Merge branch 'membrane' into tmp
This commit is contained in:
James E McClure
@@ -6,6 +6,7 @@ ADD_LBPM_EXECUTABLE( lbpm_permeability_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_greyscale_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_greyscaleColor_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_electrokinetic_SingleFluid_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_cell_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_freelee_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_freelee_SingleFluidBGK_simulator )
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ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )
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@@ -58,6 +59,7 @@ ADD_LBPM_TEST( TestTopo3D )
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ADD_LBPM_TEST( TestFluxBC )
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ADD_LBPM_TEST( TestFlowAdaptor )
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ADD_LBPM_TEST( TestMap )
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ADD_LBPM_TEST( TestMembrane )
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#ADD_LBPM_TEST( TestMRT )
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#ADD_LBPM_TEST( TestColorGrad )
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ADD_LBPM_TEST( TestWideHalo )
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256
tests/TestMembrane.cpp
Normal file
256
tests/TestMembrane.cpp
Normal file
@@ -0,0 +1,256 @@
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//*************************************************************************
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// Lattice Boltzmann Simulator for Single Phase Flow in Porous Media
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// James E. McCLure
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//*************************************************************************
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#include <stdio.h>
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#include <iostream>
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#include <fstream>
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#include "common/MPI.h"
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#include "common/Membrane.h"
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#include "common/ScaLBL.h"
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using namespace std;
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std::shared_ptr<Database> loadInputs( int nprocs )
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{
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//auto db = std::make_shared<Database>( "Domain.in" );
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auto db = std::make_shared<Database>();
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db->putScalar<int>( "BC", 0 );
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db->putVector<int>( "nproc", { 1, 1, 1 } );
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db->putVector<int>( "n", { 32, 32, 32 } );
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db->putScalar<int>( "nspheres", 1 );
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db->putVector<double>( "L", { 1, 1, 1 } );
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return db;
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}
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//***************************************************************************************
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int main(int argc, char **argv)
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{
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// Initialize MPI
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Utilities::startup( argc, argv );
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Utilities::MPI comm( MPI_COMM_WORLD );
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int check=0;
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{
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int i,j,k,n;
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int rank = comm.getRank();
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if (rank == 0){
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printf("********************************************************\n");
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printf("Running unit test: TestMembrane \n");
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printf("********************************************************\n");
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}
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// Load inputs
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auto db = loadInputs( comm.getSize() );
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int Nx = db->getVector<int>( "n" )[0];
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int Ny = db->getVector<int>( "n" )[1];
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int Nz = db->getVector<int>( "n" )[2];
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auto Dm = std::make_shared<Domain>(db,comm);
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Nx += 2;
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Ny += 2;
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Nz += 2;
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int N = Nx*Ny*Nz;
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//.......................................................................
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int Np = 0;
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double distance,radius;
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DoubleArray Distance(Nx,Ny,Nz);
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for (k=0;k<Nz;k++){
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for (j=0;j<Ny;j++){
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for (i=0;i<Nx;i++){
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n = k*Nx*Ny+j*Nx+i;
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Dm->id[n] = 1;
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radius = double(Nx)/4;
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distance = sqrt(double((i-0.5*Nx)*(i-0.5*Nx)+ (j-0.5*Ny)*(j-0.5*Ny)+ (k-0.5*Nz)*(k-0.5*Nz)))-radius;
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if (distance < 0.0 ){
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Dm->id[n] = 1;
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}
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Distance(i,j,k) = distance;
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Np++;
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}
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}
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}
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Dm->CommInit();
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// Create a communicator for the device (will use optimized layout)
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std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm(new ScaLBL_Communicator(Dm));
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//Create a second communicator based on the regular data layout
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std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm_Regular(new ScaLBL_Communicator(Dm));
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if (rank==0){
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printf("Total domain size = %i \n",N);
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printf("Reduced domain size = %i \n",Np);
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}
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// LBM variables
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if (rank==0) printf ("Set up the neighborlist \n");
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int Npad=Np+32;
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int neighborSize=18*Npad*sizeof(int);
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int *neighborList;
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IntArray Map(Nx,Ny,Nz);
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neighborList= new int[18*Npad];
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//......................device distributions.................................
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int *NeighborList;
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int *dvcMap;
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//...........................................................................
