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#define _FILE_OFFSET_BITS 64 |
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#include <iostream> |
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#include <cmath> |
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#include <math.h> |
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|
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#include <stdio.h> |
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#include <stdlib.h> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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#include "GenericData.hpp" |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif // is_mpi |
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|
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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InitializeFromFile::InitializeFromFile( char *in_name ){ |
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|
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#ifdef IS_MPI |
34 |
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if (worldRank == 0) { |
35 |
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#endif |
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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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strcpy( c_in_name, in_name); |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
48 |
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else{ |
49 |
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sprintf( c_in_name, "mpiNodeParser_%d", worldRank ); |
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} |
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|
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
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MPIcheckPoint(); |
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#endif |
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return; |
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return; |
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} |
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InitializeFromFile :: ~InitializeFromFile( ){ |
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InitializeFromFile::~InitializeFromFile( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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} |
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void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){ |
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void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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|
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int i, j, done, which_node, which_atom; // loop counter |
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int i, j; |
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|
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#ifdef IS_MPI |
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int done, which_node, which_atom; // loop counter |
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#endif //is_mpi |
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|
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const int BUFFERSIZE = 2000; // size of the read buffer |
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int n_atoms; // the number of atoms |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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#ifdef IS_MPI |
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char send_buffer[BUFFERSIZE]; |
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#endif |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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|
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char *eof_test; // ptr to see when we reach the end of the file |
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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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|
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simnfo = the_simnfo; |
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n_atoms = atoi( read_buffer ); |
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|
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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 != 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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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//read the box mat from the comment line |
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|
