int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt n = 3,ix[2][3] = {{3,5,4},{1,7,9}};
IS isx,il;
PetscMPIInt size,rank;
PetscViewer vx,vl;
PetscBool equal;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_SIZ,"Example only works with one or two processes");
ierr = ISCreateGeneral(PETSC_COMM_WORLD,n,ix[rank],PETSC_COPY_VALUES,&isx);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"testfile",FILE_MODE_WRITE,&vx);CHKERRQ(ierr);
ierr = ISView(isx,vx);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&vx);CHKERRQ(ierr);
ierr = ISCreate(PETSC_COMM_WORLD,&il);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"testfile",FILE_MODE_READ,&vl);CHKERRQ(ierr);
ierr = ISLoad(il,vl);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&vl);CHKERRQ(ierr);
ierr = ISEqual(il,isx,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Index set loaded from file does not match index set to file");
ierr = ISDestroy(&il);CHKERRQ(ierr);
ierr = ISDestroy(&isx);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
-fA <input_file> -fB <input_file> \n\n";
#include <petscmat.h>
#undef WRITEFILE
#undef __FUNCT__
#define __FUNCT__ "main"
PetscInt main(PetscInt argc,char **args)
{
Mat A,B;
PetscViewer fd;
char file[2][PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscErrorCode ierr;
PetscMPIInt size;
PetscInt ma,na,mb,nb;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
/* read the two matrices, A and B */
ierr = PetscOptionsGetString(NULL,NULL,"-fA",file[0],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate binary file with the -fA options");
ierr = PetscOptionsGetString(NULL,NULL,"-fB",file[1],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate binary file with the -fP options");
/* Load matrices */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[0],FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
printf("\n A:\n");
printf("----------------------\n");
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatGetSize(A,&ma,&na);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[1],FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatLoad(B,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
printf("\n B:\n");
printf("----------------------\n");
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatGetSize(B,&mb,&nb);CHKERRQ(ierr);
/* Compute B = -A + B */
if (ma != mb || na != nb) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"nonconforming matrix size");
ierr = MatAXPY(B,-1.0,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
printf("\n B - A:\n");
printf("----------------------\n");
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat BAIJ,SBAIJ,*subBAIJ,*subSBAIJ;
PetscViewer viewer;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscErrorCode ierr;
PetscInt n = 2,issize,M,N;
PetscMPIInt rank;
IS isrow,iscol,irow[n],icol[n];
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&BAIJ);CHKERRQ(ierr);
ierr = MatSetType(BAIJ,MATMPIBAIJ);CHKERRQ(ierr);
ierr = MatLoad(BAIJ,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&SBAIJ);CHKERRQ(ierr);
ierr = MatSetType(SBAIJ,MATMPISBAIJ);CHKERRQ(ierr);
ierr = MatLoad(SBAIJ,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatGetSize(BAIJ,&M,&N);CHKERRQ(ierr);
issize = M/4;
ierr = ISCreateStride(PETSC_COMM_SELF,issize,0,1,&isrow);CHKERRQ(ierr);
irow[0] = irow[1] = isrow;
issize = N/2;
ierr = ISCreateStride(PETSC_COMM_SELF,issize,0,1,&iscol);CHKERRQ(ierr);
icol[0] = icol[1] = iscol;
ierr = MatGetSubMatrices(BAIJ,n,irow,icol,MAT_INITIAL_MATRIX,&subBAIJ);CHKERRQ(ierr);
/* irow and icol must be same for SBAIJ matrices! */
icol[0] = icol[1] = isrow;
ierr = MatGetSubMatrices(SBAIJ,n,irow,icol,MAT_INITIAL_MATRIX,&subSBAIJ);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (!rank) {
ierr = MatView(subBAIJ[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatView(subSBAIJ[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
/* Free data structures */
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
ierr = MatDestroyMatrices(n,&subBAIJ);CHKERRQ(ierr);
ierr = MatDestroyMatrices(n,&subSBAIJ);CHKERRQ(ierr);
ierr = MatDestroy(&BAIJ);CHKERRQ(ierr);
ierr = MatDestroy(&SBAIJ);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,B;
PetscErrorCode ierr;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscViewer fd;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/*
Open another binary file. Note that we use FILE_MODE_WRITE to indicate writing to the file
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fileoutput",FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
ierr = PetscViewerBinarySetFlowControl(fd,3);CHKERRQ(ierr);
/*
Save the matrix and vector; then destroy the viewer.
