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#define _FILE_OFFSET_BITS 64 |
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gezelter |
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#include <iostream> |
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#include <cmath> |
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mmeineke |
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#include <vector> |
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gezelter |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <unistd.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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#ifdef IS_MPI |
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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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mmeineke |
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#endif // is_mpi |
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namespace dumpRead{ |
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#ifdef IS_MPI |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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#endif // is_mpi |
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mmeineke |
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class FilePos{ |
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public: |
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FilePos(){ myPos = NULL; } |
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FilePos( fpos_t* thePos ) { myPos = thePos; } |
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~FilePos(){ if( myPos != NULL ) delete myPos; } |
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FilePos &operator=(fpos_t *thePos){ myPos = thePos; return *this; } |
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void setPos( fpos_t *thePos ){ myPos = thePos; } |
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fpos_t *getPos( void ){ return myPos; } |
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mmeineke |
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private: |
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mmeineke |
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fpos_t *myPos |
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mmeineke |
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}; |
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bool operator<(FilePos a, FilePos b){ |
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return (a.getPos())->__pos < (b.getPos())->__pos; } |
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bool operator==(FilePos a, FilePos b){ |
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return (a.getPos())->__pos == (b.getPos())->__pos; } |
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mmeineke |
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vector<FilePos> frameStart; |
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gezelter |
637 |
} |
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using namespace dumpRead; |
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DumpReader :: DumpReader( char *in_name ){ |
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mmeineke |
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isScanned = false; |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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mmeineke |
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inFile = fopen(in_name, "r"); |
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if(inFile == NULL){ |
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sprintf(painCave.errMsg, |
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"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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mmeineke |
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strcpy( inName, in_name); |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
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MPIcheckPoint(); |
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#endif |
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return; |
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} |
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DumpReader :: ~DumpReader( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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int error; |
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mmeineke |
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error = fclose( inFile ); |
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if( error ){ |
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sprintf( painCave.errMsg, |
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mmeineke |
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"Error closing %s\n", inName ); |
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simError(); |
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} |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Dump file closed successfully." ); |
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MPIcheckPoint(); |
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#endif |
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return; |
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} |
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mmeineke |
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int DumpReader::getNframes( void ){ |
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mmeineke |
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if( !isScanned ) scanFile(); |
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return nFrames; |
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} |
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mmeineke |
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mmeineke |
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void DumpReader::scanFile( void ){ |
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int vectorSize; |
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int i, j, k; |
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int lineNum = 0; |
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char readBuffer[2000]; |
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char* foo; |
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fpos_t *currPos; |
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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rewind( inFile ); |
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currPos = new fpos_t; |
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fgetpos( inFile, currPos ); |
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fgets( readBuffer, sizeof( readBuffer ), in_file ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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inName, |
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lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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while( !feof( in_file ) ){ |
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frameStart.push_back( FilePos( currPos ) ); |
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i = atoi(readBuffer); |
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fgets( readBuffer, sizeof( readBuffer ), in_file ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d\n", |
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inName, |
