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LBPM/tests/TestBubble.cpp
James McClure 20800ed7eb partial merge
2021-01-04 19:33:27 -05:00

997 lines
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#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
#include "analysis/pmmc.h"
#include "common/ScaLBL.h"
#include "common/MPI_Helpers.h"
#include "common/Communication.h"
#include "IO/Mesh.h"
#include "IO/Writer.h"
#include "ProfilerApp.h"
using namespace std;
std::shared_ptr<Database> readInput( const std::string& file )
{
if ( exists( file )
return std::make_shared<Database>( file );
auto db = std::make_shared<Database>();
db.putData( "Color", std::make_shared<Database>() );
db.putData( "Domain", std::make_shared<Database>() );
return db;
}
int main(int argc, char **argv)
{
// Initialize MPI
int provided_thread_support = -1;
MPI_Init_thread(&argc,&argv,MPI_THREAD_MULTIPLE,&provided_thread_support);
MPI_Comm comm;
MPI_Comm_dup(MPI_COMM_WORLD,&comm);
int rank = comm_rank(comm);
int nprocs = comm_size(comm);
if ( rank==0 && provided_thread_support<MPI_THREAD_MULTIPLE )
std::cerr << "Warning: Failed to start MPI with necessary thread support, thread support will be disabled" << std::endl;
{ // Limit scope so variables that contain communicators will free before MPI_Finialize
// parallel domain size (# of sub-domains)
int nprocx,nprocy,nprocz;
MPI_Request req1[18],req2[18];
MPI_Status stat1[18],stat2[18];
if (rank == 0){
printf("********************************************************\n");
printf("Running Hybrid Implementation of Color LBM \n");
printf("********************************************************\n");
}
PROFILE_ENABLE(1);
//PROFILE_ENABLE_TRACE();
//PROFILE_ENABLE_MEMORY();
PROFILE_SYNCHRONIZE();
PROFILE_START("Main");
Utilities::setErrorHandlers();
// Variables that specify the computational domain
string FILENAME;
unsigned int nBlocks, nthreads;
int Nx,Ny,Nz;
int nspheres;
double Lx,Ly,Lz;
// Color Model parameters
int i,j,k,n;
// pmmc threshold values
double fluid_isovalue,solid_isovalue;
fluid_isovalue = 0.0;
solid_isovalue = 0.0;
nBlocks = 32;
nthreads = 128;
int RESTART_INTERVAL=1000;
auto db = readInput( "input.in" );
// Read variables from Color
auto color_db = db->getDatabase( "Color" );
auto tau = color_db->getScalarWithDefault<double>( "tau", 1.0 );
auto alpha = color_db->getScalarWithDefault<double>( "alpha", 1e-3 );
auto beta = color_db->getScalarWithDefault<double>( "beta", 0.95 );
auto phi_s = color_db->getScalarWithDefault<double>( "phi_s", 0.0 );
auto Fx = color_db->getVectorWithDefault<double>( "F", { 0, 0, 0 } )[0];
auto Fy = color_db->getScalarWithDefault<double>( "F", { 0, 0, 0 } )[1];
auto Fz = color_db->getScalarWithDefault<double>( "F", { 0, 0, 0 } )[2];
auto Restart = color_db->getScalarWithDefault<bool>( "Restart", 0 );
auto pBC = color_db->getScalarWithDefault<double>( "pBC", 0 );
auto din = color_db->getScalarWithDefault<double>( "din", 1.0 );
auto dout = color_db->getScalarWithDefault<double>( "dout", 1.0 );
auto timestepMax = color_db->getScalarWithDefault<int>( "timestepMax", 3 );
auto interval = color_db->getScalarWithDefault<int>( "interval", 100 );
auto tol = color_db->getScalarWithDefault<double>( "tol", 1e-6 );
auto das = color_db->getScalarWithDefault<double>( "das", 0.1 );
auto dbs = color_db->getScalarWithDefault<double>( "dab", 0.9 );
// Read variables from Domain
auto domain_db = db->getDatabase( "Domain" );
auto n = domain_db->getVectorWithDefault<int>( "n", { 50, 50, 50 } );
auto L = domain_db->getVectorWithDefault<double>( "L", { 1.0, 1.0, 1.0 } );
auto nproc = domain_db->getVectorWithDefault<int>( "nproc", { 1, 1, 1 } );
auto nspheres = domain_db->getScalarWithDefault<int>( "nspheres", 1 );
int Nx = n[0];
int Ny = n[1];
int Nz = n[2];
int nprocx = nproc[0];
int nprocy = nproc[1];
int nprocz = nproc[2];
double Lx = L[0];
double Ly = L[1];
double Lz = L[2];
// Get the rank info
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
int iproc = rank_info.ix;
int jproc = rank_info.jy;
int kproc = rank_info.kz;
MPI_Barrier(comm);
// **************************************************************
// **************************************************************
double Ps = -(das-dbs)/(das+dbs);
double rlxA = 1.f/tau;
double rlxB = 8.f*(2.f-rlxA)/(8.f-rlxA);
double xIntPos;
xIntPos = log((1.0+phi_s)/(1.0-phi_s))/(2.0*beta);
if (nprocs != nprocx*nprocy*nprocz){
printf("Fatal error in processor number! \n");
printf(" nprocx = %i \n",nprocx);
printf(" nprocy = %i \n",nprocy);
printf(" nprocz = %i \n",nprocz);
return 1;
}
if (rank==0){
printf("********************************************************\n");
printf("tau = %f \n", tau);
printf("alpha = %f \n", alpha);
