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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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} |
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){ |
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int i, j, done, which_node, which_atom; // loop counter |
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char *eof_test; // ptr to see when we reach the end of the file |
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char *parseErr; |
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int procIndex; |
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double boxMat[9]; |
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double theBoxMat3[3][3]; |
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entry_plug = the_entry_plug; |
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simnfo = the_simnfo; |
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#ifndef IS_MPI |
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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
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Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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if( n_atoms != entry_plug->n_atoms ){ |
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if( n_atoms != simnfo->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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c_in_name, n_atoms, simnfo->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//read and toss the comment line |
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//read the box mat from the comment line |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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simError(); |
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} |
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parseErr = parseBoxLine( read_buffer, boxMat ); |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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|
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for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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MPI::Status istatus; |
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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n_atoms = atoi( read_buffer ); |
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Atom **atoms = entry_plug->atoms; |
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Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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// Check to see that the number of atoms in the intial configuration file is the |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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c_in_name, n_atoms, simnfo->n_atoms ); |
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haveError= 1; |
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simError(); |
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} |
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//read and toss the comment line |
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//read the boxMat from the comment line |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
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haveError= 1; |
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haveError = 1; |
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simError(); |
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} |
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|
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parseErr = parseBoxLine( read_buffer, boxMat ); |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
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haveError = 1; |
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simError(); |
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} |
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|
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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if(haveError) nodeZeroError(); |
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else { |
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myStatus = 1; |
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MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
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TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
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MPI_Send(&myStatus, 1, MPI_INT, which_node, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
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MPI_COMM_WORLD); |
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MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
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MPI_COMM_WORLD, &istatus); |
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if(!myStatus) nodeZeroError(); |
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} |
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} |
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myStatus = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
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TAKE_THIS_TAG_INT); |
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MPI_Send( &myStatus, 1, MPI_INT, j, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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} |
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} else { |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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done = 0; |
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while (!done) { |
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MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, istatus); |
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MPI_Recv(&myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
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if(!myStatus) anonymousNodeDie(); |
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if(myStatus < 0) break; |
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MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG_CHAR, istatus); |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, istatus); |
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MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
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MPI_Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
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myStatus = 1; |
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parseErr = parseDumpLine( read_buffer, which_atom ); |
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simError(); |
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} |
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MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT); |
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MPI_Send( &myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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} |
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} |
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// last thing last, enable fatalities. |
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painCave.isEventLoop = 0; |
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|
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for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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|
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#endif |
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} |
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double jx, jy, jz; // angular velocity placeholders; |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
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Atom **atoms = entry_plug->atoms; |
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> |
Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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int j, n_atoms, atomIndex; |
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return strdup( painCave.errMsg ); |
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} |
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#else |
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n_atoms = entry_plug->n_atoms; |
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n_atoms = simnfo->n_atoms; |
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atomIndex = globalIndex; |
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#endif // is_mpi |
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} |
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char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){ |
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|
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char *foo; // the pointer to the current string token |
545 |
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int j; |
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|
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// set the string tokenizer |
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|
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foo = strtok(readLine, " ,;\t"); |
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// ignore the first token which is the time stamp. |
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|
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|
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// get the Hx vector |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading Hx[0] from %s\n", |
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c_in_name ); |
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return strdup( painCave.errMsg ); |
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} |
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boxMat[0] = atof( foo ); |
563 |
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|
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading Hx[1] from %s\n", |
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c_in_name ); |
569 |
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return strdup( painCave.errMsg ); |
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} |
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boxMat[1] = atof( foo ); |
572 |
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|
573 |
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foo = strtok(NULL, " ,;\t"); |
574 |
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if(foo == NULL){ |
575 |
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sprintf( painCave.errMsg, |
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"error in reading Hx[2] from %s\n", |
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c_in_name ); |
578 |
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return strdup( painCave.errMsg ); |
579 |
+ |
} |
580 |
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boxMat[2] = atof( foo ); |
581 |
+ |
|
582 |
+ |
// get the Hy vector |
583 |
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|
584 |
+ |
foo = strtok(NULL, " ,;\t"); |
585 |
+ |
if(foo == NULL){ |
586 |
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sprintf( painCave.errMsg, |
587 |
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"error in reading Hy[0] from %s\n", |
588 |
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c_in_name ); |
589 |
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return strdup( painCave.errMsg ); |
590 |
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} |
591 |
+ |
boxMat[3] = atof( foo ); |
592 |
+ |
|
593 |
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foo = strtok(NULL, " ,;\t"); |
594 |
+ |
if(foo == NULL){ |
595 |
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sprintf( painCave.errMsg, |
596 |
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"error in reading Hy[1] from %s\n", |
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c_in_name ); |
598 |
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return strdup( painCave.errMsg ); |
599 |
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} |
600 |
+ |
boxMat[4] = atof( foo ); |
601 |
+ |
|
602 |
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foo = strtok(NULL, " ,;\t"); |
603 |
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if(foo == NULL){ |
604 |
+ |
sprintf( painCave.errMsg, |
605 |
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"error in reading Hy[2] from %s\n", |
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c_in_name ); |
607 |
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return strdup( painCave.errMsg ); |
608 |
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} |
609 |
+ |
boxMat[5] = atof( foo ); |
610 |
+ |
|
611 |
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// get the Hz vector |
612 |
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|
613 |
+ |
foo = strtok(NULL, " ,;\t"); |
614 |
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if(foo == NULL){ |
615 |
+ |
sprintf( painCave.errMsg, |
616 |
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"error in reading Hz[0] from %s\n", |
617 |
+ |
c_in_name ); |
618 |
+ |
return strdup( painCave.errMsg ); |
619 |
+ |
} |
620 |
+ |
boxMat[6] = atof( foo ); |
621 |
+ |
|
622 |
+ |
foo = strtok(NULL, " ,;\t"); |
623 |
+ |
if(foo == NULL){ |
624 |
+ |
sprintf( painCave.errMsg, |
625 |
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"error in reading Hz[1] from %s\n", |
626 |
+ |
c_in_name ); |
627 |
+ |
return strdup( painCave.errMsg ); |
628 |
+ |
} |
629 |
+ |
boxMat[7] = atof( foo ); |
630 |
+ |
|
631 |
+ |
foo = strtok(NULL, " ,;\t"); |
632 |
+ |
if(foo == NULL){ |
633 |
+ |
sprintf( painCave.errMsg, |
634 |
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"error in reading Hz[2] from %s\n", |
635 |
+ |
c_in_name ); |
636 |
+ |
return strdup( painCave.errMsg ); |
637 |
+ |
} |
638 |
+ |
boxMat[8] = atof( foo ); |
639 |
+ |
|
640 |
+ |
return NULL; |
641 |
+ |
} |
642 |
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|
643 |
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|
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#ifdef IS_MPI |
645 |
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|
646 |
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// a couple of functions to let us escape the read loop |
650 |
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651 |
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myStatus = 0; |
652 |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
653 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
654 |
< |
TAKE_THIS_TAG_INT); |
653 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
654 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
655 |
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} |
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