*/
ierr = MatView(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* load the new matrix */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fileoutput",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatLoad(B,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatEqual(A,B,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Matrices are not equal\n");CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode writeBC(PetscScalar tc, PetscInt iLoop, PetscInt numTracers, Vec *v, Vec *bcc, Vec *bcf)
{
PetscErrorCode ierr;
PetscInt ip;
PetscScalar zero = 0.0, one = 1.0;
/* Note: tc and iLoop are the time and step at the end of the current time step. */
if (calcDiagnostics) {
if (Iter0+iLoop>=diagTimer.startTimeStep) { /* start time averaging (note: startTimeStep is ABSOLUTE time step) */
if (diagTimer.count<=diagTimer.numTimeSteps) { /* still within same averaging block so accumulate */
ierr = VecAXPY(TRsatanomdiagavg,one,TRsatanomdiag);CHKERRQ(ierr);
ierr = VecAXPY(TReqdiagavg,one,TReqdiag);CHKERRQ(ierr);
ierr = VecAXPY(BCdiagavg,one,BCc);CHKERRQ(ierr);
diagTimer.count++; // = diagCount+1;
}
if (diagTimer.count==diagTimer.numTimeSteps) { /* time to write averages to file */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Writing diagnostics time average at time %10.5f, step %d\n", tc, Iter0+iLoop);CHKERRQ(ierr);
ierr = VecScale(TRsatanomdiagavg,1.0/diagTimer.count);CHKERRQ(ierr);
ierr = VecScale(TReqdiagavg,1.0/diagTimer.count);CHKERRQ(ierr);
ierr = VecScale(BCdiagavg,1.0/diagTimer.count);CHKERRQ(ierr);
if (!appendDiagnostics) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"TRsatanomdiagavg.petsc",FILE_MODE_WRITE,&fdTRsatanomdiagavg);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"TReqdiagavg.petsc",FILE_MODE_WRITE,&fdTReqdiagavg);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"BCdiagavg.petsc",FILE_MODE_WRITE,&fdBCdiagavg);CHKERRQ(ierr);
}
ierr = VecView(TRsatanomdiagavg,fdTRsatanomdiagavg);CHKERRQ(ierr);
ierr = VecView(TReqdiagavg,fdTReqdiagavg);CHKERRQ(ierr);
ierr = VecView(BCdiagavg,fdBCdiagavg);CHKERRQ(ierr);
appendDiagnostics=PETSC_TRUE;
/* reset diagnostic arrays */
ierr = VecSet(TRsatanomdiagavg,zero); CHKERRQ(ierr);
ierr = VecSet(TReqdiagavg,zero); CHKERRQ(ierr);
ierr = VecSet(BCdiagavg,zero); CHKERRQ(ierr);
ierr = updateStepTimer("diag_", Iter0+iLoop, &diagTimer);CHKERRQ(ierr);
// diagCount = 0;
}
}
}
return 0;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec x; /* Solution vector */
TS ts; /* Time-stepping context */
AppCtx user; /* Application context */
Mat J;
PetscViewer viewer;
PetscInitialize(&argc,&argv,"petscopt_ex6", help);
/* Get physics and time parameters */
ierr = Parameter_settings(&user);CHKERRQ(ierr);
/* Create a 2D DA with dof = 1 */
ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr);
/* Set x and y coordinates */
ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);CHKERRQ(ierr);
/* Get global vector x from DM */
ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);
ierr = ini_bou(x,&user);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
/* Get Jacobian matrix structure from the da */
ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.da,&J);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr);
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
ierr = TSSetDuration(ts,PETSC_DEFAULT,user.tmax);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,user.t0,.005);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = DMDestroy(&user.da);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
PetscErrorCode writeProfileSurfaceScalarData(char *fileName, PetscScalar *arr, PetscInt numValsPerProfile, PetscTruth appendToFile)
{
PetscErrorCode ierr;
PetscScalar *tmpArr;
PetscInt *displs, *rcounts, cumpro;
PetscInt ipro;
size_t m1, m2;
/* off_t off, offset; */
PetscViewer fd;
PetscInt fp;
/* PetscInt iShift; */
PetscMPIInt numProcessors, myId;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&myId);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&numProcessors);CHKERRQ(ierr);
m1 = numValsPerProfile*totalNumProfiles*sizeof(PetscScalar);
m2 = numProcessors*sizeof(PetscInt);
/* Allocate memory for temporary arrays */
ierr = PetscMalloc(m1,&tmpArr);CHKERRQ(ierr);
ierr = PetscMalloc(m2,&displs);CHKERRQ(ierr);
ierr = PetscMalloc(m2,&rcounts);CHKERRQ(ierr);