printf("beta = %f \n", beta);
printf("das = %f \n", das);
printf("dbs = %f \n", dbs);
printf("Value of phi at solid surface = %f \n", phi_s);
printf("Distance to phi = 0.0: %f \n", xIntPos);
printf("gamma_{wn} = %f \n", 5.796*alpha);
// printf("cos theta_c = %f \n", 1.05332*Ps);
printf("Force(x) = %f \n", Fx);
printf("Force(y) = %f \n", Fy);
printf("Force(z) = %f \n", Fz);
printf("Sub-domain size = %i x %i x %i\n",Nz,Nz,Nz);
printf("Parallel domain size = %i x %i x %i\n",nprocx,nprocy,nprocz);
printf("********************************************************\n");
}
// Full domain used for averaging (do not use mask for analysis)
Domain Dm(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,pBC);
Dm.CommInit();
// Mask that excludes the solid phase
Domain Mask(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,pBC);
MPI_Barrier(comm);
Nx+=2; Ny+=2; Nz += 2;
int N = Nx*Ny*Nz;
int dist_mem_size = N*sizeof(double);
int S = N/nthreads/nBlocks+1;
// unsigned int nBlocks = N/nthreads + (N%nthreads == 0?0:1);
// dim3 grid(nBlocks,1,1);
if (rank==0) printf("Number of blocks = %i \n", nBlocks);
if (rank==0) printf("Threads per block = %i \n", nthreads);
if (rank==0) printf("Sweeps per thread = %i \n", S);
if (rank==0) printf("Number of nodes per side = %i \n", Nx);
if (rank==0) printf("Total Number of nodes = %i \n", N);
if (rank==0) printf("********************************************************\n");
//.......................................................................
if (rank == 0) printf("Read input media... \n");
//.......................................................................
//.......................................................................
// Filenames used
char LocalRankString[8];
char LocalRankFilename[40];
char LocalRestartFile[40];
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
// printf("Local File Name = %s \n",LocalRankFilename);
// .......... READ THE INPUT FILE .......................................
// char value;
char *id;
id = new char[N];
int sum = 0;
double iVol_global = 1.0/(1.0*Nx*Ny*Nz*nprocs);
double porosity = 0;
DoubleArray SDs(Nx,Ny,Nz);
DoubleArray SDn(Nx,Ny,Nz);
//.......................................................................
double BubbleRadius = 15.5; // Radius of the capillary tube
sum=0;
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n = k*Nx*Ny + j*Nz + i;
// Cylindrical capillary tube aligned with the z direction
SDs(i,j,k) = 100;
// Initialize phase positions field
if (SDs(i,j,k) < 0.0){
id[n] = 0;
}
else {
id[n] = 1;
sum++;
}
}
}
}
// Set up MPI communication structurese
if (rank==0) printf ("Setting up communication control structures \n");
// Initialize communication structures in averaging domain
for (i=0; i<Mask.Nx*Mask.Ny*Mask.Nz; i++) Mask.id[i] = id[i];
Mask.CommInit(comm);
//......................................................................................
// Create a communicator for the device
ScaLBL_Communicator ScaLBL_Comm(Mask);
//...........device phase ID.................................................
if (rank==0) printf ("Copying phase ID to device \n");
char *ID;
ScaLBL_AllocateDeviceMemory((void **) &ID, N); // Allocate device memory
// Copy to the device
ScaLBL_CopyToDevice(ID, id, N);
ScaLBL_DeviceBarrier();
//...........................................................................
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
// LBM variables
if (rank==0) printf ("Allocating distributions \n");
//......................device distributions.................................
double *f_even,*f_odd;
double *A_even,*A_odd,*B_even,*B_odd;
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &f_even, 10*dist_mem_size); // Allocate device memory
ScaLBL_AllocateDeviceMemory((void **) &f_odd, 9*dist_mem_size); // Allocate device memory
ScaLBL_AllocateDeviceMemory((void **) &A_even, 4*dist_mem_size); // Allocate device memory
ScaLBL_AllocateDeviceMemory((void **) &A_odd, 3*dist_mem_size); // Allocate device memory
ScaLBL_AllocateDeviceMemory((void **) &B_even, 4*dist_mem_size); // Allocate device memory
ScaLBL_AllocateDeviceMemory((void **) &B_odd, 3*dist_mem_size); // Allocate device memory
//...........................................................................
double *Phi,*Den;
double *ColorGrad, *Velocity, *Pressure;
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &Phi, dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Pressure, dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Den, 2*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &ColorGrad, 3*dist_mem_size);
//...........................................................................
//...........................................................................
