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update to membrane capability

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This commit is contained in:
James McClure 2022-03-14 16:16:47 -04:00
parent abf5823de6
commit 12026f54d4
4 changed files with 130 additions and 3 deletions
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34
analysis/Membrane.cpp
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@ -1161,8 +1161,40 @@ void Membrane::RecvD37AA(double *dist){
}
void Membrane::AssignCoefficients(double *dvcPsi, double *dvcDistance, double *dvcMap, std::string method){
void Membrane::AssignCoefficients(int *Map, double *Psi, double *Distance, std::string method){
/* Assign mass transfer coefficients to the membrane data structure */
double Threshold;
double MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut;
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(-1,0,0,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_X,dvcRecvLinks_X,coefficient_X,0,linkCount_X[0],recvCount_X,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(1,0,0,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_x,dvcRecvLinks_x,coefficient_x,0,linkCount_x[0],recvCount_x,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,-1,0,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_Y,dvcRecvLinks_Y,coefficient_Y,0,linkCount_Y[0],recvCount_Y,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,1,0,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_y,dvcRecvLinks_y,coefficient_y,0,linkCount_y[0],recvCount_y,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,-1,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_Z,dvcRecvLinks_Z,coefficient_Z,0,linkCount_Z[0],recvCount_Z,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,1,Map,Distance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_z,dvcRecvLinks_z,coefficient_z,0,linkCount_z[0],recvCount_z,
Np,Nx,Ny,Nz);
}

2
analysis/Membrane.h
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@ -92,7 +92,7 @@ public:
void RecvD3Q19AA(double *dist);
void SendD3Q7AA(double *dist);
void RecvD37AA(double *dist);
void AssignCoefficients(double *dvcPsi, double *dvcDistance, double *dvcMap, std::string method);
void AssignCoefficients(int *Map, double *Psi, double *Distance, std::string method);
//......................................................................................
// Buffers to store data sent and recieved by this MPI process
double *sendbuf_x, *sendbuf_y, *sendbuf_z, *sendbuf_X, *sendbuf_Y, *sendbuf_Z;

11
common/ScaLBL.h
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@ -221,6 +221,17 @@ extern "C" void ScaLBL_D3Q19_AAodd_BGK(int *neighborList, double *dist, int star
extern "C" void ScaLBL_D3Q7_Membrane_IonTransport(int *membrane, double *coef, double *dist, double *Den, int memLinks, int Np);
extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef(int *membrane, int *Map, double *Distance, double *Psi, double *coef,
double Threshold, double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
int memLinks, int Nx, int Ny, int Nz, int Np);
extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
const int Cqx, const int Cqy, int const Cqz,
int *Map, double *Distance, double *Psi, double Threshold,
double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
int *d3q7_recvlist, int *d3q7_linkList, double *coef, int start, int nlinks, int count,
const int N, const int Nx, const int Ny, const int Nz);
extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
double *recvbuf, double *dist, int N, double *coef);

86
cpu/Ion.cpp
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@ -1,7 +1,91 @@
#include <stdio.h>
extern "C" void ScaLBL_D3Q7_AssignLinkCoef(){
extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef(int *membrane, int *Map, double *Distance, double *Psi, double *coef,
double Threshold, double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
int memLinks, int Nx, int Ny, int Nz, int Np){
int link,iq,ip,nq,np,nqm,npm;
double aq, ap, membranePotential;
/* Interior Links */
for (link=0; link<memLinks; link++){
// inside //outside
aq = MassFractionIn; ap = MassFractionOut;
iq = membrane[2*link]; ip = membrane[2*link+1];
nq = iq%Np; np = ip%Np;
nqm = Map[nq]; npm = Map[np]; // strided layout
/* membrane potential for this link */
membranePotential = Psi[nqm] - Psi[npm];
if (membranePotential > Threshold){
aq = ThresholdMassFractionIn; ap = ThresholdMassFractionOut;
}
/* Save the mass transfer coefficients */
coef[2*link] = aq; coef[2*link+1] = ap;
}
}
extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
const int Cqx, const int Cqy, int const Cqz,
int *Map, double *Distance, double *Psi, double Threshold,
double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
int *d3q7_recvlist, int *d3q7_linkList, double *coef, int start, int nlinks, int count,
const int N, const int Nx, const int Ny, const int Nz) {
//....................................................................................
// Unack distribution from the recv buffer
// Distribution q matche Cqx, Cqy, Cqz
// swap rule means that the distributions in recvbuf are OPPOSITE of q
// dist may be even or odd distributions stored by stream layout
//....................................................................................
int n, idx, link, nqm, npm, i, j, k;
double distanceLocal, distanceNonlocal;
double psiLocal, psiNonlocal, membranePotential;
double ap,aq; // coefficient
/* second enforce custom rule for membrane links */
for (link = nlinks; link < count; link++) {
// get the index for the recv list (deal with reordering of links)
idx = d3q7_linkList[link];
// get the distribution index
n = d3q7_recvlist[start+idx];
// get the index in strided layout
nqm = Map[n];
distanceLocal = Distance[nqm];
psiLocal = Psi[nqm];
// Get the 3-D indices from the send process
k = nqm/(Nx*Ny); j = (nqm-Nx*Ny*k)/Nx; i = nqm-Nx*Ny*k-Nx*j;
// Streaming link the non-local distribution
i -= Cqx; j -= Cqy; k -= Cqz;
npm = k*Nx*Ny + j*Nx + i;
distanceNonlocal = Distance[npm];
psiNonlocal = Psi[npm];
membranePotential = psiLocal - psiNonlocal;
aq = MassFractionIn;
ap = MassFractionOut;
/* link is inside membrane */
if (distanceLocal > 0.0){
if (membranePotential < Threshold*(-1.0)){
ap = MassFractionIn;
aq = MassFractionOut;
}
else {
ap = ThresholdMassFractionIn;
aq = ThresholdMassFractionOut;
}
}
else if (membranePotential > Threshold){
aq = ThresholdMassFractionIn;
ap = ThresholdMassFractionOut;
}
// update link based on mass transfer coefficients
coef[2*(link-nlinks)] = aq;
coef[2*(link-nlinks)+1] = ap;
}
}