cumpro=0;
for (ipro=1; ipro<=numProcessors; ipro++) {
displs[ipro-1]=numValsPerProfile*cumpro;
rcounts[ipro-1]=numValsPerProfile*gNumProfiles[ipro-1];
cumpro = cumpro + gNumProfiles[ipro-1];
/* ierr=PetscPrintf(PETSC_COMM_WORLD,"cumpro=%d, displs=%d\n",cumpro,displs[ipro-1],rcounts[ipro-1]);CHKERRQ(ierr); */
}
MPI_Gatherv(arr,numValsPerProfile*lNumProfiles,MPI_DOUBLE,tmpArr,rcounts,displs,MPI_DOUBLE,0, PETSC_COMM_WORLD);
if (myId==0) { /* this shouldn't really be necessary, but without it, all processors seem to be writing in append mode */
if (appendToFile) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_APPEND,&fd);CHKERRQ(ierr);
} else {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr);
ierr = PetscBinaryWrite(fp,tmpArr,numValsPerProfile*totalNumProfiles,PETSC_SCALAR,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
}
ierr = PetscFree(tmpArr);CHKERRQ(ierr);
ierr = PetscFree(displs);CHKERRQ(ierr);
ierr = PetscFree(rcounts);CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat BAIJ,SBAIJ,*subBAIJ,*subSBAIJ;
PetscViewer viewer;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscErrorCode ierr;
PetscInt n = 2,issize;
PetscMPIInt rank;
IS is,iss[2];
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&BAIJ);CHKERRQ(ierr);
ierr = MatSetType(BAIJ,MATMPIBAIJ);CHKERRQ(ierr);
ierr = MatLoad(BAIJ,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&SBAIJ);CHKERRQ(ierr);
ierr = MatSetType(SBAIJ,MATMPISBAIJ);CHKERRQ(ierr);
ierr = MatLoad(SBAIJ,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = MatGetSize(BAIJ,&issize,0);CHKERRQ(ierr);
issize = 9;
ierr = ISCreateStride(PETSC_COMM_SELF,issize,0,1,&is);CHKERRQ(ierr);
iss[0] = is;iss[1] = is;
ierr = MatGetSubMatrices(BAIJ,n,iss,iss,MAT_INITIAL_MATRIX,&subBAIJ);CHKERRQ(ierr);
ierr = MatGetSubMatrices(SBAIJ,n,iss,iss,MAT_INITIAL_MATRIX,&subSBAIJ);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
#if defined(PETSC_USE_SOCKET_VIEWER)
if (!rank) {
ierr = MatView(subBAIJ[0],PETSC_VIEWER_SOCKET_SELF);CHKERRQ(ierr);
ierr = MatView(subSBAIJ[0],PETSC_VIEWER_SOCKET_SELF);CHKERRQ(ierr);
}
#endif
/* Free data structures */
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = MatDestroyMatrices(n,&subBAIJ);CHKERRQ(ierr);
ierr = MatDestroyMatrices(n,&subSBAIJ);CHKERRQ(ierr);
ierr = MatDestroy(&BAIJ);CHKERRQ(ierr);
ierr = MatDestroy(&SBAIJ);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec x; /* Solution vector */
TS ts; /* Time-stepping context */
AppCtx user; /* Application context */
PetscViewer viewer;
PetscInitialize(&argc,&argv,"petscopt_ex7", help);
/* Get physics and time parameters */
ierr = Parameter_settings(&user);CHKERRQ(ierr);
/* Create a 2D DA with dof = 1 */
ierr = DMDACreate2d(PETSC_COMM_WORLD,user.bx,user.by,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,user.st_width,NULL,NULL,&user.da);CHKERRQ(ierr);
/* Set x and y coordinates */
ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,0,0);CHKERRQ(ierr);
ierr = DMDASetCoordinateName(user.da,0,"X - the angle");
ierr = DMDASetCoordinateName(user.da,1,"Y - the speed");
/* Get global vector x from DM */
ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr);
ierr = ini_bou(x,&user);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetDM(ts,user.da);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr);
/* ierr = TSSetIJacobian(ts,NULL,NULL,IJacobian,&user);CHKERRQ(ierr); */
ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,.005);CHKERRQ(ierr);
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr);
ierr = TSSolve(ts,x);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = VecView(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = DMDestroy(&user.da);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt M = PETSC_DECIDE,N = PETSC_DECIDE;
DM da;
Vec global;
PetscViewer bviewer;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"daoutput",FILE_MODE_READ,&bviewer);CHKERRQ(ierr);
ierr = DMCreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMLoad(da,bviewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = VecLoad(global,bviewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&bviewer);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode TSTrajectoryGet_Basic(TSTrajectory tj,TS ts,PetscInt stepnum,PetscReal *t)
{
Vec Sol,*Y;
PetscInt Nr,i;
PetscViewer viewer;
PetscReal timepre;