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|
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//read the box mat from the comment line |
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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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simError(); |
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} |
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parseErr = parseBoxLine( read_buffer, boxMat ); |
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|
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|
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parseErr = parseCommentLine( read_buffer, simnfo); |
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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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//parse dump lines |
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|
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simnfo->setBoxM( theBoxMat3 ); |
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|
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|
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for( i=0; i < n_atoms; i++){ |
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|
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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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simError(); |
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} |
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|
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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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|
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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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|
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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|
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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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"Error reading 1st line of %s \n ",c_in_name); |
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haveError = 1; |
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simError(); |
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} |
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|
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|
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n_atoms = atoi( read_buffer ); |
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|
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Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
190 |
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|
187 |
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|
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// Check to see that the number of atoms in the intial configuration file is the |
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// same as declared in simBass. |
190 |
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|
190 |
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|
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if( n_atoms != mpiSim->getTotAtoms() ){ |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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haveError= 1; |
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simError(); |
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} |
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|
200 |
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//read the boxMat from the comment line |
201 |
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|
199 |
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|
200 |
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//read the boxMat from the comment line |
201 |
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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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haveError = 1; |
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simError(); |
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} |
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|
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< |
parseErr = parseBoxLine( read_buffer, boxMat ); |
209 |
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|
210 |
> |
//Every single processor will parse the comment line by itself |
211 |
> |
//By using this way, we might lose some efficiency, but if we want to add |
212 |
> |
