sendtag+16,Comm,&req1[16]);
MPI_Irecv(&recvCount_yZ, 1,MPI_INT,rank_yZ(),recvtag+16,Comm,&req2[16]);
MPI_Isend(&sendCount_yZ, 1,MPI_INT,rank_yZ(),sendtag+17,Comm,&req1[17]);
MPI_Irecv(&recvCount_Yz, 1,MPI_INT,rank_Yz(),recvtag+17,Comm,&req2[17]);
MPI_Waitall(18,req1,stat1);
MPI_Waitall(18,req2,stat2);
MPI_Barrier(Comm);
//......................................................................................
// recv buffers
recvList_x = new int [recvCount_x];
recvList_y = new int [recvCount_y];
recvList_z = new int [recvCount_z];
recvList_X = new int [recvCount_X];
recvList_Y = new int [recvCount_Y];
recvList_Z = new int [recvCount_Z];
recvList_xy = new int [recvCount_xy];
recvList_yz = new int [recvCount_yz];
recvList_xz = new int [recvCount_xz];
recvList_Xy = new int [recvCount_Xy];
recvList_Yz = new int [recvCount_Yz];
recvList_xZ = new int [recvCount_xZ];
recvList_xY = new int [recvCount_xY];
recvList_yZ = new int [recvCount_yZ];
recvList_Xz = new int [recvCount_Xz];
recvList_XY = new int [recvCount_XY];
recvList_YZ = new int [recvCount_YZ];
recvList_XZ = new int [recvCount_XZ];
//......................................................................................
MPI_Isend(sendList_x, sendCount_x,MPI_INT,rank_x(),sendtag,Comm,&req1[0]);
MPI_Irecv(recvList_X, recvCount_X,MPI_INT,rank_X(),recvtag,Comm,&req2[0]);
MPI_Isend(sendList_X, sendCount_X,MPI_INT,rank_X(),sendtag,Comm,&req1[1]);
MPI_Irecv(recvList_x, recvCount_x,MPI_INT,rank_x(),recvtag,Comm,&req2[1]);
MPI_Isend(sendList_y, sendCount_y,MPI_INT,rank_y(),sendtag,Comm,&req1[2]);
MPI_Irecv(recvList_Y, recvCount_Y,MPI_INT,rank_Y(),recvtag,Comm,&req2[2]);
MPI_Isend(sendList_Y, sendCount_Y,MPI_INT,rank_Y(),sendtag,Comm,&req1[3]);
MPI_Irecv(recvList_y, recvCount_y,MPI_INT,rank_y(),recvtag,Comm,&req2[3]);
MPI_Isend(sendList_z, sendCount_z,MPI_INT,rank_z(),sendtag,Comm,&req1[4]);
MPI_Irecv(recvList_Z, recvCount_Z,MPI_INT,rank_Z(),recvtag,Comm,&req2[4]);
MPI_Isend(sendList_Z, sendCount_Z,MPI_INT,rank_Z(),sendtag,Comm,&req1[5]);
MPI_Irecv(recvList_z, recvCount_z,MPI_INT,rank_z(),recvtag,Comm,&req2[5]);
MPI_Isend(sendList_xy, sendCount_xy,MPI_INT,rank_xy(),sendtag,Comm,&req1[6]);
MPI_Irecv(recvList_XY, recvCount_XY,MPI_INT,rank_XY(),recvtag,Comm,&req2[6]);
MPI_Isend(sendList_XY, sendCount_XY,MPI_INT,rank_XY(),sendtag,Comm,&req1[7]);
MPI_Irecv(recvList_xy, recvCount_xy,MPI_INT,rank_xy(),recvtag,Comm,&req2[7]);
MPI_Isend(sendList_Xy, sendCount_Xy,MPI_INT,rank_Xy(),sendtag,Comm,&req1[8]);
MPI_Irecv(recvList_xY, recvCount_xY,MPI_INT,rank_xY(),recvtag,Comm,&req2[8]);
MPI_Isend(sendList_xY, sendCount_xY,MPI_INT,rank_xY(),sendtag,Comm,&req1[9]);
MPI_Irecv(recvList_Xy, recvCount_Xy,MPI_INT,rank_Xy(),recvtag,Comm,&req2[9]);
MPI_Isend(sendList_xz, sendCount_xz,MPI_INT,rank_xz(),sendtag,Comm,&req1[10]);
MPI_Irecv(recvList_XZ, recvCount_XZ,MPI_INT,rank_XZ(),recvtag,Comm,&req2[10]);