char filename[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = TSGetTotalSteps(ts,&stepnum);CHKERRQ(ierr);
ierr = PetscSNPrintf(filename,sizeof filename,"SA-data/SA-%06d.bin",stepnum);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&Sol);CHKERRQ(ierr);
ierr = VecLoad(Sol,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,t,1,NULL,PETSC_REAL);CHKERRQ(ierr);
if (stepnum != 0) {
ierr = TSGetStages(ts,&Nr,&Y);CHKERRQ(ierr);
for (i=0;i<Nr ;i++) {
ierr = VecLoad(Y[i],viewer);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryRead(viewer,&timepre,1,NULL,PETSC_REAL);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,-(*t)+timepre);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A,B,MA;
PetscViewer fd;
char file[PETSC_MAX_PATH_LEN];
PetscInt m,n,M,N,dof=1;
PetscMPIInt rank,size;
PetscErrorCode ierr;
PetscBool flg;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example does not work with complex numbers");
#else
/* Load aij matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate binary file with the -f option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Get dof, then create maij matrix MA */
ierr = PetscOptionsGetInt(NULL,"-dof",&dof,NULL);CHKERRQ(ierr);
ierr = MatCreateMAIJ(A,dof,&MA);CHKERRQ(ierr);
ierr = MatGetLocalSize(MA,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(MA,&M,&N);CHKERRQ(ierr);
if (size == 1) {
ierr = MatConvert(MA,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
} else {
ierr = MatConvert(MA,MATMPIAIJ,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr);
}
/* Test MatMult() */
ierr = MatMultEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Error: MatMul() for MAIJ matrix");
/* Test MatMultAdd() */
ierr = MatMultAddEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Error: MatMulAdd() for MAIJ matrix");
/* Test MatMultTranspose() */
ierr = MatMultTransposeEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Error: MatMulAdd() for MAIJ matrix");
/* Test MatMultTransposeAdd() */
ierr = MatMultTransposeAddEqual(MA,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_CONV_FAILED,"Error: MatMulTransposeAdd() for MAIJ matrix");
ierr = MatDestroy(&MA);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
#endif
return 0;
}
int main(int argc,char **args)
{
Mat A;
PetscErrorCode ierr;
PetscReal *norms;
char file[PETSC_MAX_PATH_LEN];
PetscBool flg;
PetscViewer fd;
PetscInt n;
PetscMPIInt rank;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate binary file with the -f option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetSize(A,PETSC_NULL,&n);CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscReal),&norms);CHKERRQ(ierr);
ierr = MatGetColumnNorms(A,NORM_2,norms);CHKERRQ(ierr);
if (!rank) {
ierr = PetscRealView(n,norms,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
ierr = PetscFree(norms);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode readProfileSurfaceScalarDataRecord(char *fileName, PetscScalar *arr, PetscInt numValsPerProfile, PetscInt iRec)
{
/* Random access version of readProfileSurfaceScalarData */
/* This version takes 1 additional argument: */
/* iRec: the record to read (iRec=1 is the first record) */
PetscErrorCode ierr;
off_t off, offset;
PetscViewer fd;
PetscInt fp;
PetscInt iShift;
PetscMPIInt numProcessors, myId;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&myId);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&numProcessors);CHKERRQ(ierr);
/* Shift file pointer to start of data owned by local process */
iShift = (iRec-1)*numValsPerProfile*totalNumProfiles + numValsPerProfile*numPrevProfiles;
off = PETSC_BINARY_SCALAR_SIZE*iShift;
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,fileName,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr);
ierr = PetscBinarySeek(fp,off,PETSC_BINARY_SEEK_SET,&offset);CHKERRQ(ierr);
ierr = PetscBinaryRead(fp,arr,numValsPerProfile*lNumProfiles,PETSC_SCALAR);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
return 0;
}
int main( int argc, char **args)
{
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &args, (char *) 0, ""); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Start\n"); CHKERRQ(ierr);
DA da;
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,
64,64,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0, &da); CHKERRQ(ierr);