//more parameters into comment line, we only need to modify function |
213 |
> |
//parseCommentLine |
214 |
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|
215 |
> |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
216 |
> |
|
217 |
> |
parseErr = parseCommentLine( read_buffer, simnfo); |
218 |
> |
|
219 |
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if( parseErr != NULL ){ |
220 |
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strcpy( painCave.errMsg, parseErr ); |
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haveError = 1; |
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simError(); |
223 |
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} |
224 |
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|
220 |
– |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
221 |
– |
|
222 |
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if(haveError) nodeZeroError(); |
223 |
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|
225 |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
226 |
< |
|
226 |
> |
|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
228 |
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if(eof_test == NULL){ |
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sprintf(painCave.errMsg, |
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haveError= 1; |
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simError(); |
236 |
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} |
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|
237 |
> |
|
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if(haveError) nodeZeroError(); |
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|
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// Get the Node number which wants this atom: |
241 |
< |
which_node = AtomToProcMap[i]; |
241 |
> |
which_node = AtomToProcMap[i]; |
242 |
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if (which_node == 0) { |
243 |
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parseErr = parseDumpLine( read_buffer, i ); |
244 |
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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(); |
248 |
< |
} |
248 |
> |
} |
249 |
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if(haveError) nodeZeroError(); |
250 |
< |
} |
251 |
< |
|
250 |
> |
} |
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> |
|
252 |
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else { |
253 |
< |
|
253 |
> |
|
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myStatus = 1; |
255 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
255 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
256 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
257 |
< |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
257 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
258 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
259 |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
260 |
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MPI_COMM_WORLD); |
261 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
261 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
262 |
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MPI_COMM_WORLD, &istatus); |
263 |
< |
|
263 |
> |
|
264 |
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if(!myStatus) nodeZeroError(); |
265 |
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} |
266 |
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} |
267 |
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myStatus = -1; |
268 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
269 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
268 |
> |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
269 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
270 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
271 |
|
} |
272 |
< |
|
272 |
> |
|
273 |
|
} else { |
273 |
– |
|
274 |
– |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
274 |
|
|
275 |
+ |
MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); |
276 |
+ |
|
277 |
+ |
parseErr = parseCommentLine( read_buffer, simnfo); |
278 |
+ |
|
279 |
+ |
if( parseErr != NULL ){ |
280 |
+ |
strcpy( painCave.errMsg, parseErr ); |
281 |
+ |
haveError = 1; |
282 |
+ |
simError(); |
283 |
+ |
} |
284 |
+ |
|
285 |
+ |
|
286 |
|
done = 0; |
287 |
|
while (!done) { |
288 |
|
|
289 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
289 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
290 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
291 |
< |
|
291 |
> |
|
292 |
|
if(!myStatus) anonymousNodeDie(); |
293 |
< |
|
293 |
> |
|
294 |
|
