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testing membrane ion transport

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This commit is contained in:
James McClure 2022-04-06 22:25:05 -04:00
parent cca06f7964
commit 9c013e6169
3 changed files with 74 additions and 8 deletions
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14
common/Membrane.cpp
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@ -1356,7 +1356,11 @@ void Membrane::RecvD3Q7AA(double *dist){
//...................................................................................
Lock=false; // unlock the communicator after communications complete
//...................................................................................
}
void Membrane::IonTransport(double *dist, double *den){
ScaLBL_D3Q7_Membrane_IonTransport(MembraneLinks,MembraneCoef, dist, den, membraneLinkCount, Np);
}
// std::shared_ptr<Database> db){
@ -1372,12 +1376,22 @@ void Membrane::AssignCoefficients(int *Map, double *Psi, string method){
ThresholdMassFractionOut = 0.0;
ThresholdMassFractionIn = 0.0;
if (method == "ones"){
/* Initializing */
printf(".... initialize permeable membrane \n");
MassFractionIn = 1.0;
MassFractionOut = 1.0;
ThresholdMassFractionOut = 1.0;
ThresholdMassFractionIn = 1.0;
}
if (method == "Voltage Gated Potassium"){
MassFractionIn = 0.0;
MassFractionOut = 0.0;
ThresholdMassFractionOut = 0.0;
ThresholdMassFractionIn = 1.0;
}
ScaLBL_D3Q7_Membrane_AssignLinkCoef(MembraneLinks, Map, MembraneDistance, Psi, MembraneCoef,
Threshold, MassFractionIn, MassFractionOut, ThresholdMassFractionIn, ThresholdMassFractionOut,
membraneLinkCount, Nx, Ny, Nz, Np);

1
common/Membrane.h
View File

@ -96,6 +96,7 @@ public:
void SendD3Q7AA(double *dist);
void RecvD3Q7AA(double *dist);
void AssignCoefficients(int *Map, double *Psi, std::string method);
void IonTransport(double *dist, double *den);
//......................................................................................
// Buffers to store data sent and recieved by this MPI process
double *sendbuf_x, *sendbuf_y, *sendbuf_z, *sendbuf_X, *sendbuf_Y, *sendbuf_Z;

67
tests/TestMembrane.cpp
View File

@ -98,10 +98,10 @@ int main(int argc, char **argv)
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Npad);
ScaLBL_CopyToDevice(NeighborList, neighborList, 18*Np*sizeof(int));
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Dm->id.data(),Np,1);
comm.barrier();
ScaLBL_CopyToDevice(NeighborList, neighborList, 18*Np*sizeof(int));
double *dist;
dist = new double [19*Np];
@ -162,7 +162,64 @@ int main(int argc, char **argv)
}
if (argc > 1)
Dm->AggregateLabels("membrane.raw");
/* create a pair of distributions to test membrane mass transport routine */
double *fq, *gq, *Ci, *Cj, *Psi, *Ci_host;
Ci_host = new double [Np];
ScaLBL_AllocateDeviceMemory((void **)&fq, 19 * sizeof(double) * Np);
ScaLBL_AllocateDeviceMemory((void **)&gq, 19 * sizeof(double) * Np);
ScaLBL_AllocateDeviceMemory((void **)&Ci, sizeof(double) * Np);
ScaLBL_AllocateDeviceMemory((void **)&Cj, sizeof(double) * Np);
ScaLBL_AllocateDeviceMemory((void **)&Psi, sizeof(double) * Np);
/* initialize concentration inside membrane */
for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){
n = k*Nx*Ny+j*Nx+i;
int idx = Map(i,j,k);
if (Distance(i,j,k) > 0.0)
Ci_host[idx] = 1.0;
else
Ci_host[idx] = 0.0;
}
}
}
ScaLBL_CopyToDevice(Ci, Ci_host, sizeof(double) * Np);
/* initialize the distributions */
ScaLBL_D3Q7_Ion_Init_FromFile(fq, Ci, Np);
ScaLBL_D3Q7_Ion_Init_FromFile(gq, Ci, Np);
/* Streaming with the usual neighborlist */
ScaLBL_D3Q19_AAodd_Compact(NeighborList, fq, Np);
/* Streaming with the membrane neighborlist*/
ScaLBL_D3Q19_AAodd_Compact(M.NeighborList, gq, Np);
/* explicit mass transfer step with the membrane*/
M.AssignCoefficients(dvcMap, Psi, "ones");
M.IonTransport(gq, Cj);
ScaLBL_CopyToHost(Ci_host, Cj, sizeof(double) * Np);
double ionError = 0.0;
for (int n=0; n<Np; n++){
ionError += Ci_host[n];
}
if (ionError > 1e-12) {
printf(" Failed error tolerance in membrane ion transport routine! \n");
check = 2;
}
DoubleArray Ions(Nx,Ny,Nz);
ScaLBL_Comm->RegularLayout(Map, Cj, Ions);
Dm->AggregateLabels("membrane2.raw",Ions);
/* now check that the two values agree*/
//...........................................................................
// Update GPU data structures
if (rank==0) printf ("Setting up device map and neighbor list \n");
@ -198,9 +255,6 @@ int main(int argc, char **argv)
}
/* Run dummy communications */
double * gq, *fq;
ScaLBL_AllocateDeviceMemory((void **) &gq, sizeof(double)*7*Np);
ScaLBL_AllocateDeviceMemory((void **) &fq, sizeof(double)*7*Np);
/*initialize fq from host data */
ScaLBL_CopyToDevice(fq, fq_host, sizeof(double)*7*Np);
@ -210,9 +264,6 @@ int main(int argc, char **argv)
//ScaLBL_CopyToHost(fq_host, gq, sizeof(double)*7*Np);
if (rank==0) printf ("Sum result \n");
double *Ci;
Ci = new double [Np];
ScaLBL_D3Q7_AAeven_IonConcentration(&gq[0 * Np * 7], &Ci[0 * Np],
0, ScaLBL_Comm->LastExterior(),
Np);