int rank;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
printf("[%d] rank\n", rank);
Vec p;
ierr = DACreateGlobalVector(da,&p); CHKERRQ(ierr);
ierr = VecSet( p, 1.);
char file[256] = "vec";
sprintf( file, "vec-%d", rank);
PetscViewer view;
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_WRITE,&view
); CHKERRQ(ierr);
ierr = VecView(p, view); CHKERRQ(ierr);
ierr = PetscViewerDestroy(view); CHKERRQ(ierr);
ierr = VecDestroy( p );
ierr = DADestroy( da );
ierr = PetscPrintf(PETSC_COMM_WORLD, "End\n"); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
}
int main(int argc,char **args)
{
Mat A;
PetscViewer fd;
char file[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscBool flg;
PetscMPIInt rank;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Determine files from which we read the matrix */
ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate binary file with the -f");
/* Load matrices */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetBlockSize(A,2);CHKERRQ(ierr);
if (!rank) {
ierr = MatSetSizes(A, 4, PETSC_DETERMINE, PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
} else {
ierr = MatSetSizes(A, 8, PETSC_DETERMINE, PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
}
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char *argv[])
{
PetscErrorCode ierr;
params params;
Mat H;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscPrintf(PETSC_COMM_WORLD,"--------------------------------------------------------------------------------------\n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," _______ __ __ _______ _______ ______ _______ \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," |__ __| \\/ |/ ____\\ \\ / /_ _| ____|__ __| \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," | | | \\ / | (___ \\ \\ /\\ / / | | | |__ | | \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," | | | |\\/| |\\___ \\ \\ \\/ \\/ / | | | __| | | \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," | | | | | |____) | \\ /\\ / _| |_| | | | \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," |_| |_| |_|_____/ \\/ \\/ |_____|_| |_| \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," True Muonium Solver with Iterative Front-Form Techniques \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," \n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"--------------------------------------------------------------------------------------\n");CHKERRQ(ierr);
read_input(ierr,argv,¶ms);
print_input(ierr,¶ms);
if(check_file(params.hfile))
{
PetscViewer viewer_H;
PetscViewerBinaryOpen(PETSC_COMM_WORLD,params.hfile.c_str(),FILE_MODE_READ,&viewer_H);
MatCreate(PETSC_COMM_WORLD,&H);
MatSetFromOptions(H);
MatLoad(H,viewer_H);
PetscViewerDestroy(&viewer_H);
}else
{
discretize(ierr,¶ms);
// ierr = VecView(params.mu,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
// ierr = VecView(params.theta,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
write_output(ierr,¶ms);
coulomb_trick(ierr,¶ms);
// ierr = VecView(params.CT,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ct_discrete(ierr,¶ms);
// ierr = VecView(params.CT,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
hamiltonian(ierr,¶ms,H);
// ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_DENSE);//DENSE<-->COMMON
// MatView(H,PETSC_VIEWER_STDOUT_WORLD);
}
cleanup(ierr,¶ms);
eigensolver(ierr,¶ms,H,argc,argv);
ierr = MatDestroy(&H);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
PetscErrorCode loadMatrix(Mat * A){
char file[PETSC_MAX_PATH_LEN];
char err[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscBool flag;
PetscViewer fd;
PetscInt sizex,sizey;
/*check args, if no matrix then no work... matrix file is mandatory*/
ierr=PetscOptionsGetString(PETSC_NULL,"-mfile",file,PETSC_MAX_PATH_LEN-1,&flag);CHKERRQ(ierr);
if (!flag) {
sprintf(err,"Error : mfile is not properly set -> %s\n",file);
SETERRQ(PETSC_COMM_WORLD,(PetscErrorCode)83,err);
}
/* read matrix file */
PetscPrintf(PETSC_COMM_WORLD,"Loading Matrix : %s\n",file);
ierr=MatCreate(PETSC_COMM_WORLD,A);CHKERRQ(ierr);
ierr=MatSetType(*A,MATAIJ);CHKERRQ(ierr);
ierr=PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr=MatLoad(*A,fd);CHKERRQ(ierr);
ierr=PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr=MatGetSize(*A,&sizex,&sizey);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"Loaded Matrix of size : %d %d\n",sizex,sizey);
