add barrier to membrane transport
This commit is contained in:
James McClure
parent
9e74f49812
commit
e677b0395f
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@ -1285,30 +1285,30 @@ void Membrane::SendD3Q7AA(double *dist){
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// Pack the distributions
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//...Packing for x face(q=2)................................
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ScaLBL_D3Q19_Pack(2,dvcSendList_x,0,sendCount_x,sendbuf_x,dist,Np);
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req1[0] = MPI_COMM_SCALBL.Isend(sendbuf_x, sendCount_x,rank_x,sendtag);
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req2[0] = MPI_COMM_SCALBL.Irecv(recvbuf_X, recvCount_X,rank_X,recvtag);
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req1[0] = MPI_COMM_SCALBL.Isend(sendbuf_x, sendCount_x,rank_x,sendtag);
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//...Packing for X face(q=1)................................
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ScaLBL_D3Q19_Pack(1,dvcSendList_X,0,sendCount_X,sendbuf_X,dist,Np);
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req1[1] = MPI_COMM_SCALBL.Isend(sendbuf_X, sendCount_X,rank_X,sendtag);
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req2[1] = MPI_COMM_SCALBL.Irecv(recvbuf_x, recvCount_x,rank_x,recvtag);
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req1[1] = MPI_COMM_SCALBL.Isend(sendbuf_X, sendCount_X,rank_X,sendtag);
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//for (int idx=0; idx<sendCount_X; idx++) printf(" SendX(%i)=%e \n",idx,sendbuf_X[idx]);
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//...Packing for y face(q=4).................................
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ScaLBL_D3Q19_Pack(4,dvcSendList_y,0,sendCount_y,sendbuf_y,dist,Np);
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req1[2] = MPI_COMM_SCALBL.Isend(sendbuf_y, sendCount_y,rank_y,sendtag);
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req2[2] = MPI_COMM_SCALBL.Irecv(recvbuf_Y, recvCount_Y,rank_Y,recvtag);
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req1[2] = MPI_COMM_SCALBL.Isend(sendbuf_y, sendCount_y,rank_y,sendtag);
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//...Packing for Y face(q=3).................................
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ScaLBL_D3Q19_Pack(3,dvcSendList_Y,0,sendCount_Y,sendbuf_Y,dist,Np);
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req1[3] = MPI_COMM_SCALBL.Isend(sendbuf_Y, sendCount_Y,rank_Y,sendtag);
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req2[3] = MPI_COMM_SCALBL.Irecv(recvbuf_y, recvCount_y,rank_y,recvtag);
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req1[3] = MPI_COMM_SCALBL.Isend(sendbuf_Y, sendCount_Y,rank_Y,sendtag);
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//for (int idx=0; idx<sendCount_Y; idx++) printf(" SendY(%i)=%e \n",idx,sendbuf_Y[idx]);
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//...Packing for z face(q=6)................................
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ScaLBL_D3Q19_Pack(6,dvcSendList_z,0,sendCount_z,sendbuf_z,dist,Np);
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req1[4] = MPI_COMM_SCALBL.Isend(sendbuf_z, sendCount_z,rank_z,sendtag);
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req2[4] = MPI_COMM_SCALBL.Irecv(recvbuf_Z, recvCount_Z,rank_Z,recvtag);
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req1[4] = MPI_COMM_SCALBL.Isend(sendbuf_z, sendCount_z,rank_z,sendtag);
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//...Packing for Z face(q=5)................................
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ScaLBL_D3Q19_Pack(5,dvcSendList_Z,0,sendCount_Z,sendbuf_Z,dist,Np);
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req1[5] = MPI_COMM_SCALBL.Isend(sendbuf_Z, sendCount_Z,rank_Z,sendtag);
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req2[5] = MPI_COMM_SCALBL.Irecv(recvbuf_z, recvCount_z,rank_z,recvtag);
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req1[5] = MPI_COMM_SCALBL.Isend(sendbuf_Z, sendCount_Z,rank_Z,sendtag);
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}
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@ -1341,6 +1341,7 @@ void Membrane::RecvD3Q7AA(double *dist){
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ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,Np,coefficient_Z);
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//..................................................................................
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MPI_COMM_SCALBL.barrier();
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//...................................................................................
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Lock=false; // unlock the communicator after communications complete
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//...................................................................................