MPI_Isend(sendList_XZ, sendCount_XZ,MPI_INT,rank_XZ(),sendtag,Comm,&req1[11]);
MPI_Irecv(recvList_xz, recvCount_xz,MPI_INT,rank_xz(),recvtag,Comm,&req2[11]);
MPI_Isend(sendList_Xz, sendCount_Xz,MPI_INT,rank_Xz(),sendtag,Comm,&req1[12]);
MPI_Irecv(recvList_xZ, recvCount_xZ,MPI_INT,rank_xZ(),recvtag,Comm,&req2[12]);
MPI_Isend(sendList_xZ, sendCount_xZ,MPI_INT,rank_xZ(),sendtag,Comm,&req1[13]);
MPI_Irecv(recvList_Xz, recvCount_Xz,MPI_INT,rank_Xz(),recvtag,Comm,&req2[13]);
MPI_Isend(sendList_yz, sendCount_yz,MPI_INT,rank_yz(),sendtag,Comm,&req1[14]);
MPI_Irecv(recvList_YZ, recvCount_YZ,MPI_INT,rank_YZ(),recvtag,Comm,&req2[14]);
MPI_Isend(sendList_YZ, sendCount_YZ,MPI_INT,rank_YZ(),sendtag,Comm,&req1[15]);
MPI_Irecv(recvList_yz, recvCount_yz,MPI_INT,rank_yz(),recvtag,Comm,&req2[15]);
MPI_Isend(sendList_Yz, sendCount_Yz,MPI_INT,rank_Yz(),sendtag,Comm,&req1[16]);
MPI_Irecv(recvList_yZ, recvCount_yZ,MPI_INT,rank_yZ(),recvtag,Comm,&req2[16]);
MPI_Isend(sendList_yZ, sendCount_yZ,MPI_INT,rank_yZ(),sendtag,Comm,&req1[17]);
MPI_Irecv(recvList_Yz, recvCount_Yz,MPI_INT,rank_Yz(),recvtag,Comm,&req2[17]);
MPI_Waitall(18,req1,stat1);
MPI_Waitall(18,req2,stat2);
//......................................................................................
for (int idx=0; idx<recvCount_x; idx++) recvList_x[idx] -= (Nx-2);
for (int idx=0; idx<recvCount_X; idx++) recvList_X[idx] += (Nx-2);
for (int idx=0; idx<recvCount_y; idx++) recvList_y[idx] -= (Ny-2)*Nx;
for (int idx=0; idx<recvCount_Y; idx++) recvList_Y[idx] += (Ny-2)*Nx;
for (int idx=0; idx<recvCount_z; idx++) recvList_z[idx] -= (Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_Z; idx++) recvList_Z[idx] += (Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_xy; idx++) recvList_xy[idx] -= (Nx-2)+(Ny-2)*Nx;
for (int idx=0; idx<recvCount_XY; idx++) recvList_XY[idx] += (Nx-2)+(Ny-2)*Nx;
for (int idx=0; idx<recvCount_xY; idx++) recvList_xY[idx] -= (Nx-2)-(Ny-2)*Nx;
for (int idx=0; idx<recvCount_Xy; idx++) recvList_Xy[idx] += (Nx-2)-(Ny-2)*Nx;
for (int idx=0; idx<recvCount_xz; idx++) recvList_xz[idx] -= (Nx-2)+(Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_XZ; idx++) recvList_XZ[idx] += (Nx-2)+(Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_xZ; idx++) recvList_xZ[idx] -= (Nx-2)-(Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_Xz; idx++) recvList_Xz[idx] += (Nx-2)-(Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_yz; idx++) recvList_yz[idx] -= (Ny-2)*Nx + (Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_YZ; idx++) recvList_YZ[idx] += (Ny-2)*Nx + (Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_yZ; idx++) recvList_yZ[idx] -= (Ny-2)*Nx - (Nz-2)*Nx*Ny;
for (int idx=0; idx<recvCount_Yz; idx++) recvList_Yz[idx] += (Ny-2)*Nx - (Nz-2)*Nx*Ny;
//......................................................................................