// Phase indicator (in array form as needed by PMMC algorithm)
DoubleArray Phase(Nx,Ny,Nz);
// Extra copies of phi needed to compute time derivatives on CPU
DoubleArray Phase_tminus(Nx,Ny,Nz);
DoubleArray Phase_tplus(Nx,Ny,Nz);
DoubleArray dPdt(Nx,Ny,Nz);
//copies of data needed to perform checkpointing from cpu
double *cDen, *cDistEven, *cDistOdd;
cDen = new double[2*N];
cDistEven = new double[10*N];
cDistOdd = new double[9*N];
// data needed to perform CPU-based averaging
//double *Vel = new double[3*N]; // fluid velocity
DoubleArray MeanCurvature(Nx,Ny,Nz);
DoubleArray GaussCurvature(Nx,Ny,Nz);
DoubleArray SDs_x(Nx,Ny,Nz); // Gradient of the signed distance
DoubleArray SDs_y(Nx,Ny,Nz);
DoubleArray SDs_z(Nx,Ny,Nz);
DoubleArray Phase_x(Nx,Ny,Nz); // Gradient of the phase indicator field
DoubleArray Phase_y(Nx,Ny,Nz);
DoubleArray Phase_z(Nx,Ny,Nz);
DoubleArray Press(Nx,Ny,Nz);
MeanCurvature.fill(0);
GaussCurvature.fill(0);
SDs_x.fill(0);
SDs_y.fill(0);
SDs_z.fill(0);
Phase_x.fill(0);
Phase_y.fill(0);
Phase_z.fill(0);
Press.fill(0);
/*****************************************************************
VARIABLES FOR THE PMMC ALGORITHM
****************************************************************** */
//...........................................................................
// Averaging variables
//...........................................................................
// local averages (to each MPI process)
double awn,ans,aws,lwns,nwp_volume;
double As;
double vol_w, vol_n; // volumes the exclude the interfacial region
double sat_w;
double pan,paw; // local phase averaged pressure
// double vx_w,vy_w,vz_w,vx_n,vy_n,vz_n; // local phase averaged velocity
// Global averages (all processes)
double vol_w_global, vol_n_global; // volumes the exclude the interfacial region
double awn_global,ans_global,aws_global;
double lwns_global;
double efawns,efawns_global; // averaged contact angle
double Jwn,Jwn_global; // average mean curavture - wn interface
DoubleArray van(3);
DoubleArray vaw(3);
DoubleArray vawn(3);
DoubleArray Gwn(6);
DoubleArray Gns(6);
DoubleArray Gws(6);
double nwp_volume_global; // volume for the wetting phase (for saturation)
// double p_n_global,p_w_global; // global phase averaged pressure
// double vx_w_global,vy_w_global,vz_w_global; // global phase averaged velocity
// double vx_n_global,vy_n_global,vz_n_global; // global phase averaged velocity
double As_global;
double dEs,dAwn,dAns; // Global surface energy (calculated by rank=0)
double pan_global,paw_global; // local phase averaged pressure
DoubleArray van_global(3);
DoubleArray vaw_global(3);
DoubleArray vawn_global(3);
DoubleArray Gwn_global(6);
DoubleArray Gns_global(6);
DoubleArray Gws_global(6);
//...........................................................................
// bool add=1; // Set to false if any corners contain nw-phase ( F > fluid_isovalue)
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}}; // cube corners
DoubleArray CubeValues(2,2,2);
// int count_in=0,count_out=0;
// int nodx,nody,nodz;
// initialize lists for vertices for surfaces, common line
DTMutableList<Point> nw_pts(20);
DTMutableList<Point> ns_pts(20);
DTMutableList<Point> ws_pts(20);
DTMutableList<Point> nws_pts(20);
// initialize triangle lists for surfaces
IntArray nw_tris(3,20);
IntArray ns_tris(3,20);
IntArray ws_tris(3,20);
// initialize list for line segments
IntArray nws_seg(2,20);
DTMutableList<Point> tmp(20);
DoubleArray Values(20);
DoubleArray ContactAngle(20);
DoubleArray Curvature(20);
DoubleArray InterfaceSpeed(20);
DoubleArray NormalVector(60);
// IntArray store;
int n_nw_pts=0,n_ns_pts=0,n_ws_pts=0,n_nws_pts=0;
int n_nw_tris=0, n_ns_tris=0, n_ws_tris=0, n_nws_seg=0;
// double s,s1,s2,s3; // Triangle sides (lengths)
Point A,B,C,P;
// double area;
// Initialize arrays for local solid surface
DTMutableList<Point> local_sol_pts(20);
int n_local_sol_pts = 0;
IntArray local_sol_tris(3,18);
int n_local_sol_tris;
DoubleArray values(20);
DTMutableList<Point> local_nws_pts(20);
int n_local_nws_pts;
//int n_nw_tris_beg, n_ns_tris_beg, n_ws_tris_beg;
int c;
//int newton_steps = 0;
//...........................................................................
int ncubes = (Nx-2)*(Ny-2)*(Nz-2); // Exclude the "upper" halo
IntArray cubeList(3,ncubes);
int nc=0;
//...........................................................................
// Set up the cube list (very regular in this case due to lack of blob-ID)
for (k=0; k<Nz-2; k++){
for (j=0; j<Ny-2; j++){
for (i=0; i<Nx-2; i++){
cubeList(0,nc) = i;
cubeList(1,nc) = j;
cubeList(2,nc) = k;
nc++;
}
}
}
//...........................................................................
