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debug crusher

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This commit is contained in:
James E McClure 2022-04-24 14:55:59 -04:00
parent eadb420d06
commit 9043751281
4 changed files with 14 additions and 53 deletions
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4
common/Membrane.cpp
View File

@ -1323,7 +1323,7 @@ void Membrane::RecvD3Q7AA(double *dist){
// Unpack the distributions on the device
//...................................................................................
//...Unpacking for x face(q=2)................................
ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, dvcRecvLinks_x,0,linkCount_x[0],recvCount_x,recvbuf_x,dist,Np,coefficient_x);
/* ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, dvcRecvLinks_x,0,linkCount_x[0],recvCount_x,recvbuf_x,dist,Np,coefficient_x);
//...................................................................................
//...Packing for X face(q=1)................................
ScaLBL_D3Q7_Membrane_Unpack(1,dvcRecvDist_X, dvcRecvLinks_X,0,linkCount_X[0],recvCount_X,recvbuf_X,dist,Np,coefficient_X);
@ -1339,7 +1339,7 @@ void Membrane::RecvD3Q7AA(double *dist){
//...Packing for Z face(q=5)................................
ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,Np,coefficient_Z);
//..................................................................................
*/
//...................................................................................
Lock=false; // unlock the communicator after communications complete
//...................................................................................

49
models/IonModel.cpp
View File

@ -441,7 +441,6 @@ void ScaLBL_IonModel::ReadParams(string filename) {
}
}
}
//Read solid boundary condition specific to Ion model
BoundaryConditionSolid = 0;
if (ion_db->keyExists("BC_Solid")) {
@ -1375,12 +1374,7 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
timestep++;
//LB-Ion collison
IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 1 \n");
fflush(stdout);
IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
ScaLBL_D3Q7_AAodd_Ion(
IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
@ -1389,12 +1383,7 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt,
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 2 \n");
fflush(stdout);
// IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_D3Q7_AAodd_Ion(
IonMembrane->NeighborList, &fq[ic * Np * 7], &Ci[ic * Np],
@ -1403,18 +1392,9 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
IonDiffusivity[ic], IonValence[ic], rlx[ic], Vt, 0,
ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 3 \n");
fflush(stdout);
IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 4 \n");
fflush(stdout);
/* if (BoundaryConditionSolid == 1) {
//TODO IonSolid may also be species-dependent
@ -1428,15 +1408,6 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//LB-Ion collison
IonMembrane->SendD3Q7AA(&fq[ic * Np * 7]); //READ FORM NORMAL
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
comm.barrier();
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 5 \n");
fflush(stdout);
ScaLBL_D3Q7_AAeven_Ion(
&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
@ -1445,30 +1416,20 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
rlx[ic], Vt, ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np);
//IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 6 \n");
fflush(stdout);
IonMembrane->RecvD3Q7AA(&fq[ic * Np * 7]); //WRITE INTO OPPOSITE
ScaLBL_D3Q7_AAeven_Ion(
&fq[ic * Np * 7], &Ci[ic * Np], &FluxDiffusive[3 * ic * Np],
&FluxAdvective[3 * ic * Np], &FluxElectrical[3 * ic * Np],
Velocity, ElectricField, IonDiffusivity[ic], IonValence[ic],
rlx[ic], Vt, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 7 \n");
fflush(stdout);
IonMembrane->IonTransport(&fq[ic * Np * 7],&Ci[ic * Np]);
ScaLBL_Comm->Barrier();
comm.barrier();
if (rank==0) printf(" IonMembrane: completeted # 8 \n");
fflush(stdout);
/*
if (BoundaryConditionSolid == 1) {
//TODO IonSolid may also be species-dependent

10
models/PoissonSolver.cpp
View File

@ -560,9 +560,10 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
// Check convergence of steady-state solution
if (timestep==2){
//save electric potential for convergence check
ScaLBL_CopyToHost(Psi_previous.data(),Psi,sizeof(double)*Nx*Ny*Nz);
}
if (timestep%analysis_interval==0){
/* get the elecric potential */
ScaLBL_CopyToHost(Psi_host.data(),Psi,sizeof(double)*Nx*Ny*Nz);
if (rank==0) printf(" ... getting Poisson solver error \n");
double err = 0.0;
double max_error = 0.0;
@ -684,10 +685,10 @@ void ScaLBL_Poisson::SolveElectricPotentialAAeven(int timestep_from_Study, doubl
void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVelBC){
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
//ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAodd_Poisson(NeighborList, dvcMap, fq, ChargeDensity, Psi, ElectricField, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
//TODO: perhaps add another ScaLBL_Comm routine to update Psi values on solid boundary nodes.
@ -698,9 +699,8 @@ void ScaLBL_Poisson::SolvePoissonAAodd(double *ChargeDensity, bool UseSlippingVe
void ScaLBL_Poisson::SolvePoissonAAeven(double *ChargeDensity, bool UseSlippingVelBC){
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_Comm->Barrier();
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, epsilon_LB, UseSlippingVelBC, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAeven_Poisson(dvcMap, fq, ChargeDensity, Psi, ElectricField, ResidualError, tau, epsilon_LB, UseSlippingVelBC, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();

4
tests/lbpm_cell_simulator.cpp
View File

@ -124,7 +124,7 @@ int main(int argc, char **argv)
fflush(stdout);
timestep++;//AA operations
/*
if (timestep%Study.analysis_interval==0){
Analysis.Basic(IonModel,PoissonSolver,StokesModel,timestep);
@ -137,7 +137,7 @@ int main(int argc, char **argv)
//StokesModel.getVelocity(timestep);
}
*/
}
if (rank==0) printf("Save simulation raw data at maximum timestep\n");