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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 0 |
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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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namespace initFile{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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} |
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|
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using namespace initFile; |
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|
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#endif // is_mpi |
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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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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|
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|
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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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|
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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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|
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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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simnfo->setBoxM( boxMat ); |
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|
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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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// MPI Section of code.......... |
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#else //IS_MPI |
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MPI::Status istatus; |
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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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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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|
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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haveError = 0; |
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if (worldRank == 0) { |
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|
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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 reading 1st line of %d \n ",c_in_name); |
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painCave.isFatal = 1; |
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haveError = 1; |
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simError(); |
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} |
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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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painCave.isFatal = 1; |
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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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|
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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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painCave.isFatal = 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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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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haveError= 1; |
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simError(); |
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} |
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if(haveError) nodeZeroError(); |
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|
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
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< |
if (which_node == mpiSim->getMyNode()) { |
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> |
if (which_node == 0) { |
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parseErr = parseDumpLine( read_buffer, i ); |
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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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> |
haveError = 1; |
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simError(); |
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} |
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} else { |
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< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
245 |
> |
if(haveError) nodeZeroError(); |
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} |
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|
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else { |
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> |
|
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myStatus = 1; |
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MPI_Send(&myStatus, 1, MPI_INT, which_node, |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
253 |
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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); |
257 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
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MPI_COMM_WORLD, &istatus); |
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|
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if(!myStatus) nodeZeroError(); |
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} |
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} |
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sprintf(read_buffer, "GAMEOVER"); |
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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(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
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TAKE_THIS_TAG); |
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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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< |
|
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|
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} else { |
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|
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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|
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done = 0; |
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while (!done) { |
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< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG, istatus); |
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if (strcmp(read_buffer, "GAMEOVER")) { |
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done = 1; |
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continue; |
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} else { |
281 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
282 |
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TAKE_THIS_TAG, istatus); |
283 |
< |
parseErr = parseDumpLine( read_buffer, which_atom ); |
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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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} |
275 |
> |
|
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> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
277 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
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> |
|
279 |
