OilfieldToolsNet/LBPM
4
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

add barrier to membrane transport

Browse Source
This commit is contained in:
James McClure
2022-05-09 06:32:58 -04:00
parent 9e74f49812
commit e677b0395f
2 changed files with 70 additions and 69 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
common/Membrane.cpp
View File

@@ -1285,30 +1285,30 @@ void Membrane::SendD3Q7AA(double *dist){
// Pack the distributions // Pack the distributions
//...Packing for x face(q=2)................................ //...Packing for x face(q=2)................................
ScaLBL_D3Q19_Pack(2,dvcSendList_x,0,sendCount_x,sendbuf_x,dist,Np); ScaLBL_D3Q19_Pack(2,dvcSendList_x,0,sendCount_x,sendbuf_x,dist,Np);
req1[0] = MPI_COMM_SCALBL.Isend(sendbuf_x, sendCount_x,rank_x,sendtag);
req2[0] = MPI_COMM_SCALBL.Irecv(recvbuf_X, recvCount_X,rank_X,recvtag); req2[0] = MPI_COMM_SCALBL.Irecv(recvbuf_X, recvCount_X,rank_X,recvtag);
req1[0] = MPI_COMM_SCALBL.Isend(sendbuf_x, sendCount_x,rank_x,sendtag);
//...Packing for X face(q=1)................................ //...Packing for X face(q=1)................................
ScaLBL_D3Q19_Pack(1,dvcSendList_X,0,sendCount_X,sendbuf_X,dist,Np); ScaLBL_D3Q19_Pack(1,dvcSendList_X,0,sendCount_X,sendbuf_X,dist,Np);
req1[1] = MPI_COMM_SCALBL.Isend(sendbuf_X, sendCount_X,rank_X,sendtag);
req2[1] = MPI_COMM_SCALBL.Irecv(recvbuf_x, recvCount_x,rank_x,recvtag); req2[1] = MPI_COMM_SCALBL.Irecv(recvbuf_x, recvCount_x,rank_x,recvtag);
req1[1] = MPI_COMM_SCALBL.Isend(sendbuf_X, sendCount_X,rank_X,sendtag);
//for (int idx=0; idx<sendCount_X; idx++) printf(" SendX(%i)=%e \n",idx,sendbuf_X[idx]); //for (int idx=0; idx<sendCount_X; idx++) printf(" SendX(%i)=%e \n",idx,sendbuf_X[idx]);
//...Packing for y face(q=4)................................. //...Packing for y face(q=4).................................
ScaLBL_D3Q19_Pack(4,dvcSendList_y,0,sendCount_y,sendbuf_y,dist,Np); ScaLBL_D3Q19_Pack(4,dvcSendList_y,0,sendCount_y,sendbuf_y,dist,Np);
req1[2] = MPI_COMM_SCALBL.Isend(sendbuf_y, sendCount_y,rank_y,sendtag);
req2[2] = MPI_COMM_SCALBL.Irecv(recvbuf_Y, recvCount_Y,rank_Y,recvtag); req2[2] = MPI_COMM_SCALBL.Irecv(recvbuf_Y, recvCount_Y,rank_Y,recvtag);
req1[2] = MPI_COMM_SCALBL.Isend(sendbuf_y, sendCount_y,rank_y,sendtag);
//...Packing for Y face(q=3)................................. //...Packing for Y face(q=3).................................
ScaLBL_D3Q19_Pack(3,dvcSendList_Y,0,sendCount_Y,sendbuf_Y,dist,Np); ScaLBL_D3Q19_Pack(3,dvcSendList_Y,0,sendCount_Y,sendbuf_Y,dist,Np);
req1[3] = MPI_COMM_SCALBL.Isend(sendbuf_Y, sendCount_Y,rank_Y,sendtag);
req2[3] = MPI_COMM_SCALBL.Irecv(recvbuf_y, recvCount_y,rank_y,recvtag); req2[3] = MPI_COMM_SCALBL.Irecv(recvbuf_y, recvCount_y,rank_y,recvtag);
req1[3] = MPI_COMM_SCALBL.Isend(sendbuf_Y, sendCount_Y,rank_Y,sendtag);
//for (int idx=0; idx<sendCount_Y; idx++) printf(" SendY(%i)=%e \n",idx,sendbuf_Y[idx]); //for (int idx=0; idx<sendCount_Y; idx++) printf(" SendY(%i)=%e \n",idx,sendbuf_Y[idx]);
//...Packing for z face(q=6)................................ //...Packing for z face(q=6)................................
ScaLBL_D3Q19_Pack(6,dvcSendList_z,0,sendCount_z,sendbuf_z,dist,Np); ScaLBL_D3Q19_Pack(6,dvcSendList_z,0,sendCount_z,sendbuf_z,dist,Np);
req1[4] = MPI_COMM_SCALBL.Isend(sendbuf_z, sendCount_z,rank_z,sendtag);
req2[4] = MPI_COMM_SCALBL.Irecv(recvbuf_Z, recvCount_Z,rank_Z,recvtag); req2[4] = MPI_COMM_SCALBL.Irecv(recvbuf_Z, recvCount_Z,rank_Z,recvtag);
req1[4] = MPI_COMM_SCALBL.Isend(sendbuf_z, sendCount_z,rank_z,sendtag);
//...Packing for Z face(q=5)................................ //...Packing for Z face(q=5)................................
ScaLBL_D3Q19_Pack(5,dvcSendList_Z,0,sendCount_Z,sendbuf_Z,dist,Np); ScaLBL_D3Q19_Pack(5,dvcSendList_Z,0,sendCount_Z,sendbuf_Z,dist,Np);
req1[5] = MPI_COMM_SCALBL.Isend(sendbuf_Z, sendCount_Z,rank_Z,sendtag);
req2[5] = MPI_COMM_SCALBL.Irecv(recvbuf_z, recvCount_z,rank_z,recvtag); req2[5] = MPI_COMM_SCALBL.Irecv(recvbuf_z, recvCount_z,rank_z,recvtag);
req1[5] = MPI_COMM_SCALBL.Isend(sendbuf_Z, sendCount_Z,rank_Z,sendtag);
} }
@@ -1341,6 +1341,7 @@ void Membrane::RecvD3Q7AA(double *dist){
ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,Np,coefficient_Z); ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,Np,coefficient_Z);
//.................................................................................. //..................................................................................
MPI_COMM_SCALBL.barrier();
//................................................................................... //...................................................................................
Lock=false; // unlock the communicator after communications complete Lock=false; // unlock the communicator after communications complete
//................................................................................... //...................................................................................