// Grids used to pack faces on the GPU for MPI
int faceGrid,edgeGrid,packThreads;
packThreads=512;
edgeGrid=1;
faceGrid=Nx*Ny/packThreads;
NULL_USE(faceGrid);
NULL_USE(edgeGrid);
//...........................................................................
//...........................................................................
int timestep = 0;
if (rank==0) printf("********************************************************\n");
if (rank==0) printf("No. of timesteps: %i \n", timestepMax);
//.......create a stream for the LB calculation.......
// cudaStream_t stream;
// cudaStreamCreate(&stream);
//.......create and start timer............
double starttime,stoptime,cputime;
MPI_Barrier(comm);
starttime = MPI_Wtime();
//.........................................
//...........................................................................
// MAIN VARIABLES INITIALIZED HERE
//...........................................................................
double BubRad[5];
BubRad[0] = 8.0;
BubRad[1] = 10.0;
BubRad[2] = 12.0;
BubRad[3] = 15.0;
BubRad[4] = 20.0;
//...........................................................................
if (rank==0){
printf("--------------------------------------------------------------------------------------\n");
printf("radius "); // Timestep, Change in Surface Energy
printf("sw pw pn awn Jwn "); // Scalar averages
printf("Gwn [xx, yy, zz, xy, xz, yz] "); // Orientation tensors
printf("--------------------------------------------------------------------------------------\n");
}
for (int bubbleCount=0; bubbleCount<4; bubbleCount++){
char bubbleCountName[20];
sprintf(bubbleCountName,"bubbleCount-%i",bubbleCount);
PROFILE_START(bubbleCountName);
BubbleRadius = BubRad[bubbleCount]; // Radius of the current bubble
// Initialize the bubble
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n = k*Nx*Ny + j*Nz + i;
int iglobal= i+(Nx-2)*iproc;
int jglobal= j+(Ny-2)*jproc;
int kglobal= k+(Nz-2)*kproc;
// Cylindrical capillary tube aligned with the z direction
SDs(i,j,k) = 100;
// Initialize phase positions field
// if ((i-0.5*Nx)*(i-0.5*Nx)+(j-0.5*Ny)*(j-0.5*Ny)+(k-0.5*Nz)*(k-0.5*Nz) < BubbleRadius*BubbleRadius){
// id[n] = 2;
// }
// Initialize phase position field for parallel bubble test
if ((iglobal-0.5*(Nx-2)*nprocx)*(iglobal-0.5*(Nx-2)*nprocx)
+(jglobal-0.5*(Ny-2)*nprocy)*(jglobal-0.5*(Ny-2)*nprocy)
+(kglobal-0.5*(Nz-2)*nprocz)*(kglobal-0.5*(Nz-2)*nprocz) < BubbleRadius*BubbleRadius){
id[n] = 2;
}
else{
id[n]=1;
}
}
}
}
// Copy the bubble to the device and initialize
ScaLBL_CopyToDevice(ID, id, N);
//...........................................................................
//...........................................................................
ScaLBL_D3Q19_Init(ID, f_even, f_odd, Nx, Ny, Nz);
//......................................................................
//ScaLBL_Color_InitDistance(ID, Den, Phi, SDs.data(), das, dbs, beta, xIntPos, Nx, Ny, Nz);
ScaLBL_Color_Init(ID, Den, Phi, das, dbs, Nx, Ny, Nz);
ScaLBL_D3Q7_Init(ID, A_even, A_odd, &Den[0], Nx, Ny, Nz);
ScaLBL_D3Q7_Init(ID, B_even, B_odd, &Den[N], Nx, Ny, Nz);
//......................................................................
// Once phase has been initialized, map solid to account for 'smeared' interface
//......................................................................
for (i=0; i<N; i++) SDs(i) -= (1.0); //
//......................................................................
//.......................................................................
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
WriteLocalSolidID(LocalRankFilename, id, N);
sprintf(LocalRankFilename,"%s%s","SDs.",LocalRankString);
WriteLocalSolidDistance(LocalRankFilename, SDs.data(), N);
//.......................................................................
if (Restart == true){
if (rank==0) printf("Reading restart file! \n");
// Read in the restart file to CPU buffers
ReadCheckpoint(LocalRestartFile, cDen, cDistEven, cDistOdd, N);
// Copy the restart data to the GPU
ScaLBL_CopyToDevice(f_even,cDistEven,10*N*sizeof(double));
ScaLBL_CopyToDevice(f_odd,cDistOdd,9*N*sizeof(double));
ScaLBL_CopyToDevice(Den,cDen,2*N*sizeof(double));
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
}
//*************************************************************************
// Compute the phase indicator field and reset Copy, Den
//*************************************************************************
ScaLBL_ComputePhaseField(ID, Phi, Den, N);
//*************************************************************************
ScaLBL_DeviceBarrier();
ScaLBL_Comm.SendHalo(Phi);
ScaLBL_Comm.RecvHalo(Phi);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
//*************************************************************************
if (rank==0 && pBC){
printf("Setting inlet pressure = %f \n", din);
printf("Setting outlet pressure = %f \n", dout);
}
if (pBC && kproc == 0) {
ScaLBL_D3Q19_Pressure_BC_z(f_even,f_odd,din,Nx,Ny,Nz);
ScaLBL_Color_BC_z(Phi,Den,Velocity,A_even,A_odd,B_even,B_odd,Nx,Ny,Nz);
}
if (pBC && kproc == nprocz-1){
ScaLBL_D3Q19_Pressure_BC_Z(f_even,f_odd,dout,Nx,Ny,Nz,Nx*Ny*(Nz-2));
ScaLBL_Color_BC_Z(Phi,Den,Velocity,A_even,A_odd,B_even,B_odd,Nx,Ny,Nz);
}
//...........................................................................