// allocate recv buffers
recvBuf_x = new int [recvCount_x];
recvBuf_y = new int [recvCount_y];
recvBuf_z = new int [recvCount_z];
recvBuf_X = new int [recvCount_X];
recvBuf_Y = new int [recvCount_Y];
recvBuf_Z = new int [recvCount_Z];
recvBuf_xy = new int [recvCount_xy];
recvBuf_yz = new int [recvCount_yz];
recvBuf_xz = new int [recvCount_xz];
recvBuf_Xy = new int [recvCount_Xy];
recvBuf_Yz = new int [recvCount_Yz];
recvBuf_xZ = new int [recvCount_xZ];
recvBuf_xY = new int [recvCount_xY];
recvBuf_yZ = new int [recvCount_yZ];
recvBuf_Xz = new int [recvCount_Xz];
recvBuf_XY = new int [recvCount_XY];
recvBuf_YZ = new int [recvCount_YZ];
recvBuf_XZ = new int [recvCount_XZ];
//......................................................................................
// send buffers
sendData_x = new double [sendCount_x];
sendData_y = new double [sendCount_y];
sendData_z = new double [sendCount_z];
sendData_X = new double [sendCount_X];
sendData_Y = new double [sendCount_Y];
sendData_Z = new double [sendCount_Z];
sendData_xy = new double [sendCount_xy];
sendData_yz = new double [sendCount_yz];
sendData_xz = new double [sendCount_xz];
sendData_Xy = new double [sendCount_Xy];
sendData_Yz = new double [sendCount_Yz];
sendData_xZ = new double [sendCount_xZ];
sendData_xY = new double [sendCount_xY];
sendData_yZ = new double [sendCount_yZ];
sendData_Xz = new double [sendCount_Xz];
sendData_XY = new double [sendCount_XY];
sendData_YZ = new double [sendCount_YZ];
sendData_XZ = new double [sendCount_XZ];
//......................................................................................
// recv buffers
recvData_x = new double [recvCount_x];
recvData_y = new double [recvCount_y];
recvData_z = new double [recvCount_z];
recvData_X = new double [recvCount_X];
recvData_Y = new double [recvCount_Y];
recvData_Z = new double [recvCount_Z];
recvData_xy = new double [recvCount_xy];
recvData_yz = new double [recvCount_yz];
recvData_xz = new double [recvCount_xz];
recvData_Xy = new double [recvCount_Xy];
recvData_xZ = new double [recvCount_xZ];
recvData_xY = new double [recvCount_xY];
recvData_yZ = new double [recvCount_yZ];
recvData_Yz = new double [recvCount_Yz];
recvData_Xz = new double [recvCount_Xz];
recvData_XY = new double [recvCount_XY];
recvData_YZ = new double [recvCount_YZ];
recvData_XZ = new double [recvCount_XZ];
//......................................................................................
}
void Domain::ReadIDs(){
// Read the IDs from input file
int nprocs=nprocx()*nprocy()*nprocz();
size_t readID;
char LocalRankString[8];
char LocalRankFilename[40];
//.......................................................................
if (rank() == 0) printf("Read input media... \n");
//.......................................................................
sprintf(LocalRankString,"%05d",rank());
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
// .......... READ THE INPUT FILE .......................................
if (rank()==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
sprintf(LocalRankFilename,"ID.%05i",rank());
FILE *IDFILE = fopen(LocalRankFilename,"rb");
if (IDFILE==NULL) ERROR("Domain::ReadIDs -- Error opening file: ID.xxxxx");
readID=fread(id,1,N,IDFILE);
if (readID != size_t(N)) printf("Domain::ReadIDs -- Error reading ID (rank=%i) \n",rank());
fclose(IDFILE);
// Compute the porosity
double sum;
double sum_local=0.0;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
if (BoundaryCondition > 0 && BoundaryCondition !=5) iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-6));
//.........................................................
// If external boundary conditions are applied remove solid
if (BoundaryCondition > 0 && BoundaryCondition !=5 && kproc() == 0){
if (inlet_layers_z < 4) inlet_layers_z=4;
for (int k=0; k<inlet_layers_z; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = 1;
}
}
}
}
if (BoundaryCondition > 0 && BoundaryCondition !=5 && kproc() == nprocz()-1){
if (outlet_layers_z < 4) outlet_layers_z=4;
for (int k=Nz-outlet_layers_z; k<Nz; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = 2;
}
}
}
}
for (int k=inlet_layers_z+1; k<Nz-outlet_layers_z-1;k++){
for (int j=1;j<Ny-1;j++){
for (int i=1;i<Nx-1;i++){
int n = k*Nx*Ny+j*Nx+i;
if (id[n] > 0){
sum_local+=1.0;
}
}
}
}
MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,Comm);
porosity = sum*iVol_global;
if (rank()==0) printf("Media porosity = %f \n",porosity);
//.........................................................