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ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
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ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Npad);
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ScaLBL_CopyToDevice(NeighborList, neighborList, 18*Np*sizeof(int));
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Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Dm->id.data(),Np,1);
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comm.barrier();
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double *dist;
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dist = new double [19*Np];
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// Check the neighborlist
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printf("Check neighborlist: exterior %i, first interior %i last interior %i \n",ScaLBL_Comm->LastExterior(),ScaLBL_Comm->FirstInterior(),ScaLBL_Comm->LastInterior());
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for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
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for (int q=0; q<18; q++){
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int nn = neighborList[q*Np+idx]%Np;
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if (nn>Np) printf("neighborlist error (exterior) at q=%i, idx=%i \n",q,idx);
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dist[q*Np + idx] = 0.0;
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}
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}
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for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
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for (int q=0; q<18; q++){
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int nn = neighborList[q*Np+idx]%Np;
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if (nn>Np) printf("neighborlist error (exterior) at q=%i, idx=%i \n",q,idx);
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dist[q*Np + idx] = 0.0;
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}
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}
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/* create a membrane data structure */
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Membrane M(Dm, NeighborList, Np);
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int MembraneCount = M.Create(Dm, Distance, Map);
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if (rank==0) printf (" Number of membrane links: %i \n", MembraneCount);
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/* create a tagged array to show where the mebrane is*/
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double *MembraneLinks;
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MembraneLinks = new double [Nx*Ny*Nz];
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for (int n=0; n<Nx*Ny*Nz; n++) {
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MembraneLinks[n] = 0.0;
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}
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for (int mlink=0; mlink<MembraneCount; mlink++){
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int iq = M.membraneLinks[2*mlink];
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int jq = M.membraneLinks[2*mlink+1];
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dist[iq] = -1.0; // set these distributions to non-zero
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dist[jq] = 1.0;
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}
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for (k=1;k<Nz-1;k++){
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for (j=1;j<Ny-1;j++){
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for (i=1;i<Nx-1;i++){
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int idx = Map(i,j,k);
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double sum = 0.0;
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for (int q=0; q<19; q++){
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sum += dist[q*Np + idx];
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}
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int n = k*Nx*Ny + j*Nx + i;
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MembraneLinks[n] = sum;
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if (sum > 0.f){
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Dm->id[n] = 127;
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}
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if (sum < 0.f){
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Dm->id[n] = 64;
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}
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}
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}
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}
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if (argc > 1)
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Dm->AggregateLabels("membrane.raw");
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//...........................................................................
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// Update GPU data structures
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if (rank==0) printf ("Setting up device map and neighbor list \n");
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int *TmpMap;
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TmpMap=new int[Np*sizeof(int)];
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for (k=1; k<Nz-1; k++){
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for (j=1; j<Ny-1; j++){
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for (i=1; i<Nx-1; i++){
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int idx=Map(i,j,k);
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if (!(idx < 0))
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TmpMap[idx] = k*Nx*Ny+j*Nx+i;
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}
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}
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}
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ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
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ScaLBL_DeviceBarrier();
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// Create a dummy distribution data structure
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double *fq_host;
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fq_host = new double[19*Np];
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if (rank==0) printf ("Setting up Np=%i distributions \n",Np);
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for (k=1; k<Nz-1; k++){
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for (j=1; j<Ny-1; j++){
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for (i=1; i<Nx-1; i++){
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int idx=Map(i,j,k);
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if (!(idx<0)){
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for (int q=0; q<19; q++){
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fq_host[q*Np+idx]=(k*Nx*Ny+j*Nx+i)+0.01*q;
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}
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}
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}
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}
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}
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/* Run dummy communications */
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double * gq, *fq;
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ScaLBL_AllocateDeviceMemory((void **) &gq, sizeof(double)*7*Np);
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ScaLBL_AllocateDeviceMemory((void **) &fq, sizeof(double)*7*Np);
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/*initialize fq from host data */
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ScaLBL_CopyToDevice(fq, fq_host, sizeof(double)*7*Np);
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M.SendD3Q7AA(&fq[0]);
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M.RecvD3Q7AA(&gq[0]);
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// this has only the communicated values
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//ScaLBL_CopyToHost(fq_host, gq, sizeof(double)*7*Np);
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if (rank==0) printf ("Sum result \n");
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double *Ci;
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Ci = new double [Np];
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ScaLBL_D3Q7_AAeven_IonConcentration(&gq[0 * Np * 7], &Ci[0 * Np],
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0, ScaLBL_Comm->LastExterior(),
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Np);
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DoubleArray Result(Nx,Ny,Nz);
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ScaLBL_Comm->RegularLayout(Map, Ci, Result);
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/* for (k=1; k<Nz-1; k++){
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for (j=1; j<Ny-1; j++){
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for (i=1; i<Nx-1; i++){
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int idx=Map(i,j,k);
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double sum = 0.0;
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if (!(idx<0)){
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for (int q=1; q<3; q++){
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sum += fq_host[q*Np+idx];
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}
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Result[k*Nx*Ny+j*Nx+i] = sum;
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}
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}
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}
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}
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*/
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FILE *OUTFILE;
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OUTFILE = fopen("D3Q7.raw","wb");
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fwrite(Result.data(),8,Nx*Ny*Nz,OUTFILE);
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fclose(OUTFILE);
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FILE *MAPFILE;
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MAPFILE = fopen("Map.raw","wb");