// Copy the phase indicator field for the earlier timestep
ScaLBL_DeviceBarrier();
ScaLBL_CopyToHost(Phase_tplus.data(),Phi,N*sizeof(double));
//...........................................................................
//...........................................................................
// Copy the data for for the analysis timestep
//...........................................................................
// Copy the phase from the GPU -> CPU
//...........................................................................
ScaLBL_DeviceBarrier();
ScaLBL_D3Q19_Pressure(ID,f_even,f_odd,Pressure,Nx,Ny,Nz);
ScaLBL_CopyToHost(Phase.data(),Phi,N*sizeof(double));
ScaLBL_CopyToHost(Press.data(),Pressure,N*sizeof(double));
MPI_Barrier(comm);
//...........................................................................
int timestep = 0;
//************ MAIN ITERATION LOOP ***************************************/
PROFILE_START("Time-loop");
while (timestep < timestepMax){
//*************************************************************************
// Fused Color Gradient and Collision
//*************************************************************************
ScaLBL_D3Q19_ColorCollide( ID,f_even,f_odd,Phi,ColorGrad,
Velocity,Nx,Ny,Nz,rlxA,rlxB,alpha,beta,Fx,Fy,Fz);
//*************************************************************************
ScaLBL_DeviceBarrier();
//*************************************************************************
// Pack and send the D3Q19 distributions
ScaLBL_Comm.SendD3Q19(f_even, f_odd);
//*************************************************************************
//*************************************************************************
// Carry out the density streaming step for mass transport
//*************************************************************************
ScaLBL_D3Q7_ColorCollideMass(ID, A_even, A_odd, B_even, B_odd, Den, Phi,
ColorGrad, Velocity, beta, N, pBC);
//*************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
//*************************************************************************
// Swap the distributions for momentum transport
//*************************************************************************
ScaLBL_D3Q19_Swap(ID, f_even, f_odd, Nx, Ny, Nz);
//*************************************************************************
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
//*************************************************************************
// Wait for communications to complete and unpack the distributions
ScaLBL_Comm.RecvD3Q19(f_even, f_odd);
//*************************************************************************
ScaLBL_DeviceBarrier();
//*************************************************************************
// Pack and send the D3Q7 distributions
ScaLBL_Comm.BiSendD3Q7(A_even, A_odd, B_even, B_odd);
//*************************************************************************
ScaLBL_DeviceBarrier();
ScaLBL_D3Q7_Swap(ID, A_even, A_odd, Nx, Ny, Nz);
ScaLBL_D3Q7_Swap(ID, B_even, B_odd, Nx, Ny, Nz);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
//*************************************************************************
// Wait for communication and unpack the D3Q7 distributions
ScaLBL_Comm.BiRecvD3Q7(A_even, A_odd, B_even, B_odd);
//*************************************************************************
ScaLBL_DeviceBarrier();
//..................................................................................
ScaLBL_D3Q7_Density(ID, A_even, A_odd, &Den[0], Nx, Ny, Nz);
ScaLBL_D3Q7_Density(ID, B_even, B_odd, &Den[N], Nx, Ny, Nz);
//*************************************************************************
// Compute the phase indicator field
//*************************************************************************
// ScaLBL_ComputePhaseField(ID, Phi, Copy, Den, N);
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
ScaLBL_ComputePhaseField(ID, Phi, Den, N);
//*************************************************************************
ScaLBL_Comm.SendHalo(Phi);
ScaLBL_DeviceBarrier();
ScaLBL_Comm.RecvHalo(Phi);
//*************************************************************************
ScaLBL_DeviceBarrier();
// Pressure boundary conditions
if (pBC && kproc == 0) {
ScaLBL_D3Q19_Pressure_BC_z(f_even,f_odd,din,Nx,Ny,Nz);
ScaLBL_D3Q19_Velocity(ID,f_even,f_odd,Velocity,Nx,Ny,Nz);
ScaLBL_Color_BC_z(Phi,Den,Velocity,A_even,A_odd,B_even,B_odd,Nx,Ny,Nz);
}
if (pBC && kproc == nprocz-1){
ScaLBL_D3Q19_Pressure_BC_Z(f_even,f_odd,dout,Nx,Ny,Nz,Nx*Ny*(Nz-2));
ScaLBL_D3Q19_Velocity(ID,f_even,f_odd,Velocity,Nx,Ny,Nz);
ScaLBL_Color_BC_Z(Phi,Den,Velocity,A_even,A_odd,B_even,B_odd,Nx,Ny,Nz);
}
//...................................................................................