return 0;
}
int main(int argc,char **args)
{
Vec x; /* exact solution, RHS, temp */
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
char file2[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr,ierrp;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscPrintf(PETSC_COMM_WORLD,"initializing...\n");CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f1",file,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f2",file2,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierrp = VecLoad(fd,PETSC_NULL,&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
PetscScalar *a;
VecGetArray(x,&a);
PetscInt n;
VecGetSize(x,&n);
std::ofstream f(file2);
for (int i=0;i<n;i++)
f << a[i] << " ";
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat A,B;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec v;
PetscInitialize(&argc,&args,(char *)0,help);
/*
Determine files from which we read the two linear systems
(matrix and right-hand-side vector).
*/
ierr = PetscOptionsGetString(PETSC_NULL,"-f0",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f0 option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
ierr = VecLoad(v,fd);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PadMatrix(A,v,3.0,&B);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A;
Vec x;
PetscErrorCode ierr;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscReal norm;
PetscBool flg;
PetscInitialize(&argc,&args,(char*)0,help);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatCreateVecs(A,&x,NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,x);CHKERRQ(ierr);
ierr = VecScale(x,-1.0);CHKERRQ(ierr);
ierr = MatDiagonalSet(A,x,ADD_VALUES);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,x);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm %g\n",(double)norm);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/*@C
PETSC_VIEWER_BINARY_ - Creates a binary PetscViewer shared by all processors
in a communicator.
Collective on MPI_Comm
Input Parameter:
. comm - the MPI communicator to share the binary PetscViewer
Level: intermediate
Options Database Keys:
+ -viewer_binary_filename <name>
. -viewer_binary_skip_info
- -viewer_binary_skip_options
Environmental variables:
- PETSC_VIEWER_BINARY_FILENAME
Notes:
Unlike almost all other PETSc routines, PETSC_VIEWER_BINARY_ does not return
an error code. The binary PetscViewer is usually used in the form
$ XXXView(XXX object,PETSC_VIEWER_BINARY_(comm));
.seealso: PETSC_VIEWER_BINARY_WORLD, PETSC_VIEWER_BINARY_SELF, PetscViewerBinaryOpen(), PetscViewerCreate(),
PetscViewerDestroy()
@*/
PetscViewer PETSC_VIEWER_BINARY_(MPI_Comm comm)
{
PetscErrorCode ierr;
PetscBool flg;
PetscViewer viewer;
char fname[PETSC_MAX_PATH_LEN];
MPI_Comm ncomm;
PetscFunctionBegin;
ierr = PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
if (Petsc_Viewer_Binary_keyval == MPI_KEYVAL_INVALID) {
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_Binary_keyval,0);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
}
ierr = MPI_Attr_get(ncomm,Petsc_Viewer_Binary_keyval,(void**)&viewer,(int*)&flg);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
if (!flg) { /* PetscViewer not yet created */
ierr = PetscOptionsGetenv(ncomm,"PETSC_VIEWER_BINARY_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
if (!flg) {
ierr = PetscStrcpy(fname,"binaryoutput");
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
}
ierr = PetscViewerBinaryOpen(ncomm,fname,FILE_MODE_WRITE,&viewer);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
ierr = PetscObjectRegisterDestroy((PetscObject)viewer);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
ierr = MPI_Attr_put(ncomm,Petsc_Viewer_Binary_keyval,(void*)viewer);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
}
ierr = PetscCommDestroy(&ncomm);
if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_BINARY_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(0);}
PetscFunctionReturn(viewer);
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec U,cv,eta;
DM da,da2;
PetscViewer viewer,view_vtk_cv,view_vtk_eta;
char filename[PETSC_MAX_PATH_LEN],cv_filename[PETSC_MAX_PATH_LEN],eta_filename[PETSC_MAX_PATH_LEN];
PetscBool flg,sflg = PETSC_FALSE;
PetscInt i,n=10000;
PetscInt seed;
PetscInitialize(&argc,&argv, (char*)0, help);
