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update membrane structure

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This commit is contained in:
James McClure
2021-12-25 17:58:53 -05:00
parent d59c78b0ce
commit 26766ef69a
4 changed files with 52 additions and 120 deletions
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151
analysis/Membrane.cpp
View File

@@ -12,7 +12,7 @@ Membrane::~Membrane() {
}
int Membrane::Create(DoubleArray &Distance, IntArray &Map, int *neighborList, int *membrane, int Np){
int Membrane::Create(DoubleArray &Distance, IntArray &Map, int *neighborList, int Np){
int mlink = 0;
int n, idx, neighbor;
double dist, locdist;
@@ -32,7 +32,6 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map, int *neighborList, in
else if (!(idx<0)){
int neighbor; // cycle through the neighbors of lattice site idx
neighbor=Map(i-1,j,k);
dist=Distance(i-1,j,k);
if (dist*locdist < 0.0){
@@ -155,7 +154,8 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map, int *neighborList, in
}
/* allocate memory */
membrane = new int [2*mlink];
membraneLinks = new int [2*mlink];
membraneDist = new double [2*mlink];
/* construct the membrane*/
mlink = 0;
@@ -167,167 +167,94 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map, int *neighborList, in
locdist=Distance(i,j,k);
else if (!(idx<0)){
int neighbor; // cycle through the neighbors of lattice site idx
neighbor=Map(i-1,j,k);
dist=Distance(i-1,j,k);
if (dist*locdist < 0.0){
neighborList[idx]=idx + 2*Np;
//membrane[2*mlink] = idx + 2*Np;
//membrane[2*mlink+1] = neighbor + 1*Np;
//mlink++;
}
neighbor=Map(i+1,j,k);
dist=Distance(i+1,j,k);
if (dist*locdist < 0.0){
neighborList[Np+idx] = idx + 1*Np;
membrane[2*mlink] = idx + 1*Np;
membrane[2*mlink+1] = neighbor + 2*Np;
membraneLinks[2*mlink] = idx + 1*Np;
membraneLinks[2*mlink+1] = neighbor + 2*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i,j-1,k);
dist=Distance(i,j-1,k);
if (dist*locdist < 0.0){
neighborList[2*Np+idx]=idx + 4*Np;
//membrane[2*mlink] = idx + 4*Np;
//membrane[2*mlink+1] = neighbor + 3*Np;
//mlink++;
}
neighbor=Map(i,j+1,k);
dist=Distance(i,j+1,k);
if (dist*locdist < 0.0){
neighborList[3*Np+idx]=idx + 3*Np;
membrane[2*mlink] = idx + 3*Np;
membrane[2*mlink+1] = neighbor + 4*Np;
membraneLinks[2*mlink] = idx + 3*Np;
membraneLinks[2*mlink+1] = neighbor + 4*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i,j,k-1);
dist=Distance(i,j,k-1);
if (dist*locdist < 0.0){
neighborList[4*Np+idx]=idx + 6*Np;
//membrane[2*mlink] = idx + 6*Np;
//membrane[2*mlink+1] = neighbor + 5*Np;
//mlink++;
}
neighbor=Map(i,j,k+1);
dist=Distance(i,j,k+1);
if (dist*locdist < 0.0){
neighborList[5*Np+idx]=idx + 5*Np;
membrane[2*mlink] = idx + 5*Np;
membrane[2*mlink+1] = neighbor + 6*Np;
membraneLinks[2*mlink] = idx + 5*Np;
membraneLinks[2*mlink+1] = neighbor + 6*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i-1,j-1,k);
dist=Distance(i-1,j-1,k);
if (dist*locdist < 0.0){
neighborList[6*Np+idx]=idx + 8*Np;
//membrane[2*mlink] = idx + 8*Np;
//membrane[2*mlink+1] = neighbor + 7*Np
//mlink++;
}
neighbor=Map(i+1,j+1,k);
dist=Distance(i+1,j+1,k);
if (dist*locdist < 0.0){
neighborList[7*Np+idx]=idx + 7*Np;
membrane[2*mlink] = idx + 7*Np;
membrane[2*mlink+1] = neighbor+8*Np;
membraneLinks[2*mlink] = idx + 7*Np;
membraneLinks[2*mlink+1] = neighbor+8*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i-1,j+1,k);
dist=Distance(i-1,j+1,k);
if (dist*locdist < 0.0){
neighborList[8*Np+idx]=idx + 10*Np;
//membrane[2*mlink] = idx + 10*Np;
//membrane[2*mlink+1] = neighbor + 9*Np;
//mlink++;
}
neighbor=Map(i+1,j-1,k);
dist=Distance(i+1,j-1,k);
if (dist*locdist < 0.0){
neighborList[9*Np+idx]=idx + 9*Np;
membrane[2*mlink] = idx + 9*Np;
membrane[2*mlink+1] = neighbor + 10*Np;
membraneLinks[2*mlink] = idx + 9*Np;
membraneLinks[2*mlink+1] = neighbor + 10*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i-1,j,k-1);
dist=Distance(i-1,j,k-1);
if (dist*locdist < 0.0){
neighborList[10*Np+idx]=idx + 12*Np;
//membrane[2*mlink] = idx + 12*Np;
//membrane[2*mlink+1] = neighbor + 11*Np;;
//mlink++;
}
neighbor=Map(i+1,j,k+1);
dist=Distance(i+1,j,k+1);
if (dist*locdist < 0.0){
neighborList[11*Np+idx]=idx + 11*Np;
membrane[2*mlink] = idx + 11*Np;
membrane[2*mlink+1] = neighbor + 12*Np;
membraneLinks[2*mlink] = idx + 11*Np;
membraneLinks[2*mlink+1] = neighbor + 12*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i-1,j,k+1);
dist=Distance(i-1,j,k+1);
if (dist*locdist < 0.0){
neighborList[12*Np+idx]=idx + 14*Np;
//membrane[2*mlink] = idx + 14*Np;
//membrane[2*mlink+1] = neighbor + 13*Np;
//mlink++;
}
neighbor=Map(i+1,j,k-1);
dist=Distance(i+1,j,k-1);
if (dist*locdist < 0.0){
neighborList[13*Np+idx]=idx + 13*Np;
membrane[2*mlink] = idx + 13*Np;
membrane[2*mlink+1] = neighbor + 14*Np;
membraneLinks[2*mlink] = idx + 13*Np;
membraneLinks[2*mlink+1] = neighbor + 14*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i,j-1,k-1);
dist=Distance(i,j-1,k-1);
if (dist*locdist < 0.0){
neighborList[14*Np+idx]=idx + 16*Np;
//membrane[2*mlink] = idx + 16*Np;
//membrane[2*mlink+1] = neighbor + 15*Np;
//mlink++;
}
neighbor=Map(i,j+1,k+1);
dist=Distance(i,j+1,k+1);
if (dist*locdist < 0.0){
neighborList[15*Np+idx]=idx + 15*Np;
membrane[2*mlink] = idx + 15*Np;
membrane[2*mlink+1] =neighbor + 16*Np;
membraneLinks[2*mlink] = idx + 15*Np;
membraneLinks[2*mlink+1] =neighbor + 16*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
neighbor=Map(i,j-1,k+1);
dist=Distance(i,j-1,k+1);
if (dist*locdist < 0.0){
neighborList[16*Np+idx]=idx + 18*Np;
//membrane[2*mlink] = idx + 18*Np;
//membrane[2*mlink+1] = neighbor + 17*Np;
//mlink++;
}
neighbor=Map(i,j+1,k-1);
dist=Distance(i,j+1,k-1);
if (dist*locdist < 0.0){
neighborList[17*Np+idx]=idx + 17*Np;
membrane[2*mlink] = idx + 17*Np;
membrane[2*mlink+1] = neighbor + 18*Np;
membraneLinks[2*mlink] = idx + 17*Np;
membraneLinks[2*mlink+1] = neighbor + 18*Np;
membraneDist[2*mlink] = locdist;
membraneDist[2*mlink+1] = dist;
mlink++;
}
}