if(myStatus < 0) break; |
295 |
|
|
296 |
< |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
296 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
297 |
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
298 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
298 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
299 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
300 |
< |
|
300 |
> |
|
301 |
|
myStatus = 1; |
302 |
|
parseErr = parseDumpLine( read_buffer, which_atom ); |
303 |
|
if( parseErr != NULL ){ |
305 |
|
myStatus = 0;; |
306 |
|
simError(); |
307 |
|
} |
308 |
< |
|
309 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
308 |
> |
|
309 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
310 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
311 |
< |
|
311 |
> |
|
312 |
|
} |
313 |
|
} |
314 |
< |
|
314 |
> |
|
315 |
|
// last thing last, enable fatalities. |
316 |
|
painCave.isEventLoop = 0; |
317 |
|
|
308 |
– |
for(i=0;i<3;i++) |
309 |
– |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
318 |
|
|
311 |
– |
simnfo->setBoxM( theBoxMat3 ); |
319 |
|
|
313 |
– |
|
320 |
|
#endif |
321 |
|
} |
322 |
|
|
323 |
|
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
324 |
|
|
325 |
< |
char *foo; // the pointer to the current string token |
326 |
< |
|
327 |
< |
double rx, ry, rz; // position place holders |
328 |
< |
double vx, vy, vz; // velocity placeholders |
325 |
> |
char *foo; // the pointer to the current string token |
326 |
> |
|
327 |
> |
double pos[3]; // position place holders |
328 |
> |
double vel[3]; // velocity placeholders |
329 |
|
double q[4]; // the quaternions |
330 |
|
double jx, jy, jz; // angular velocity placeholders; |
331 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
332 |
< |
|
332 |
> |
|
333 |
|
Atom **atoms = simnfo->atoms; |
334 |
|
DirectionalAtom* dAtom; |
329 |
– |
|
330 |
– |
int j, n_atoms, atomIndex; |
335 |
|
|
336 |
+ |
int n_atoms, atomIndex; |
337 |
+ |
|
338 |
|
#ifdef IS_MPI |
339 |
+ |
int j; |
340 |
+ |
|
341 |
|
n_atoms = mpiSim->getTotAtoms(); |
342 |
< |
atomIndex=-1; |
342 |
> |
atomIndex=-1; |
343 |
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
344 |
|
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
345 |
|
} |
349 |
|
"in file %s does not exist on processor %d .\n", |
350 |
|
globalIndex, c_in_name, mpiSim->getMyNode() ); |
351 |
|
return strdup( painCave.errMsg ); |
352 |
< |
} |
352 |
> |
} |
353 |
|
#else |
354 |
|
n_atoms = simnfo->n_atoms; |
355 |
|
atomIndex = globalIndex; |
356 |
|
#endif // is_mpi |
357 |
|
|
358 |
|
// set the string tokenizer |
359 |
< |
|
359 |
> |
|
360 |
|
foo = strtok(readLine, " ,;\t"); |
361 |
< |
|
361 |
> |
|
362 |
|
// check the atom name to the current atom |
363 |
< |
|
363 |
> |
|
364 |
|
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
365 |
|
sprintf( painCave.errMsg, |
366 |
|
"Initialize from file error. Atom %s at index %d " |
369 |
|
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
370 |
|
return strdup( painCave.errMsg ); |
371 |
|
} |
372 |
< |
|
372 |
> |
|
373 |
|
// get the positions |
374 |
|
|
375 |
|
foo = strtok(NULL, " ,;\t"); |
380 |
|
c_in_name, n_atoms, atomIndex ); |
381 |
|
return strdup( painCave.errMsg ); |
382 |
|
} |
383 |
< |
rx = atof( foo ); |
384 |
< |
|
383 |
> |
pos[0] = atof( foo ); |
384 |
> |
|
385 |
|
foo = strtok(NULL, " ,;\t"); |
386 |
|
if(foo == NULL){ |
387 |
|
sprintf( painCave.errMsg, |
390 |
|
c_in_name, n_atoms, atomIndex ); |
391 |
|
return strdup( painCave.errMsg ); |
392 |
|
} |
393 |
< |
ry = atof( foo ); |
394 |
< |
|
393 |
> |
pos[1] = atof( foo ); |
394 |
> |
|
395 |
|
foo = strtok(NULL, " ,;\t"); |
396 |
|
if(foo == NULL){ |
397 |
|
sprintf( painCave.errMsg, |
400 |
|
c_in_name, n_atoms, atomIndex ); |
401 |
|
return strdup( painCave.errMsg ); |
402 |
|
} |
403 |
< |
rz = atof( foo ); |
403 |
> |
pos[2] = atof( foo ); |
404 |
|
|
405 |
|
|
406 |
|
// get the velocities |
413 |
|
c_in_name, n_atoms, atomIndex ); |
414 |
|
return strdup( painCave.errMsg ); |
415 |
|
} |
416 |
< |
vx = atof( foo ); |
417 |
< |
|
416 |
> |
vel[0] = atof( foo ); |
417 |
> |
|
418 |
|
foo = strtok(NULL, " ,;\t"); |
419 |
|
if(foo == NULL){ |
420 |
|
sprintf( painCave.errMsg, |
423 |
|
c_in_name, n_atoms, atomIndex ); |
424 |
|
return strdup( painCave.errMsg ); |
425 |
|
} |
426 |
< |
vy = atof( foo ); |
427 |
< |
|
426 |
> |
vel[1] = atof( foo ); |
427 |
> |
|
428 |
|
foo = strtok(NULL, " ,;\t"); |
429 |
|
if(foo == NULL){ |
430 |
|
sprintf( painCave.errMsg, |
433 |
|
c_in_name, n_atoms, atomIndex ); |
434 |
|
return strdup( painCave.errMsg ); |
435 |
|
} |
436 |
< |
vz = atof( foo ); |