> |
if(!myStatus) anonymousNodeDie(); |
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|
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> |
if(myStatus < 0) break; |
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> |
|
283 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
284 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
285 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
286 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
287 |
> |
|
288 |
> |
myStatus = 1; |
289 |
> |
parseErr = parseDumpLine( read_buffer, which_atom ); |
290 |
> |
if( parseErr != NULL ){ |
291 |
> |
strcpy( painCave.errMsg, parseErr ); |
292 |
> |
myStatus = 0;; |
293 |
> |
simError(); |
294 |
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} |
295 |
+ |
|
296 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
297 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
298 |
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|
299 |
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} |
300 |
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} |
301 |
< |
|
301 |
> |
|
302 |
> |
// last thing last, enable fatalities. |
303 |
> |
painCave.isEventLoop = 0; |
304 |
> |
simnfo->setBoxM( boxMat ); |
305 |
> |
|
306 |
> |
|
307 |
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#endif |
308 |
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} |
309 |
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|
310 |
< |
char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
310 |
> |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
311 |
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|
312 |
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char *foo; // the pointer to the current string token |
313 |
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|
317 |
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double jx, jy, jz; // angular velocity placeholders; |
318 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
319 |
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|
320 |
< |
Atom **atoms = entry_plug->atoms; |
320 |
> |
Atom **atoms = simnfo->atoms; |
321 |
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DirectionalAtom* dAtom; |
322 |
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|
323 |
< |
int n_atoms; |
323 |
> |
int j, n_atoms, atomIndex; |
324 |
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|
325 |
|
#ifdef IS_MPI |
326 |
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n_atoms = mpiSim->getTotAtoms(); |
327 |
+ |
atomIndex=-1; |
328 |
+ |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
329 |
+ |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
330 |
+ |
} |
331 |
+ |
if (atomIndex == -1) { |
332 |
+ |
sprintf( painCave.errMsg, |
333 |
+ |
"Initialize from file error. Atom at index %d " |
334 |
+ |
"in file %s does not exist on processor %d .\n", |
335 |
+ |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
336 |
+ |
return strdup( painCave.errMsg ); |
337 |
+ |
} |
338 |
|
#else |
339 |
< |
n_atoms = entry_plug->n_atoms; |
339 |
> |
n_atoms = simnfo->n_atoms; |
340 |
> |
atomIndex = globalIndex; |
341 |
|
#endif // is_mpi |
342 |
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|
262 |
– |
|
343 |
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// set the string tokenizer |
344 |
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|
345 |
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foo = strtok(readLine, " ,;\t"); |
530 |
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|
531 |
|
return NULL; |
532 |
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} |
533 |
+ |
|
534 |
+ |
|
535 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){ |
536 |
+ |
|
537 |
+ |
char *foo; // the pointer to the current string token |
538 |
+ |
int j; |
539 |
+ |
|
540 |
+ |
// set the string tokenizer |
541 |
+ |
|
542 |
+ |
foo = strtok(readLine, " ,;\t"); |
543 |
+ |
// ignore the first token which is the time stamp. |
544 |
+ |
|
545 |
+ |
|
546 |
+ |
// get the Hx vector |
547 |
+ |
|
548 |
+ |
foo = strtok(NULL, " ,;\t"); |
549 |
+ |
if(foo == NULL){ |
550 |
+ |
sprintf( painCave.errMsg, |
551 |
+ |
"error in reading Hx[0] from %s\n", |
552 |
+ |
c_in_name ); |
553 |
+ |
return strdup( painCave.errMsg ); |
554 |
+ |
} |
555 |
+ |
boxMat[0] = atof( foo ); |
556 |
+ |
|
557 |
+ |
foo = strtok(NULL, " ,;\t"); |
558 |
+ |
if(foo == NULL){ |
559 |
+ |
sprintf( painCave.errMsg, |
560 |
+ |
"error in reading Hx[1] from %s\n", |
561 |
+ |
c_in_name ); |
562 |
+ |
return strdup( painCave.errMsg ); |
563 |
+ |
} |
564 |
+ |
boxMat[1] = atof( foo ); |
565 |
+ |
|
566 |
+ |
foo = strtok(NULL, " ,;\t"); |
567 |
+ |
if(foo == NULL){ |
568 |
+ |
sprintf( painCave.errMsg, |
569 |
+ |
"error in reading Hx[2] from %s\n", |
570 |
+ |
c_in_name ); |
571 |
+ |
return strdup( painCave.errMsg ); |
572 |
+ |
} |
573 |
+ |
boxMat[2] = atof( foo ); |
574 |
+ |
|
575 |
+ |
// get the Hy vector |
576 |
+ |
|
577 |
+ |
foo = strtok(NULL, " ,;\t"); |
578 |
+ |
if(foo == NULL){ |
579 |
+ |
sprintf( painCave.errMsg, |
580 |
+ |
"error in reading Hy[0] from %s\n", |
581 |
+ |
c_in_name ); |
582 |
+ |
return strdup( painCave.errMsg ); |
583 |
+ |
} |
584 |
+ |
boxMat[3] = atof( foo ); |
585 |
+ |
|
586 |
+ |
foo = strtok(NULL, " ,;\t"); |
587 |
+ |
if(foo == NULL){ |
588 |
+ |
sprintf( painCave.errMsg, |
589 |
+ |
"error in reading Hy[1] from %s\n", |
590 |
+ |
c_in_name ); |
591 |
+ |
return strdup( painCave.errMsg ); |
592 |
+ |
} |
593 |
+ |
boxMat[4] = atof( foo ); |
594 |
+ |
|
595 |
+ |
foo = strtok(NULL, " ,;\t"); |
596 |
+ |
if(foo == NULL){ |
597 |
+ |
sprintf( painCave.errMsg, |
598 |
+ |
"error in reading Hy[2] from %s\n", |
599 |
+ |
c_in_name ); |
600 |
+ |
return strdup( painCave.errMsg ); |
601 |
+ |
} |
602 |
+ |
boxMat[5] = atof( foo ); |
603 |
+ |
|
604 |
+ |
// get the Hz vector |
605 |
+ |
|
606 |
+ |
foo = strtok(NULL, " ,;\t"); |
607 |
+ |
if(foo == NULL){ |
608 |
+ |
sprintf( painCave.errMsg, |
609 |
+ |
"error in reading Hz[0] from %s\n", |
610 |
+ |
c_in_name ); |
611 |
+ |
return strdup( painCave.errMsg ); |
612 |
+ |
} |
613 |
+ |
boxMat[6] = atof( foo ); |
614 |
+ |
|
615 |
+ |
foo = strtok(NULL, " ,;\t"); |
616 |
+ |
if(foo == NULL){ |
617 |
+ |
sprintf( painCave.errMsg, |
618 |
+ |
"error in reading Hz[1] from %s\n", |
619 |
+ |
c_in_name ); |
620 |
+ |
return strdup( painCave.errMsg ); |
621 |
+ |
} |
622 |
+ |
boxMat[7] = atof( foo ); |
623 |
+ |
|
624 |
+ |
foo = strtok(NULL, " ,;\t"); |
625 |
+ |
if(foo == NULL){ |
626 |
+ |
sprintf( painCave.errMsg, |
627 |
+ |
"error in reading Hz[2] from %s\n", |
628 |
+ |
c_in_name ); |
629 |
+ |
return strdup( painCave.errMsg ); |
630 |
+ |
} |
631 |
+ |
boxMat[8] = atof( foo ); |
632 |
+ |
|
633 |
+ |
return NULL; |
634 |
+ |
} |
635 |
+ |
|
636 |
+ |
|
637 |
+ |
#ifdef IS_MPI |
638 |
+ |
|
639 |
+ |
// a couple of functions to let us escape the read loop |
640 |
+ |
|
641 |
+ |
void initFile::nodeZeroError( void ){ |
642 |
+ |
int j, myStatus; |
643 |
+ |
|
644 |
+ |
myStatus = 0; |
645 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
646 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, j, |
647 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
648 |
+ |
} |
649 |
+ |
|
650 |
+ |
|
651 |
+ |
MPI_Finalize(); |
652 |
+ |
exit (0); |
653 |
+ |
|
654 |
+ |
} |
655 |
+ |
|
656 |
+ |
void initFile::anonymousNodeDie( void ){ |
657 |
+ |
|
658 |
+ |
MPI_Finalize(); |
659 |
+ |
exit (0); |
660 |
+ |
} |
661 |
+ |
|
662 |
+ |
#endif //is_mpi |