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@ -1447,100 +1447,100 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField) {
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void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, double *Psi) {
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//Input parameter:
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//1. Velocity is from StokesModel
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//2. ElectricField is from Poisson model
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//Input parameter:
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//1. Velocity is from StokesModel
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//2. ElectricField is from Poisson model
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//LB-related parameter
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vector<double> rlx;
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for (size_t ic = 0; ic < tau.size(); ic++) {
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rlx.push_back(1.0 / tau[ic]);
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}
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//LB-related parameter
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vector<double> rlx;
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for (size_t ic = 0; ic < tau.size(); ic++) {
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rlx.push_back(1.0 / tau[ic]);
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}
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//.......create and start timer............
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//double starttime,stoptime,cputime;
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//ScaLBL_Comm->Barrier(); comm.barrier();
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//auto t1 = std::chrono::system_clock::now();
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//.......create and start timer............
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//double starttime,stoptime,cputime;
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//ScaLBL_Comm->Barrier(); comm.barrier();
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//auto t1 = std::chrono::system_clock::now();
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for (size_t ic = 0; ic < number_ion_species; ic++) {
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/* set the mass transfer coefficients for the membrane */
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for (size_t ic = 0; ic < number_ion_species; ic++) {
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/* set the mass transfer coefficients for the membrane */
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IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic],
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MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]);
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timestep = 0;
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while (timestep < timestepMax[ic]) {
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//************************************************************************/
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// *************ODD TIMESTEP*************//
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timestep++;
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timestep = 0;
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while (timestep < timestepMax[ic]) {
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//************************************************************************/
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// *************ODD TIMESTEP*************//
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timestep++;
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//LB-Ion collison
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IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
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//LB-Ion collison
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IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
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ScaLBL_D3Q7_AAodd_Ion(
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IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
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&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
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&FluxElectrical[3 * ic * Np], Velocity, ElectricField,
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IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt,
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ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
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IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
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ScaLBL_D3Q7_AAodd_Ion(
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IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
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&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
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&FluxElectrical[3 * ic * Np], Velocity, ElectricField,
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IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt,
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ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
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ScaLBL_D3Q7_AAodd_Ion(
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IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
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&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
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&FluxElectrical[3 * ic * Np], Velocity, ElectricField,
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IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, 0,
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ScaLBL_Comm->LastExterior(), Np);
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IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
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ScaLBL_D3Q7_AAodd_Ion(
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IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
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&FluxDiffusive[3 * ic * Np], &FluxAdvective[3 * ic * Np],
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&FluxElectrical[3 * ic * Np], Velocity, ElectricField,
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IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, 0,
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ScaLBL_Comm->LastExterior(), Np);
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IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
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IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
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/* if (BoundaryConditionSolid == 1) {
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/* if (BoundaryConditionSolid == 1) {
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//TODO IonSolid may also be species-dependent
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ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid);
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}
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ScaLBL_Comm->Barrier();
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comm.barrier();
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*/
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// *************EVEN TIMESTEP*************//
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timestep++;
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*/
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// *************EVEN TIMESTEP*************//
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timestep++;
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//LB-Ion collison
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IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
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//LB-Ion collison
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IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
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ScaLBL_D3Q7_AAeven_Ion(
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&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
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&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
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Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
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rlx[ic], Vt, ScaLBL_Comm->FirstInterior(),
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ScaLBL_Comm->LastInterior(), Np);
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ScaLBL_D3Q7_AAeven_Ion(
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&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
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&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
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Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
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rlx[ic], Vt, ScaLBL_Comm->FirstInterior(),
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ScaLBL_Comm->LastInterior(), Np);
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IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
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IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
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ScaLBL_D3Q7_AAeven_Ion(
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&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
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&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
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Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
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rlx[ic], Vt, 0, ScaLBL_Comm->LastExterior(), Np);
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IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
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ScaLBL_D3Q7_AAeven_Ion(
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&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
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&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
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Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
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rlx[ic], Vt, 0, ScaLBL_Comm->LastExterior(), Np);
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ScaLBL_Comm->Barrier();
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comm.barrier();
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IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
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/*
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ScaLBL_Comm->Barrier();
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comm.barrier();
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/*
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if (BoundaryConditionSolid == 1) {
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//TODO IonSolid may also be species-dependent
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ScaLBL_Comm->SolidDirichletD3Q7(&fq[ic * Np * 7], IonSolid);
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}
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ScaLBL_Comm->Barrier();
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comm.barrier();
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*/
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}
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}
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*/
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}
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}
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//Compute charge density for Poisson equation
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for (size_t ic = 0; ic < number_ion_species; ic++) {
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