MPI_Barrier(comm);
// Timestep completed!
timestep++;
if (timestep%RESTART_INTERVAL == 0){
// Copy the data to the CPU
ScaLBL_CopyToHost(cDistEven,f_even,10*N*sizeof(double));
ScaLBL_CopyToHost(cDistOdd,f_odd,9*N*sizeof(double));
ScaLBL_CopyToHost(cDen,Den,2*N*sizeof(double));
// Read in the restart file to CPU buffers
WriteCheckpoint(LocalRestartFile, cDen, cDistEven, cDistOdd, N);
}
}
PROFILE_STOP("Time-loop");
// End the bubble loop
//...........................................................................
// Copy the phase indicator field for the later timestep
ScaLBL_DeviceBarrier();
ScaLBL_D3Q19_Pressure(ID,f_even,f_odd,Pressure,Nx,Ny,Nz);
ScaLBL_CopyToHost(Phase_tminus.data(),Phi,N*sizeof(double));
ScaLBL_CopyToHost(Phase_tplus.data(),Phi,N*sizeof(double));
ScaLBL_CopyToHost(Phase.data(),Phi,N*sizeof(double));
ScaLBL_CopyToHost(Press.data(),Pressure,N*sizeof(double));
double temp=0.5/beta;
for (n=0; n<N; n++){
double value = Phase.data()[n];
SDn(n) = temp*log((1.0+value)/(1.0-value));
}
//...........................................................................
// Calculate the time derivative of the phase indicator field
for (n=0; n<N; n++) dPdt(n) = 0.1*(Phase_tplus(n) - Phase_tminus(n));
//...........................................................................
// Compute the gradients of the phase indicator and signed distance fields
pmmc_MeshGradient(Phase,Phase_x,Phase_y,Phase_z,Nx,Ny,Nz);
pmmc_MeshGradient(SDs,SDs_x,SDs_y,SDs_z,Nx,Ny,Nz);
//...........................................................................
// Compute the mesh curvature of the phase indicator field
pmmc_MeshCurvature(SDn, MeanCurvature, GaussCurvature, Nx, Ny, Nz);
//...........................................................................
// Fill in the halo region for the mesh gradients and curvature
//...........................................................................
// Pressure
Dm.CommunicateMeshHalo(Press);
// Mean Curvature
Dm.CommunicateMeshHalo(MeanCurvature);
// Gaussian Curvature
Dm.CommunicateMeshHalo(GaussCurvature);
// Gradient of the phase indicator field
Dm.CommunicateMeshHalo(Phase_x);
Dm.CommunicateMeshHalo(Phase_y);
Dm.CommunicateMeshHalo(Phase_z);
//...........................................................................
// Compute areas using porous medium marching cubes algorithm
// McClure, Adalsteinsson, et al. (2007)
//...........................................................................
awn = aws = ans = lwns = 0.0;
nwp_volume = 0.0;
As = 0.0;
// Compute phase averages
pan = paw = 0.0;
vaw(0) = vaw(1) = vaw(2) = 0.0;
van(0) = van(1) = van(2) = 0.0;
vawn(0) = vawn(1) = vawn(2) = 0.0;
Gwn(0) = Gwn(1) = Gwn(2) = 0.0;
Gwn(3) = Gwn(4) = Gwn(5) = 0.0;
Gws(0) = Gws(1) = Gws(2) = 0.0;
Gws(3) = Gws(4) = Gws(5) = 0.0;
Gns(0) = Gns(1) = Gns(2) = 0.0;
Gns(3) = Gns(4) = Gns(5) = 0.0;
vol_w = vol_n =0.0;
Jwn = efawns = 0.0;
for (c=0;c<ncubes;c++){
// Get cube from the list
i = cubeList(0,c);
j = cubeList(1,c);
k = cubeList(2,c);
//...........................................................................
// Compute volume averages
for (int p=0;p<8;p++){
double delphi;
if ( SDs(i+cube[p][0],j+cube[p][1],k+cube[p][2]) > 0 ){
// 1-D index for this cube corner
n = i+cube[p][0] + (j+cube[p][1])*Nx + (k+cube[p][2])*Nx*Ny;
// compute the norm of the gradient of the phase indicator field
delphi = sqrt(Phase_x(n)*Phase_x(n)+Phase_y(n)*Phase_y(n)+Phase_z(n)*Phase_z(n));
// Compute the non-wetting phase volume contribution
if ( Phase(i+cube[p][0],j+cube[p][1],k+cube[p][2]) > 0 ){
nwp_volume += 0.125;
// volume the excludes the interfacial region
if (delphi < 1e-4){
vol_n += 0.125;
// pressure
pan += 0.125*Press(n);
}
}
else if (delphi < 1e-4){
// volume the excludes the interfacial region
vol_w += 0.125;
// pressure
paw += 0.125*Press(n);
}
}
}
//...........................................................................