437 |
< |
|
438 |
< |
|
436 |
> |
vel[2] = atof( foo ); |
437 |
> |
|
438 |
> |
|
439 |
|
// get the quaternions |
440 |
< |
|
440 |
> |
|
441 |
|
if( atoms[atomIndex]->isDirectional() ){ |
442 |
< |
|
442 |
> |
|
443 |
|
foo = strtok(NULL, " ,;\t"); |
444 |
|
if(foo == NULL){ |
445 |
|
sprintf(painCave.errMsg, |
449 |
|
return strdup( painCave.errMsg ); |
450 |
|
} |
451 |
|
q[0] = atof( foo ); |
452 |
< |
|
452 |
> |
|
453 |
|
foo = strtok(NULL, " ,;\t"); |
454 |
|
if(foo == NULL){ |
455 |
|
sprintf( painCave.errMsg, |
459 |
|
return strdup( painCave.errMsg ); |
460 |
|
} |
461 |
|
q[1] = atof( foo ); |
462 |
< |
|
462 |
> |
|
463 |
|
foo = strtok(NULL, " ,;\t"); |
464 |
|
if(foo == NULL){ |
465 |
|
sprintf( painCave.errMsg, |
469 |
|
return strdup( painCave.errMsg ); |
470 |
|
} |
471 |
|
q[2] = atof( foo ); |
472 |
< |
|
472 |
> |
|
473 |
|
foo = strtok(NULL, " ,;\t"); |
474 |
|
if(foo == NULL){ |
475 |
|
sprintf( painCave.errMsg, |
479 |
|
return strdup( painCave.errMsg ); |
480 |
|
} |
481 |
|
q[3] = atof( foo ); |
482 |
< |
|
482 |
> |
|
483 |
|
// get the angular velocities |
484 |
< |
|
484 |
> |
|
485 |
|
foo = strtok(NULL, " ,;\t"); |
486 |
|
if(foo == NULL){ |
487 |
|
sprintf( painCave.errMsg, |
491 |
|
return strdup( painCave.errMsg ); |
492 |
|
} |
493 |
|
jx = atof( foo ); |
494 |
< |
|
494 |
> |
|
495 |
|
foo = strtok(NULL, " ,;\t"); |
496 |
|
if(foo == NULL){ |
497 |
|
sprintf( painCave.errMsg, |
501 |
|
return strdup( painCave.errMsg ); |
502 |
|
} |
503 |
|
jy = atof(foo ); |
504 |
< |
|
504 |
> |
|
505 |
|
foo = strtok(NULL, " ,;\t"); |
506 |
|
if(foo == NULL){ |
507 |
|
sprintf( painCave.errMsg, |
511 |
|
return strdup( painCave.errMsg ); |
512 |
|
} |
513 |
|
jz = atof( foo ); |
514 |
< |
|
514 |
> |
|
515 |
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
516 |
|
|
517 |
|
// check that the quaternion vector is normalized |
518 |
|
|
519 |
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
520 |
< |
|
520 |
> |
|
521 |
|
qLength = sqrt( qSqr ); |
522 |
|
q[0] = q[0] / qLength; |
523 |
|
q[1] = q[1] / qLength; |
524 |
|
q[2] = q[2] / qLength; |
525 |
|
q[3] = q[3] / qLength; |
526 |
< |
|
526 |
> |
|
527 |
|
dAtom->setQ( q ); |
528 |
< |
|
528 |
> |
|
529 |
|
// add the angular velocities |
530 |
|
|
531 |
|
dAtom->setJx( jx ); |
532 |
|
dAtom->setJy( jy ); |
533 |
|
dAtom->setJz( jz ); |
534 |
|
} |
535 |
< |
|
535 |
> |
|
536 |
|
// add the positions and velocities to the atom |
529 |
– |
|
530 |
– |
atoms[atomIndex]->setX( rx ); |
531 |
– |
atoms[atomIndex]->setY( ry ); |
532 |
– |
atoms[atomIndex]->setZ( rz ); |
533 |
– |
|
534 |
– |
atoms[atomIndex]->set_vx( vx ); |
535 |
– |
atoms[atomIndex]->set_vy( vy ); |
536 |
– |
atoms[atomIndex]->set_vz( vz ); |
537 |
|
|
538 |
+ |
atoms[atomIndex]->setPos( pos ); |
539 |
+ |
atoms[atomIndex]->setVel( vel ); |
540 |
+ |
|
541 |
|
return NULL; |
542 |
|
} |
543 |
|
|
544 |
|
|
545 |
< |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){ |
545 |
> |
char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ |
546 |
|
|
547 |
< |
char *foo; // the pointer to the current string token |
548 |
< |
int j; |
547 |
> |
double currTime; |
548 |
> |
double boxMat[9]; |
549 |
> |
double theBoxMat3[3][3]; |
550 |
> |
double chi; |
551 |
> |
double integralOfChidt; |
552 |
> |
double eta[9]; |
553 |
|
|
554 |
+ |
char *foo; // the pointer to the current string token |
555 |
+ |
|
556 |
|
// set the string tokenizer |
557 |
< |
|
557 |
> |
|
558 |
|
foo = strtok(readLine, " ,;\t"); |
559 |
< |
// ignore the first token which is the time stamp. |
559 |
> |
// set the timeToken. |
560 |
|
|
552 |
– |
|
553 |
– |
// get the Hx vector |
554 |
– |
|
555 |
– |
foo = strtok(NULL, " ,;\t"); |
561 |
|
if(foo == NULL){ |
562 |
|
sprintf( painCave.errMsg, |
563 |
< |
"error in reading Hx[0] from %s\n", |
563 |
> |
"error in reading Time from %s\n", |
564 |
|
c_in_name ); |
565 |
|
return strdup( painCave.errMsg ); |
566 |
|
} |
562 |
– |
boxMat[0] = atof( foo ); |
563 |
– |
|
564 |
– |
foo = strtok(NULL, " ,;\t"); |
565 |
– |
if(foo == NULL){ |
566 |
– |
sprintf( painCave.errMsg, |
567 |
– |
"error in reading Hx[1] from %s\n", |
568 |
– |
c_in_name ); |
569 |
– |
return strdup( painCave.errMsg ); |
570 |
– |
} |
571 |
– |
boxMat[1] = atof( foo ); |
572 |
– |
|
573 |
– |
foo = strtok(NULL, " ,;\t"); |
574 |
– |
if(foo == NULL){ |
575 |
– |
sprintf( painCave.errMsg, |
576 |
– |
"error in reading Hx[2] from %s\n", |
577 |
– |
c_in_name ); |
578 |
– |
return strdup( painCave.errMsg ); |
579 |
– |
} |
580 |
– |
boxMat[2] = atof( foo ); |
567 |
|
|
568 |
< |
// get the Hy vector |
568 |
> |
currTime = atof( foo ); |
569 |
> |