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lineNum ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if(outTime){ |
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foo = strtok( readBuffer, " ,;\t" ); |
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time = atof( foo ); |
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} |
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for(j=0; j<i; j++){ |
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fgets( readBuffer, sizeof( readBuffer ), in_file ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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sprintf( painCave.errMsg, |
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"File \"%s\" ended unexpectedly at line %d," |
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" with atom %d\n", |
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inName, |
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lineNum, |
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j ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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currPos = new fpos_t; |
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fgetpos( inFile, currPos ); |
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fgets( readBuffer, sizeof( readBuffer ), in_file ); |
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lineNum++; |
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} |
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delete currPos; |
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vectorSize = frameStart.size(); |
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rewind( inFile ); |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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nFrames = vectorSize; |
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isScanned = true; |
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} |
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gezelter |
637 |
void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){ |
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int i, j, done, which_node, which_atom; // loop counter |
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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 *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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simnfo = the_simnfo; |
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#ifndef IS_MPI |
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mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
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gezelter |
637 |
if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"DumpReader error: error reading 1st line of \"%s\"\n", |
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mmeineke |
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inName ); |
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gezelter |
637 |
painCave.isFatal = 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 = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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if( n_atoms != simnfo->n_atoms ){ |
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sprintf( painCave.errMsg, |
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"DumpReader error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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mmeineke |
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inName, n_atoms, simnfo->n_atoms ); |
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gezelter |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//read the box mat from the comment line |
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mmeineke |
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eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
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gezelter |
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if(eof_test == NULL){ |
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sprintf( painCave.errMsg, |
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mmeineke |
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"error in reading commment in %s\n", inName); |
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gezelter |
637 |
painCave.isFatal = 1; |
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simError(); |
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} |
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parseErr = parseCommentLine( read_buffer, time, boxMat ); |
254 |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
256 |
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painCave.isFatal = 1; |
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simError(); |
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} |
259 |
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260 |
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simnfo->setTime( time ); |
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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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simnfo->setBoxM( theBoxMat3 ); |
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268 |
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for( i=0; i < n_atoms; i++){ |
270 |
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271 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
272 |
gezelter |
637 |
if(eof_test == NULL){ |
273 |
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sprintf(painCave.errMsg, |
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"error in reading file %s\n" |
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
277 |
mmeineke |
647 |
inName, n_atoms, i ); |
278 |
gezelter |
637 |
painCave.isFatal = 1; |
279 |
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simError(); |
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} |
281 |
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282 |
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283 |
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parseErr = parseDumpLine( read_buffer, i ); |
284 |
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if( parseErr != NULL ){ |
285 |
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strcpy( painCave.errMsg, parseErr ); |
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painCave.isFatal = 1; |
287 |
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simError(); |
288 |
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} |
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} |
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291 |
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292 |
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// MPI Section of code.......... |
293 |
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#else //IS_MPI |
294 |
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295 |
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// first thing first, suspend fatalities. |
296 |
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painCave.isEventLoop = 1; |
297 |
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298 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
299 |
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int haveError; |
300 |
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301 |
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MPI_Status istatus; |
302 |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