}
int Domain::PoreCount(){
/*
* count the number of nodes occupied by mobile phases
*/
int Npore=0; // number of local pore nodes
for (int k=1;k<Nz-1;k++){
for (int j=1;j<Ny-1;j++){
for (int i=1;i<Nx-1;i++){
int n = k*Nx*Ny+j*Nx+i;
if (id[n] > 0){
Npore++;
}
}
}
}
return Npore;
}
void Domain::CommunicateMeshHalo(DoubleArray &Mesh)
{
int sendtag, recvtag;
sendtag = recvtag = 7;
double *MeshData = Mesh.data();
PackMeshData(sendList_x, sendCount_x ,sendData_x, MeshData);
PackMeshData(sendList_X, sendCount_X ,sendData_X, MeshData);
PackMeshData(sendList_y, sendCount_y ,sendData_y, MeshData);
PackMeshData(sendList_Y, sendCount_Y ,sendData_Y, MeshData);
PackMeshData(sendList_z, sendCount_z ,sendData_z, MeshData);
PackMeshData(sendList_Z, sendCount_Z ,sendData_Z, MeshData);
PackMeshData(sendList_xy, sendCount_xy ,sendData_xy, MeshData);
PackMeshData(sendList_Xy, sendCount_Xy ,sendData_Xy, MeshData);
PackMeshData(sendList_xY, sendCount_xY ,sendData_xY, MeshData);
PackMeshData(sendList_XY, sendCount_XY ,sendData_XY, MeshData);
PackMeshData(sendList_xz, sendCount_xz ,sendData_xz, MeshData);
PackMeshData(sendList_Xz, sendCount_Xz ,sendData_Xz, MeshData);
PackMeshData(sendList_xZ, sendCount_xZ ,sendData_xZ, MeshData);
PackMeshData(sendList_XZ, sendCount_XZ ,sendData_XZ, MeshData);
PackMeshData(sendList_yz, sendCount_yz ,sendData_yz, MeshData);
PackMeshData(sendList_Yz, sendCount_Yz ,sendData_Yz, MeshData);
PackMeshData(sendList_yZ, sendCount_yZ ,sendData_yZ, MeshData);
PackMeshData(sendList_YZ, sendCount_YZ ,sendData_YZ, MeshData);
//......................................................................................
MPI_Sendrecv(sendData_x,sendCount_x,MPI_DOUBLE,rank_x(),sendtag,
recvData_X,recvCount_X,MPI_DOUBLE,rank_X(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_X,sendCount_X,MPI_DOUBLE,rank_X(),sendtag,
recvData_x,recvCount_x,MPI_DOUBLE,rank_x(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_y,sendCount_y,MPI_DOUBLE,rank_y(),sendtag,
recvData_Y,recvCount_Y,MPI_DOUBLE,rank_Y(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_Y,sendCount_Y,MPI_DOUBLE,rank_Y(),sendtag,
recvData_y,recvCount_y,MPI_DOUBLE,rank_y(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_z,sendCount_z,MPI_DOUBLE,rank_z(),sendtag,
recvData_Z,recvCount_Z,MPI_DOUBLE,rank_Z(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_Z,sendCount_Z,MPI_DOUBLE,rank_Z(),sendtag,
recvData_z,recvCount_z,MPI_DOUBLE,rank_z(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_xy,sendCount_xy,MPI_DOUBLE,rank_xy(),sendtag,
recvData_XY,recvCount_XY,MPI_DOUBLE,rank_XY(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_XY,sendCount_XY,MPI_DOUBLE,rank_XY(),sendtag,
recvData_xy,recvCount_xy,MPI_DOUBLE,rank_xy(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_Xy,sendCount_Xy,MPI_DOUBLE,rank_Xy(),sendtag,
recvData_xY,recvCount_xY,MPI_DOUBLE,rank_xY(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_xY,sendCount_xY,MPI_DOUBLE,rank_xY(),sendtag,
recvData_Xy,recvCount_Xy,MPI_DOUBLE,rank_Xy(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_xz,sendCount_xz,MPI_DOUBLE,rank_xz(),sendtag,
recvData_XZ,recvCount_XZ,MPI_DOUBLE,rank_XZ(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_XZ,sendCount_XZ,MPI_DOUBLE,rank_XZ(),sendtag,
recvData_xz,recvCount_xz,MPI_DOUBLE,rank_xz(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_Xz,sendCount_Xz,MPI_DOUBLE,rank_Xz(),sendtag,