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fwrite(Map.data(),4,Nx*Ny*Nz,MAPFILE);
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fclose(MAPFILE);
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delete [] TmpMap;
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delete [] fq_host;
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}
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Utilities::shutdown();
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return check;
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}
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131
tests/lbpm_cell_simulator.cpp
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131
tests/lbpm_cell_simulator.cpp
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@@ -0,0 +1,131 @@
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#include <stdio.h>
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#include <stdlib.h>
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#include <sys/stat.h>
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#include <iostream>
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#include <exception>
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#include <stdexcept>
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#include <fstream>
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#include <math.h>
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#include "models/IonModel.h"
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#include "models/StokesModel.h"
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#include "models/PoissonSolver.h"
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#include "models/MultiPhysController.h"
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#include "common/Utilities.h"
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#include "analysis/ElectroChemistry.h"
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using namespace std;
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//***************************************************************************
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// Test lattice-Boltzmann Ion Model coupled with Poisson equation
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//***************************************************************************
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int main(int argc, char **argv)
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{
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// Initialize MPI and error handlers
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Utilities::startup( argc, argv );
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Utilities::MPI comm( MPI_COMM_WORLD );
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int rank = comm.getRank();
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int nprocs = comm.getSize();
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{ // Limit scope so variables that contain communicators will free before MPI_Finialize
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if (rank == 0){
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printf("********************************************************\n");
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printf("Running LBPM electrokinetic single-fluid solver \n");
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printf("********************************************************\n");
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}
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// Initialize compute device
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int device=ScaLBL_SetDevice(rank);
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NULL_USE( device );
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ScaLBL_DeviceBarrier();
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comm.barrier();
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PROFILE_ENABLE(1);
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//PROFILE_ENABLE_TRACE();
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//PROFILE_ENABLE_MEMORY();
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PROFILE_SYNCHRONIZE();
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PROFILE_START("Main");
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Utilities::setErrorHandlers();
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auto filename = argv[1];
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ScaLBL_StokesModel StokesModel(rank,nprocs,comm);
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ScaLBL_IonModel IonModel(rank,nprocs,comm);
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ScaLBL_Poisson PoissonSolver(rank,nprocs,comm);
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ScaLBL_Multiphys_Controller Study(rank,nprocs,comm);//multiphysics controller coordinating multi-model coupling
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// Load controller information
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Study.ReadParams(filename);
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// Load user input database files for Navier-Stokes and Ion solvers
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StokesModel.ReadParams(filename);
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IonModel.ReadParams(filename);
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// Setup other model specific structures
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StokesModel.SetDomain();
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StokesModel.ReadInput();
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StokesModel.Create(); // creating the model will create data structure to match the pore structure and allocate variables
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IonModel.SetDomain();
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IonModel.ReadInput();
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IonModel.Create();
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IonModel.SetMembrane();
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// Create analysis object
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ElectroChemistryAnalyzer Analysis(IonModel.Dm);
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// Get internal iteration number
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StokesModel.timestepMax = Study.getStokesNumIter_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
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StokesModel.Initialize(); // initializing the model will set initial conditions for variables
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IonModel.timestepMax = Study.getIonNumIter_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
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IonModel.Initialize();
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// Get maximal time converting factor based on Sotkes and Ion solvers
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Study.getTimeConvMax_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
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// Initialize LB-Poisson model
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PoissonSolver.ReadParams(filename);
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PoissonSolver.SetDomain();
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PoissonSolver.ReadInput();
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PoissonSolver.Create();
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PoissonSolver.Initialize(Study.time_conv_max);
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int timestep=0;
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while (timestep < Study.timestepMax){
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timestep++;
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PoissonSolver.Run(IonModel.ChargeDensity,timestep);//solve Poisson equtaion to get steady-state electrical potental
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StokesModel.Run_Lite(IonModel.ChargeDensity, PoissonSolver.ElectricField);// Solve the N-S equations to get velocity
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IonModel.RunMembrane(StokesModel.Velocity,PoissonSolver.ElectricField,PoissonSolver.Psi); //solve for ion transport with membrane
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timestep++;//AA operations
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if (timestep%Study.analysis_interval==0){
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Analysis.Basic(IonModel,PoissonSolver,StokesModel,timestep);
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}
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if (timestep%Study.visualization_interval==0){
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Analysis.WriteVis(IonModel,PoissonSolver,StokesModel,Study.db,timestep);
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/* PoissonSolver.getElectricPotential(timestep);
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PoissonSolver.getElectricField(timestep);
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IonModel.getIonConcentration(timestep);
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StokesModel.getVelocity(timestep);
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*/
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}
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}
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if (rank==0) printf("Save simulation raw data at maximum timestep\n");
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Analysis.WriteVis(IonModel,PoissonSolver,StokesModel,Study.db,timestep);
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if (rank==0) printf("Maximum timestep is reached and the simulation is completed\n");
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if (rank==0) printf("*************************************************************\n");
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PROFILE_STOP("Main");
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PROFILE_SAVE("lbpm_electrokinetic_SingleFluid_simulator",1);
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// ****************************************************
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} // Limit scope so variables that contain communicators will free before MPI_Finialize
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Utilities::shutdown();
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}
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