// Construct the interfaces and common curve
pmmc_ConstructLocalCube(SDs, SDn, solid_isovalue, fluid_isovalue,
nw_pts, nw_tris, values, ns_pts, ns_tris, ws_pts, ws_tris,
local_nws_pts, nws_pts, nws_seg, local_sol_pts, local_sol_tris,
n_local_sol_tris, n_local_sol_pts, n_nw_pts, n_nw_tris,
n_ws_pts, n_ws_tris, n_ns_tris, n_ns_pts, n_local_nws_pts, n_nws_pts, n_nws_seg,
i, j, k, Nx, Ny, Nz);
// Integrate the contact angle
efawns += pmmc_CubeContactAngle(CubeValues,Values,Phase_x,Phase_y,Phase_z,SDs_x,SDs_y,SDs_z,
local_nws_pts,i,j,k,n_local_nws_pts);
// Integrate the mean curvature
Jwn += pmmc_CubeSurfaceInterpValue(CubeValues,MeanCurvature,nw_pts,nw_tris,Values,i,j,k,n_nw_pts,n_nw_tris);
pmmc_InterfaceSpeed(dPdt, Phase_x, Phase_y, Phase_z, CubeValues, nw_pts, nw_tris,
NormalVector, InterfaceSpeed, vawn, i, j, k, n_nw_pts, n_nw_tris);
//...........................................................................
// Compute the Interfacial Areas, Common Line length
/* awn += pmmc_CubeSurfaceArea(nw_pts,nw_tris,n_nw_tris);
ans += pmmc_CubeSurfaceArea(ns_pts,ns_tris,n_ns_tris);
aws += pmmc_CubeSurfaceArea(ws_pts,ws_tris,n_ws_tris);
*/
As += pmmc_CubeSurfaceArea(local_sol_pts,local_sol_tris,n_local_sol_tris);
// Compute the surface orientation and the interfacial area
awn += pmmc_CubeSurfaceOrientation(Gwn,nw_pts,nw_tris,n_nw_tris);
ans += pmmc_CubeSurfaceOrientation(Gns,ns_pts,ns_tris,n_ns_tris);
aws += pmmc_CubeSurfaceOrientation(Gws,ws_pts,ws_tris,n_ws_tris);
lwns += pmmc_CubeCurveLength(local_nws_pts,n_local_nws_pts);
//...........................................................................
}
//...........................................................................
MPI_Barrier(comm);
MPI_Allreduce(&nwp_volume,&nwp_volume_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&awn,&awn_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&ans,&ans_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&aws,&aws_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&lwns,&lwns_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&As,&As_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&Jwn,&Jwn_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&efawns,&efawns_global,1,MPI_DOUBLE,MPI_SUM,comm);
// Phase averages
MPI_Allreduce(&vol_w,&vol_w_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&vol_n,&vol_n_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&paw,&paw_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&pan,&pan_global,1,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&vaw(0),&vaw_global(0),3,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&van(0),&van_global(0),3,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&vawn(0),&vawn_global(0),3,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&Gwn(0),&Gwn_global(0),6,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&Gns(0),&Gns_global(0),6,MPI_DOUBLE,MPI_SUM,comm);
MPI_Allreduce(&Gws(0),&Gws_global(0),6,MPI_DOUBLE,MPI_SUM,comm);
MPI_Barrier(comm);
//.........................................................................
// Compute the change in the total surface energy based on the defined interval
// See McClure, Prins and Miller (2013)
//.........................................................................
dAwn += awn_global;
dAns += ans_global;
dEs = 6.01603*alpha*(dAwn + 1.05332*Ps*dAns);
dAwn = -awn_global; // Get ready for the next analysis interval
dAns = -ans_global;
// Normalize the phase averages
// (density of both components = 1.0)
paw_global = paw_global / vol_w_global;
vaw_global(0) = vaw_global(0) / vol_w_global;
vaw_global(1) = vaw_global(1) / vol_w_global;
vaw_global(2) = vaw_global(2) / vol_w_global;
pan_global = pan_global / vol_n_global;
van_global(0) = van_global(0) / vol_n_global;
van_global(1) = van_global(1) / vol_n_global;
van_global(2) = van_global(2) / vol_n_global;
// Normalize surface averages by the interfacial area
Jwn_global /= awn_global;
efawns_global /= lwns_global;
if (awn_global > 0.0) for (i=0; i<3; i++) vawn_global(i) /= awn_global;
if (awn_global > 0.0) for (i=0; i<6; i++) Gwn_global(i) /= awn_global;
if (ans_global > 0.0) for (i=0; i<6; i++) Gns_global(i) /= ans_global;
if (aws_global > 0.0) for (i=0; i<6; i++) Gws_global(i) /= aws_global;
sat_w = 1.0 - nwp_volume_global*iVol_global/porosity;
// Compute the specific interfacial areas and common line length (per unit volume)
awn_global = awn_global*iVol_global;
ans_global = ans_global*iVol_global;
aws_global = aws_global*iVol_global;
lwns_global = lwns_global*iVol_global;
dEs = dEs*iVol_global;
//.........................................................................
if (rank==0){
printf("%.5g ",BubbleRadius); // bubble radius
printf("%.5g %.5g ",paw_global,pan_global); // saturation and pressure
printf("%.5g ",awn_global); // interfacial area
printf("%.5g ",Jwn_global); // curvature of wn interface
printf("%.5g %.5g %.5g %.5g %.5g %.5g \n",
Gwn_global(0),Gwn_global(1),Gwn_global(2),Gwn_global(3),Gwn_global(4),Gwn_global(5)); // orientation of wn interface
}
shared_ptr<IO::TriList> mesh( new IO::TriList() );
mesh->A.reserve(8*ncubes);
mesh->B.reserve(8*ncubes);
mesh->C.reserve(8*ncubes);
for (c=0;c<ncubes;c++){
// Get cube from the list
i = cubeList(0,c);
j = cubeList(1,c);
k = cubeList(2,c);
//...........................................................................