recvData_xZ,recvCount_xZ,MPI_DOUBLE,rank_xZ(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_xZ,sendCount_xZ,MPI_DOUBLE,rank_xZ(),sendtag,
recvData_Xz,recvCount_Xz,MPI_DOUBLE,rank_Xz(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_yz,sendCount_yz,MPI_DOUBLE,rank_yz(),sendtag,
recvData_YZ,recvCount_YZ,MPI_DOUBLE,rank_YZ(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_YZ,sendCount_YZ,MPI_DOUBLE,rank_YZ(),sendtag,
recvData_yz,recvCount_yz,MPI_DOUBLE,rank_yz(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_Yz,sendCount_Yz,MPI_DOUBLE,rank_Yz(),sendtag,
recvData_yZ,recvCount_yZ,MPI_DOUBLE,rank_yZ(),recvtag,Comm,MPI_STATUS_IGNORE);
MPI_Sendrecv(sendData_yZ,sendCount_yZ,MPI_DOUBLE,rank_yZ(),sendtag,
recvData_Yz,recvCount_Yz,MPI_DOUBLE,rank_Yz(),recvtag,Comm,MPI_STATUS_IGNORE);
//........................................................................................
UnpackMeshData(recvList_x, recvCount_x ,recvData_x, MeshData);
UnpackMeshData(recvList_X, recvCount_X ,recvData_X, MeshData);
UnpackMeshData(recvList_y, recvCount_y ,recvData_y, MeshData);
UnpackMeshData(recvList_Y, recvCount_Y ,recvData_Y, MeshData);
UnpackMeshData(recvList_z, recvCount_z ,recvData_z, MeshData);
UnpackMeshData(recvList_Z, recvCount_Z ,recvData_Z, MeshData);
UnpackMeshData(recvList_xy, recvCount_xy ,recvData_xy, MeshData);
UnpackMeshData(recvList_Xy, recvCount_Xy ,recvData_Xy, MeshData);
UnpackMeshData(recvList_xY, recvCount_xY ,recvData_xY, MeshData);
UnpackMeshData(recvList_XY, recvCount_XY ,recvData_XY, MeshData);
UnpackMeshData(recvList_xz, recvCount_xz ,recvData_xz, MeshData);
UnpackMeshData(recvList_Xz, recvCount_Xz ,recvData_Xz, MeshData);
UnpackMeshData(recvList_xZ, recvCount_xZ ,recvData_xZ, MeshData);
UnpackMeshData(recvList_XZ, recvCount_XZ ,recvData_XZ, MeshData);
UnpackMeshData(recvList_yz, recvCount_yz ,recvData_yz, MeshData);
UnpackMeshData(recvList_Yz, recvCount_Yz ,recvData_Yz, MeshData);
UnpackMeshData(recvList_yZ, recvCount_yZ ,recvData_yZ, MeshData);
UnpackMeshData(recvList_YZ, recvCount_YZ ,recvData_YZ, MeshData);
}
// Ideally stuff below here should be moved somewhere else -- doesn't really belong here
void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq, size_t Np)
{
double value;
ofstream File(FILENAME,ios::binary);
for (size_t n=0; n<Np; n++){
// Write the two density values
value = cDen[n];
File.write((char*) &value, sizeof(value));
value = cDen[Np+n];
File.write((char*) &value, sizeof(value));
// Write the even distributions
for (size_t q=0; q<19; q++){
value = cfq[q*Np+n];
File.write((char*) &value, sizeof(value));
}
}
File.close();
}
void ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq, size_t Np)
{
double value=0;
ifstream File(FILENAME,ios::binary);
for (size_t n=0; n<Np; n++){
File.read((char*) &value, sizeof(value));
cPhi[n] = value;
// Read the distributions
for (size_t q=0; q<19; q++){
File.read((char*) &value, sizeof(value));
cfq[q*Np+n] = value;
}
}
File.close();
}
void ReadBinaryFile(char *FILENAME, double *Data, size_t N)
{
double value;
ifstream File(FILENAME,ios::binary);
if (File.good()){
for (size_t n=0; n<N; n++){
// Write the two density values
File.read((char*) &value, sizeof(value));
Data[n] = value;
}
}
else {
for (size_t n=0; n<N; n++) Data[n] = 1.2e-34;
}
File.close();
}
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