ierr = PetscOptionsSetValue("-viewer_binary_skip_info","true");CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f",filename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscOptionsGetInt(PETSC_NULL,"-random_seed",&seed,&sflg);CHKERRQ(ierr);
if (!sflg) {
ierr = PetscStrcpy(filename,"ex61.data");CHKERRQ(ierr);
} else {
sprintf(filename,"ex61.data.%d",seed);
}
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
/* Get physics and time parameters */
ierr = DMCreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMLoad(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr);
ierr = DMDAGetReducedDA(da,1,&da2);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&cv);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&eta);CHKERRQ(ierr);
for (i=0; i<n; i++) {
/* when this fails it simply means the file is finished */
ierr = VecLoad(U,viewer);CHKERRQ(ierr);
ierr = VecStrideGather(U,1,cv,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecStrideGather(U,4,eta,INSERT_VALUES);CHKERRQ(ierr);
sprintf(cv_filename,"%s_cv_%d.vtk",filename,i);
sprintf(eta_filename,"%s_eta_%d.vtk",filename,i);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,cv_filename,&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,eta_filename,&view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_cv, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_eta, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_cv);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_eta);CHKERRQ(ierr);
ierr = VecView(cv,view_vtk_cv);CHKERRQ(ierr);
ierr = VecView(eta,view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_eta);CHKERRQ(ierr);
}
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = VecDestroy(&cv);CHKERRQ(ierr);
ierr = VecDestroy(&eta);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&da2);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
PetscErrorCode loadVec(const char *path, Vec* v, MPI_Comm comm, PetscViewer* fd){
PetscErrorCode err;
err = PetscViewerBinaryOpen(comm, path, FILE_MODE_READ, fd); CHKERRQ(err);
err = VecCreate(comm, v); CHKERRQ(err);
err = VecSetFromOptions(*v); CHKERRQ(err);
err = VecLoad(*v, *fd); CHKERRQ(err);
err = PetscViewerDestroy(fd); CHKERRQ(err);
return err;
}
PetscErrorCode loadMat(const char *path, Mat* A, MPI_Comm comm, MatType type, PetscViewer* fd){
PetscErrorCode err;
err = PetscViewerBinaryOpen(comm, path, FILE_MODE_READ, fd); CHKERRQ(err);
err = MatCreate(comm, A); CHKERRQ(err);
err = MatSetType(*A, type); CHKERRQ(err);
err = MatSetFromOptions(*A); CHKERRQ(err);
err = MatLoad(*A, *fd); CHKERRQ(err);
err = PetscViewerDestroy(fd); CHKERRQ(err);
return err;
}
-fout <output_file> : file for saving output matrix and vector\n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscBool flg;
Vec x;
Mat A;
char file[256];
PetscViewer fd;
PetscInitialize(&argc,&args,(char *)0,help);
/* Read matrix and RHS */
ierr = PetscOptionsGetString(PETSC_NULL,"-fin",file,256,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecLoad(x,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Write matrix and vector */
ierr = PetscOptionsGetString(PETSC_NULL,"-fout",file,256,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
ierr = MatView(A,fd);CHKERRQ(ierr);
ierr = VecView(x,fd);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
example is used for testing the subroutine MatLoad_MPI_DA\n\n";
#include <petscdm.h>
#include <petscdmda.h>
int main(int argc,char **argv)
{
PetscInt X = 10,Y = 8,Z=8;
PetscErrorCode ierr;
DM da;
PetscViewer viewer;
Mat A;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,NULL,"-X",&X,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Y",&Y,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Z",&Z,NULL);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,X,Y,Z,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
ierr = MatShift(A,X);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr);
ierr = MatLoad(A,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode iniPeriodicTimer( const char pre[], PeriodicTimer *thetimer )
{
PetscErrorCode ierr;
PetscBool flg, flg1;
PetscInt it;
PetscViewer fd;
PetscInt fp;
char timeFile[PETSC_MAX_PATH_LEN];
/* read time data */
ierr = PetscOptionsGetReal(pre,"-cycle_period",&thetimer->cyclePeriod,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ1(PETSC_COMM_WORLD,1,"Must indicate matrix cycling time with the -%scycle_period option",pre);