// Construct the interfaces and common curve
pmmc_ConstructLocalCube(SDs, Phase, solid_isovalue, fluid_isovalue,
nw_pts, nw_tris, values, ns_pts, ns_tris, ws_pts, ws_tris,
local_nws_pts, nws_pts, nws_seg, local_sol_pts, local_sol_tris,
n_local_sol_tris, n_local_sol_pts, n_nw_pts, n_nw_tris,
n_ws_pts, n_ws_tris, n_ns_tris, n_ns_pts, n_local_nws_pts, n_nws_pts, n_nws_seg,
i, j, k, Nx, Ny, Nz);
//.......................................................................................
// Write the triangle lists to text file
for (int r=0;r<n_nw_tris;r++){
A = nw_pts(nw_tris(0,r));
B = nw_pts(nw_tris(1,r));
C = nw_pts(nw_tris(2,r));
// compare the trianlge orientation against the color gradient
// Orientation of the triangle
double tri_normal_x = (A.y-B.y)*(B.z-C.z) - (A.z-B.z)*(B.y-C.y);
double tri_normal_y = (A.z-B.z)*(B.x-C.x) - (A.x-B.x)*(B.z-C.z);
double tri_normal_z = (A.x-B.x)*(B.y-C.y) - (A.y-B.y)*(B.x-C.x);
double normal_x = Phase_x(i,j,k);
double normal_y = Phase_y(i,j,k);
double normal_z = Phase_z(i,j,k);
// If the normals don't point in the same direction, flip the orientation of the triangle
// Right hand rule for triangle orientation is used to determine rendering for most software
if (normal_x*tri_normal_x + normal_y*tri_normal_y + normal_z*tri_normal_z < 0.0){
P = A;
A = C;
C = P;
}
mesh->A.push_back(A);
mesh->B.push_back(B);
mesh->C.push_back(C);
}
}
std::vector<IO::MeshDataStruct> meshData(1);
meshData[0].meshName = "wn-tris";
meshData[0].mesh = mesh;
for (size_t k=0; k<meshData.size(); k++) {
shared_ptr<IO::Variable> dist( new IO::Variable() );
dist->name = "distance";
dist->dim = 1;
dist->type = IO::VariableType::NodeVariable;
dist->data.resize(3*mesh->A.size());
for (size_t i=0; i<mesh->A.size(); i++) {
const Point& a = mesh->A[i];
const Point& b = mesh->B[i];
const Point& c = mesh->C[i];
dist->data(3*i+0) = sqrt(a.x*a.x+a.y*a.y+a.z*a.z);
dist->data(3*i+1) = sqrt(b.x*b.x+b.y*b.y+b.z*b.z);
dist->data(3*i+2) = sqrt(c.x*c.x+c.y*c.y+c.z*c.z);
}
meshData[k].vars.push_back(dist);
}
IO::writeData( bubbleCount, meshData, comm );
PROFILE_STOP(bubbleCountName);
}
NULL_USE(sat_w);
//************************************************************************/
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
stoptime = MPI_Wtime();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep
cputime = (stoptime - starttime)/timestep;
// Performance obtained from each node
double MLUPS = double(Nx*Ny*Nz)/cputime/1000000;
if (rank==0) printf("********************************************************\n");
if (rank==0) printf("CPU time = %f \n", cputime);
if (rank==0) printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
MLUPS *= nprocs;
if (rank==0) printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
if (rank==0) printf("********************************************************\n");
//************************************************************************/
// Write out the phase indicator field
//************************************************************************/
sprintf(LocalRankFilename,"%s%s","Phase.",LocalRankString);
// printf("Local File Name = %s \n",LocalRankFilename);
// ScaLBL_CopyToHost(Phase.data(),Phi,N*sizeof(double));
FILE *PHASE;
PHASE = fopen(LocalRankFilename,"wb");
fwrite(Press.data(),8,N,PHASE);
// fwrite(MeanCurvature.data(),8,N,PHASE);
fclose(PHASE);
/* double *DensityValues;
DensityValues = new double [2*N];
ScaLBL_CopyToHost(DensityValues,Copy,2*N*sizeof(double));
FILE *PHASE;
PHASE = fopen(LocalRankFilename,"wb");
fwrite(DensityValues,8,2*N,PHASE);
fclose(PHASE);
*/ //************************************************************************/
PROFILE_SAVE("TestBubble");
// ****************************************************
MPI_Barrier(comm);
} // Limit scope so variables that contain communicators will free before MPI_Finialize
Utilities::shutdown();
return 0;
}
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