126
models/IonModel.cpp
View File

@@ -1447,100 +1447,100 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField) {
void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, double *Psi) { void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, double *Psi) {
//Input parameter: //Input parameter:
//1. Velocity is from StokesModel //1. Velocity is from StokesModel
//2. ElectricField is from Poisson model //2. ElectricField is from Poisson model
//LB-related parameter //LB-related parameter
vector<double> rlx; vector<double> rlx;
for (size_t ic = 0; ic < tau.size(); ic++) { for (size_t ic = 0; ic < tau.size(); ic++) {
rlx.push_back(1.0 / tau[ic]); rlx.push_back(1.0 / tau[ic]);
} }
//.......create and start timer............ //.......create and start timer............
//double starttime,stoptime,cputime; //double starttime,stoptime,cputime;
//ScaLBL_Comm->Barrier(); comm.barrier(); //ScaLBL_Comm->Barrier(); comm.barrier();
//auto t1 = std::chrono::system_clock::now(); //auto t1 = std::chrono::system_clock::now();
for (size_t ic = 0; ic < number_ion_species; ic++) { for (size_t ic = 0; ic < number_ion_species; ic++) {
/* set the mass transfer coefficients for the membrane */ /* set the mass transfer coefficients for the membrane */
IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic], IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic],
MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]); MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]);
timestep = 0; timestep = 0;
while (timestep < timestepMax[ic]) { while (timestep < timestepMax[ic]) {
//************************************************************************/ //************************************************************************/
// *************ODD TIMESTEP*************// // *************ODD TIMESTEP*************//
timestep++; timestep++;
//LB-Ion collison //LB-Ion collison
IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
ScaLBL_D3Q7_AAodd_Ion( ScaLBL_D3Q7_AAodd_Ion(
IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np], IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np], &FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
&FluxElectrical[3 * ic * Np], Velocity, ElectricField, &FluxElectrical[3 * ic * Np], Velocity, ElectricField,
IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt,
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np); ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_D3Q7_AAodd_Ion( IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np], ScaLBL_D3Q7_AAodd_Ion(
&FluxElectrical[3 * ic * Np], Velocity, ElectricField, IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, 0, &FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
ScaLBL_Comm->LastExterior(), Np); &FluxElectrical[3 * ic * Np], Velocity, ElectricField,
IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, 0,
ScaLBL_Comm->LastExterior(), Np);
IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]); IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
/* if (BoundaryConditionSolid == 1) { /* if (BoundaryConditionSolid == 1) {
//TODO IonSolid may also be species-dependent //TODO IonSolid may also be species-dependent
ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid); ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid);
} }
ScaLBL_Comm->Barrier(); ScaLBL_Comm->Barrier();
comm.barrier(); comm.barrier();
*/ */
// *************EVEN TIMESTEP*************// // *************EVEN TIMESTEP*************//
timestep++; timestep++;
//LB-Ion collison //LB-Ion collison
IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
ScaLBL_D3Q7_AAeven_Ion( ScaLBL_D3Q7_AAeven_Ion(
&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np], &fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np], &FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic], Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
rlx[ic], Vt, ScaLBL_Comm->FirstInterior(), rlx[ic], Vt, ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np); ScaLBL_Comm->LastInterior(), Np);
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_D3Q7_AAeven_Ion( ScaLBL_D3Q7_AAeven_Ion(
&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np], &fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np], &FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic], Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
rlx[ic], Vt, 0, ScaLBL_Comm->LastExterior(), Np); rlx[ic], Vt, 0, ScaLBL_Comm->LastExterior(), Np);
IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
ScaLBL_Comm->Barrier(); IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
comm.barrier();
/* ScaLBL_Comm->Barrier();
comm.barrier();
/*
if (BoundaryConditionSolid == 1) { if (BoundaryConditionSolid == 1) {
//TODO IonSolid may also be species-dependent //TODO IonSolid may also be species-dependent
ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid); ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid);
} }
ScaLBL_Comm->Barrier(); ScaLBL_Comm->Barrier();
comm.barrier(); comm.barrier();
*/ */
} }
} }
//Compute charge density for Poisson equation //Compute charge density for Poisson equation
for (size_t ic = 0; ic < number_ion_species; ic++) { for (size_t ic = 0; ic < number_ion_species; ic++) {