ierr = PetscOptionsGetReal(pre,"-cycle_step",&thetimer->cycleStep,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"WARNING!: Cycling step has been specified for periodic object %s\n",pre);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," This is a legacy option retained for backward compatibility and will be removed in future releases\n");CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Use -%snum_per_period instead\n",pre);CHKERRQ(ierr);
thetimer->numPerPeriod=thetimer->cyclePeriod/thetimer->cycleStep;
/* array for holding extended time array */
PetscMalloc((thetimer->numPerPeriod+2)*sizeof(PetscScalar), &thetimer->tdp);
for (it=0; it<=thetimer->numPerPeriod+1; it++) {
thetimer->tdp[it]=(-thetimer->cycleStep/2.0) + it*thetimer->cycleStep;
}
} else {
ierr = PetscOptionsGetInt(pre,"-num_per_period",&thetimer->numPerPeriod,&flg1);CHKERRQ(ierr);
if (!flg1) SETERRQ1(PETSC_COMM_WORLD,1,"Must indicate number of fields per period with the -%snum_per_period option",pre);
/* array for holding extended time array */
PetscMalloc((thetimer->numPerPeriod+2)*sizeof(PetscScalar), &thetimer->tdp);
ierr = PetscOptionsGetString(pre,"-periodic_times_file",timeFile,PETSC_MAX_PATH_LEN-1,&flg1);CHKERRQ(ierr);
if (flg1) {
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,timeFile,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetDescriptor(fd,&fp);CHKERRQ(ierr);
ierr = PetscBinaryRead(fp,&thetimer->tdp[1],thetimer->numPerPeriod,PETSC_SCALAR);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
thetimer->tdp[0]=thetimer->tdp[thetimer->numPerPeriod]-thetimer->cyclePeriod;
thetimer->tdp[thetimer->numPerPeriod+1]=thetimer->tdp[1]+thetimer->cyclePeriod;
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Assuming equally-spaced fields for periodic object %s\n",pre);CHKERRQ(ierr);
thetimer->cycleStep=thetimer->cyclePeriod/thetimer->numPerPeriod;
for (it=0; it<=thetimer->numPerPeriod+1; it++) {
thetimer->tdp[it]=(-thetimer->cycleStep/2.0) + it*thetimer->cycleStep;
}
}
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"Periodic object %s specified at times:\n",pre);CHKERRQ(ierr);
for (it=0; it<=thetimer->numPerPeriod+1; it++) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"tdp=%10.5f\n", thetimer->tdp[it]);CHKERRQ(ierr);
}
return 0;
}
-fout <file> : output file name\n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
Mat A;
Vec b;
char fileout[PETSC_MAX_PATH_LEN];
PetscInt i,j,m = 6,n = 6,N = 36,Ii,J;
PetscErrorCode ierr;
PetscScalar val,v;
PetscViewer view;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,PETSC_DECIDE,N);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
for (i=0; i<N; i++) {
val = i + 1;
ierr = VecSetValues(b,1,&i,&val,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,NULL,"-fout",fileout,PETSC_MAX_PATH_LEN,NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,fileout,FILE_MODE_WRITE,&view);CHKERRQ(ierr);
ierr = MatView(A,view);CHKERRQ(ierr);
ierr = VecView(b,view);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Mat A;
PetscInt i,j;
PetscErrorCode ierr;
PetscMPIInt size;
PetscViewer fd;
PetscScalar values[16],one = 1.0;
Vec x;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,1,"Can only run on one processor");
/*
Open binary file. Note that we use FILE_MODE_WRITE to indicate
writing to this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"4by4",FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
ierr = MatCreateSeqBAIJ(PETSC_COMM_WORLD,4,12,12,0,0,&A);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i; for (i=0; i<4; i++) values[4*i+i] += 5;
i = 0; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 0; j = 2;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 1; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;for (i=0; i<4; i++) values[4*i+i] += 6;
i = 1; j = 1;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 2; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;for (i=0; i<4; i++) values[4*i+i] += 7;
i = 2; j = 2;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(A,fd);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,12,&x);CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
ierr = VecView(x,fd);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