303 |
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304 |
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305 |
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haveError = 0; |
306 |
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if (worldRank == 0) { |
307 |
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308 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
309 |
gezelter |
637 |
if( eof_test == NULL ){ |
310 |
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sprintf( painCave.errMsg, |
311 |
mmeineke |
647 |
"Error reading 1st line of %d \n ",inName); |
312 |
gezelter |
637 |
haveError = 1; |
313 |
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simError(); |
314 |
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} |
315 |
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316 |
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n_atoms = atoi( read_buffer ); |
317 |
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318 |
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Atom **atoms = simnfo->atoms; |
319 |
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DirectionalAtom* dAtom; |
320 |
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321 |
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// Check to see that the number of atoms in the intial configuration file is the |
322 |
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// same as declared in simBass. |
323 |
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324 |
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if( n_atoms != mpiSim->getTotAtoms() ){ |
325 |
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sprintf( painCave.errMsg, |
326 |
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"Initialize from File error. %s n_atoms, %d, " |
327 |
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"does not match the BASS file's n_atoms, %d.\n", |
328 |
mmeineke |
647 |
inName, n_atoms, simnfo->n_atoms ); |
329 |
gezelter |
637 |
haveError= 1; |
330 |
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simError(); |
331 |
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} |
332 |
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333 |
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//read the time and boxMat from the comment line |
334 |
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335 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
336 |
gezelter |
637 |
if(eof_test == NULL){ |
337 |
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sprintf( painCave.errMsg, |
338 |
mmeineke |
647 |
"error in reading commment in %s\n", inName); |
339 |
gezelter |
637 |
haveError = 1; |
340 |
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simError(); |
341 |
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} |
342 |
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343 |
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parseErr = parseCommentLine( read_buffer, time, boxMat ); |
344 |
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if( parseErr != NULL ){ |
345 |
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strcpy( painCave.errMsg, parseErr ); |
346 |
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haveError = 1; |
347 |
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simError(); |
348 |
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} |
349 |
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350 |
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MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
351 |
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352 |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
353 |
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354 |
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if(haveError) nodeZeroError(); |
355 |
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356 |
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
357 |
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358 |
mmeineke |
647 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
359 |
gezelter |
637 |
if(eof_test == NULL){ |
360 |
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sprintf(painCave.errMsg, |
361 |
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"error in reading file %s\n" |
362 |
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"natoms = %d; index = %d\n" |
363 |
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"error reading the line from the file.\n", |
364 |
mmeineke |
647 |
inName, n_atoms, i ); |
365 |
gezelter |
637 |
haveError= 1; |
366 |
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simError(); |
367 |
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} |
368 |
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369 |
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if(haveError) nodeZeroError(); |
370 |
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371 |
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// Get the Node number which wants this atom: |
372 |
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which_node = AtomToProcMap[i]; |
373 |
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if (which_node == 0) { |
374 |
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parseErr = parseDumpLine( read_buffer, i ); |
375 |
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if( parseErr != NULL ){ |
376 |
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strcpy( painCave.errMsg, parseErr ); |
377 |
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haveError = 1; |
378 |
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simError(); |
379 |
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} |
380 |
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if(haveError) nodeZeroError(); |
381 |
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} |
382 |
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383 |
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else { |
384 |
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385 |
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myStatus = 1; |
386 |
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MPI_Send(&myStatus, 1, MPI_INT, which_node, |
387 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
388 |
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MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
389 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
390 |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
391 |
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MPI_COMM_WORLD); |
392 |
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MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
393 |
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MPI_COMM_WORLD, &istatus); |
394 |
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395 |
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if(!myStatus) nodeZeroError(); |
396 |
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} |
397 |
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} |
398 |
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myStatus = -1; |
399 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
400 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
401 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
402 |
|
|
} |
403 |
|
|
|
404 |
|
|
} else { |
405 |
|
|
|
406 |
|
|
MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
407 |
|
|
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