entry_plug->setTime( currTime ); |
570 |
|
|
571 |
< |
foo = strtok(NULL, " ,;\t"); |
572 |
< |
if(foo == NULL){ |
573 |
< |
sprintf( painCave.errMsg, |
574 |
< |
"error in reading Hy[0] from %s\n", |
575 |
< |
c_in_name ); |
576 |
< |
return strdup( painCave.errMsg ); |
571 |
> |
//get H-Matrix |
572 |
> |
|
573 |
> |
for(int i = 0 ; i < 9; i++){ |
574 |
> |
foo = strtok(NULL, " ,;\t"); |
575 |
> |
if(foo == NULL){ |
576 |
> |
sprintf( painCave.errMsg, |
577 |
> |
"error in reading H[%d] from %s\n", i, c_in_name ); |
578 |
> |
return strdup( painCave.errMsg ); |
579 |
> |
} |
580 |
> |
boxMat[i] = atof( foo ); |
581 |
|
} |
591 |
– |
boxMat[3] = atof( foo ); |
592 |
– |
|
593 |
– |
foo = strtok(NULL, " ,;\t"); |
594 |
– |
if(foo == NULL){ |
595 |
– |
sprintf( painCave.errMsg, |
596 |
– |
"error in reading Hy[1] from %s\n", |
597 |
– |
c_in_name ); |
598 |
– |
return strdup( painCave.errMsg ); |
599 |
– |
} |
600 |
– |
boxMat[4] = atof( foo ); |
601 |
– |
|
602 |
– |
foo = strtok(NULL, " ,;\t"); |
603 |
– |
if(foo == NULL){ |
604 |
– |
sprintf( painCave.errMsg, |
605 |
– |
"error in reading Hy[2] from %s\n", |
606 |
– |
c_in_name ); |
607 |
– |
return strdup( painCave.errMsg ); |
608 |
– |
} |
609 |
– |
boxMat[5] = atof( foo ); |
582 |
|
|
583 |
< |
// get the Hz vector |
583 |
> |
for(int i=0;i<3;i++) |
584 |
> |
for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
585 |
|
|
586 |
< |
foo = strtok(NULL, " ,;\t"); |
587 |
< |
if(foo == NULL){ |
588 |
< |
sprintf( painCave.errMsg, |
589 |
< |
"error in reading Hz[0] from %s\n", |
590 |
< |
c_in_name ); |
591 |
< |
return strdup( painCave.errMsg ); |
586 |
> |
//set H-Matrix |
587 |
> |
entry_plug->setBoxM( theBoxMat3 ); |
588 |
> |
|
589 |
> |
//get chi and integralOfChidt, they should appear by pair |
590 |
> |
|
591 |
> |
if( entry_plug->useInitXSstate ){ |
592 |
> |
foo = strtok(NULL, " ,;\t\n"); |
593 |
> |
if(foo != NULL){ |
594 |
> |
chi = atof(foo); |
595 |
> |
|
596 |
> |
foo = strtok(NULL, " ,;\t\n"); |
597 |
> |
if(foo == NULL){ |
598 |
> |
sprintf( painCave.errMsg, |
599 |
> |
"chi and integralOfChidt should appear by pair in %s\n", c_in_name ); |
600 |
> |
return strdup( painCave.errMsg ); |
601 |
> |
} |
602 |
> |
integralOfChidt = atof( foo ); |
603 |
> |
|
604 |
> |
//push chi and integralOfChidt into SimInfo::properties which can be |
605 |
> |
//retrieved by integrator later |
606 |
> |
DoubleData* chiValue = new DoubleData(); |
607 |
> |
chiValue->setID(CHIVALUE_ID); |
608 |
> |
chiValue->setData(chi); |
609 |
> |
entry_plug->addProperty(chiValue); |
610 |
> |
|
611 |
> |
DoubleData* integralOfChidtValue = new DoubleData(); |
612 |
> |
integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); |
613 |
> |
integralOfChidtValue->setData(integralOfChidt); |
614 |
> |
entry_plug->addProperty(integralOfChidtValue); |
615 |
> |
|
616 |
> |
} |
617 |
> |
else |
618 |
> |
return NULL; |
619 |
> |
|
620 |
> |
//get eta |
621 |
> |
for(int i = 0 ; i < 9; i++){ |
622 |
> |
foo = strtok(NULL, " ,;\t"); |
623 |
> |
if(foo == NULL){ |
624 |
> |
sprintf( painCave.errMsg, |
625 |
> |
"error in reading eta[%d] from %s\n", i, c_in_name ); |
626 |
> |
return strdup( painCave.errMsg ); |
627 |
> |
} |
628 |
> |
eta[i] = atof( foo ); |
629 |
> |
} |
630 |
> |
|
631 |
> |
//push eta into SimInfo::properties which can be |
632 |
> |
//retrieved by integrator later |
633 |
> |
//entry_plug->setBoxM( theBoxMat3 ); |
634 |
> |
DoubleArrayData* etaValue = new DoubleArrayData(); |
635 |
> |
etaValue->setID(ETAVALUE_ID); |
636 |
> |
etaValue->setData(eta, 9); |
637 |
> |
entry_plug->addProperty(etaValue); |
638 |
|
} |
620 |
– |
boxMat[6] = atof( foo ); |
621 |
– |
|
622 |
– |
foo = strtok(NULL, " ,;\t"); |
623 |
– |
if(foo == NULL){ |
624 |
– |
sprintf( painCave.errMsg, |
625 |
– |
"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 |
– |
"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 |
|
|
643 |
– |
|
643 |
|
#ifdef IS_MPI |
644 |
|
|
645 |
|
// a couple of functions to let us escape the read loop |
646 |
|
|
647 |
|
void initFile::nodeZeroError( void ){ |
648 |
|
int j, myStatus; |
649 |
< |
|
649 |
> |
|
650 |
|
myStatus = 0; |
651 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
652 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
651 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
652 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
653 |
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
654 |
< |
} |
656 |
< |
|
654 |
> |
} |
655 |
|
|
656 |
+ |
|
657 |
|
MPI_Finalize(); |
658 |
|
exit (0); |
659 |
< |
|
659 |
> |
|
660 |
|
} |
661 |
|
|
662 |
|
void initFile::anonymousNodeDie( void ){ |