7
analysis/Membrane.h
View File

@@ -21,6 +21,9 @@
class Membrane {
public:
int *membraneLinks; // D3Q19 links that cross membrane
double *membraneDist; // distance to membrane for each linked site
/**
* \brief Create a flow adaptor to operate on the LB model
* @param ScaLBL - originating data structures
@@ -45,9 +48,7 @@ public:
* @param membrane - links that form the membrane
* @param Np - number of sites in compact layout
*/
int Create(DoubleArray &Distance, IntArray &Map, int *neighborList, int *membrane, int Np);
int Create(DoubleArray &Distance, IntArray &Map, int *neighborList, int Np);
private:
};

6
common/ScaLBL.cpp
View File

@@ -1,5 +1,5 @@
/*
Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
Copyright 2013--2022 James E. McClure, Virginia Polytechnic & State University
Copyright Equnior ASA
This file is part of the Open Porous Media project (OPM).
@@ -15,10 +15,8 @@
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
#include "common/ScaLBL.h"
#include <chrono>
ScaLBL_Communicator::ScaLBL_Communicator(std::shared_ptr <Domain> Dm){
//......................................................................................
Lock=false; // unlock the communicator
@@ -324,7 +322,6 @@ ScaLBL_Communicator::ScaLBL_Communicator(std::shared_ptr <Domain> Dm){
}
ScaLBL_Communicator::~ScaLBL_Communicator()
{
@@ -988,7 +985,6 @@ int ScaLBL_Communicator::MemoryOptimizedLayoutAA(IntArray &Map, int *neighborLis
return(Np);
}
void ScaLBL_Communicator::SetupBounceBackList(IntArray &Map, signed char *id, int Np, bool SlippingVelBC)
{

8
common/ScaLBL.h
View File

@@ -699,6 +699,14 @@ public:
double GetPerformance(int *NeighborList, double *fq, int Np);
int MemoryOptimizedLayoutAA(IntArray &Map, int *neighborList, signed char *id, int Np, int width);
/**
* \brief Create membrane data structure
* - cut lattice links based on distance map
* @param Distance - signed distance to membrane
* @param neighborList - data structure that retains lattice links
* @param Np - number of lattice sites
* @param width - halo width for the model
*/
void Barrier(){
ScaLBL_DeviceBarrier();
MPI_COMM_SCALBL.barrier();