408 |
|
|
|
409 |
|
|
done = 0; |
410 |
|
|
while (!done) { |
411 |
|
|
|
412 |
|
|
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
413 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
414 |
|
|
|
415 |
|
|
if(!myStatus) anonymousNodeDie(); |
416 |
|
|
|
417 |
|
|
if(myStatus < 0) break; |
418 |
|
|
|
419 |
|
|
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
420 |
|
|
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
421 |
|
|
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
422 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
423 |
|
|
|
424 |
|
|
myStatus = 1; |
425 |
|
|
parseErr = parseDumpLine( read_buffer, which_atom ); |
426 |
|
|
if( parseErr != NULL ){ |
427 |
|
|
strcpy( painCave.errMsg, parseErr ); |
428 |
|
|
myStatus = 0;; |
429 |
|
|
simError(); |
430 |
|
|
} |
431 |
|
|
|
432 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, 0, |
433 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
434 |
|
|
|
435 |
|
|
} |
436 |
|
|
} |
437 |
|
|
|
438 |
|
|
// last thing last, enable fatalities. |
439 |
|
|
painCave.isEventLoop = 0; |
440 |
|
|
|
441 |
|
|
simnfo->setTime( time ); |
442 |
|
|
|
443 |
|
|
for(i=0;i<3;i++) |
444 |
|
|
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
445 |
|
|
|
446 |
|
|
simnfo->setBoxM( theBoxMat3 ); |
447 |
|
|
|
448 |
|
|
|
449 |
|
|
#endif |
450 |
|
|
} |
451 |
|
|
|
452 |
|
|
char* DumpReader::parseDumpLine(char* readLine, int globalIndex){ |
453 |
|
|
|
454 |
|
|
char *foo; // the pointer to the current string token |
455 |
|
|
|
456 |
|
|
double rx, ry, rz; // position place holders |
457 |
|
|
double vx, vy, vz; // velocity placeholders |
458 |
|
|
double q[4]; // the quaternions |
459 |
|
|
double jx, jy, jz; // angular velocity placeholders; |
460 |
|
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
461 |
|
|
|
462 |
|
|
Atom **atoms = simnfo->atoms; |
463 |
|
|
DirectionalAtom* dAtom; |
464 |
|
|
|
465 |
|
|
int j, n_atoms, atomIndex; |
466 |
|
|
|
467 |
|
|
#ifdef IS_MPI |
468 |
|
|
n_atoms = mpiSim->getTotAtoms(); |
469 |
|
|
atomIndex=-1; |
470 |
|
|
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
471 |
|
|
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
472 |
|
|
} |
473 |
|
|
if (atomIndex == -1) { |
474 |
|
|
sprintf( painCave.errMsg, |
475 |
|
|
"Initialize from file error. Atom at index %d " |
476 |
|
|
"in file %s does not exist on processor %d .\n", |
477 |
mmeineke |
647 |
globalIndex, inName, mpiSim->getMyNode() ); |
478 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
479 |
|
|
} |
480 |
|
|
#else |
481 |
|
|
n_atoms = simnfo->n_atoms; |
482 |
|
|
atomIndex = globalIndex; |
483 |
|
|
#endif // is_mpi |
484 |
|
|
|
485 |
|
|
// set the string tokenizer |
486 |
|
|
|
487 |
|
|
foo = strtok(readLine, " ,;\t"); |
488 |
|
|
|
489 |
|
|
// check the atom name to the current atom |
490 |
|
|
|
491 |
|
|
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
492 |
|
|
sprintf( painCave.errMsg, |
493 |
|
|
"Initialize from file error. Atom %s at index %d " |
494 |
|
|
"in file %s does not" |
495 |
|
|
" match the BASS atom %s.\n", |
496 |
mmeineke |
647 |
foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
497 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
498 |
|
|
} |
499 |
|
|
|
500 |
|
|
// get the positions |
501 |
|
|
|
502 |
|
|
foo = strtok(NULL, " ,;\t"); |
503 |
|
|
if(foo == NULL){ |
504 |
|
|
sprintf( painCave.errMsg, |
505 |
|
|
"error in reading postition x from %s\n" |
506 |
|
|
"natoms = %d, index = %d\n", |
507 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
508 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
509 |
|
|
} |
510 |
|
|
rx = atof( foo ); |
511 |
|
|
|
512 |
|
|
foo = strtok(NULL, " ,;\t"); |
513 |
|
|
if(foo == NULL){ |
514 |
|
|
sprintf( painCave.errMsg, |
515 |
|
|
"error in reading postition y from %s\n" |
516 |
|
|
"natoms = %d, index = %d\n", |
517 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
518 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
519 |
|
|
} |
520 |
|
|
ry = atof( foo ); |
521 |
|
|
|
522 |
|
|
foo = strtok(NULL, " ,;\t"); |
523 |
|
|
if(foo == NULL){ |
524 |
|
|
sprintf( painCave.errMsg, |
525 |
|
|
"error in reading postition z from %s\n" |
526 |
|
|
"natoms = %d, index = %d\n", |
527 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
528 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
529 |
|
|
} |
530 |
|
|
rz = atof( foo ); |
531 |
|
|
|
532 |
|
|
|
533 |
|
|
// get the velocities |
534 |
|
|
|
535 |
|
|
foo = strtok(NULL, " ,;\t"); |
536 |
|
|
if(foo == NULL){ |
537 |
|
|
sprintf( painCave.errMsg, |
538 |
|
|
"error in reading velocity x from %s\n" |
539 |
|
|
"natoms = %d, index = %d\n", |
540 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
541 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
542 |
|
|
} |
543 |
|
|
vx = atof( foo ); |
544 |
|
|
|
545 |
|
|
foo = strtok(NULL, " ,;\t"); |
546 |
|
|
if(foo == NULL){ |
547 |
|
|
sprintf( painCave.errMsg, |
548 |
|
|
"error in reading velocity y from %s\n" |
549 |
|
|
"natoms = %d, index = %d\n", |
550 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
551 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
552 |
|
|
} |
553 |
|
|
vy = atof( foo ); |
554 |
|
|
|
555 |
|
|
foo = strtok(NULL, " ,;\t"); |
556 |
|
|
if(foo == NULL){ |
557 |
|
|
sprintf( painCave.errMsg, |
558 |
|
|
"error in reading velocity z from %s\n" |
559 |
|
|
"natoms = %d, index = %d\n", |
560 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
561 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
562 |
|
|
} |
563 |
|
|
vz = atof( foo ); |
564 |
|
|
|
565 |
|
|
|
566 |
|
|
// get the quaternions |
567 |
|
|
|
568 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
569 |
|
|
|
570 |
|
|
foo = strtok(NULL, " ,;\t"); |
571 |
|
|
if(foo == NULL){ |
572 |
|
|
sprintf(painCave.errMsg, |
573 |
|
|
"error in reading quaternion 0 from %s\n" |
574 |
|
|
"natoms = %d, index = %d\n", |
575 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
576 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
577 |
|
|
} |
578 |
|
|
q[0] = atof( foo ); |
579 |
|
|
|
580 |
|
|
foo = strtok(NULL, " ,;\t"); |
581 |
|
|
if(foo == NULL){ |
582 |
|
|
sprintf( painCave.errMsg, |
583 |
|
|
"error in reading quaternion 1 from %s\n" |
584 |
|
|
"natoms = %d, index = %d\n", |
585 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
586 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
587 |
|
|
} |
588 |
|
|
q[1] = atof( foo ); |
589 |
|
|
|
590 |
|
|
foo = strtok(NULL, " ,;\t"); |
591 |
|
|
if(foo == NULL){ |
592 |
|
|
sprintf( painCave.errMsg, |
593 |
|
|
"error in reading quaternion 2 from %s\n" |
594 |
|
|
"natoms = %d, index = %d\n", |
595 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
596 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
597 |
|
|
} |
598 |
|
|
q[2] = atof( foo ); |
599 |
|
|
|
600 |
|
|
foo = strtok(NULL, " ,;\t"); |
601 |
|
|
if(foo == NULL){ |
602 |
|
|
sprintf( painCave.errMsg, |
603 |
|
|
"error in reading quaternion 3 from %s\n" |
604 |
|
|
"natoms = %d, index = %d\n", |
605 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
606 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
607 |
|
|
} |
608 |
|
|
q[3] = atof( foo ); |
609 |
|
|
|
610 |
|
|
// get the angular velocities |
611 |
|
|
|
612 |
|
|
foo = strtok(NULL, " ,;\t"); |
613 |
|
|
if(foo == NULL){ |
614 |
|
|
sprintf( painCave.errMsg, |
615 |
|
|
"error in reading angular momentum jx from %s\n" |
616 |
|
|
"natoms = %d, index = %d\n", |
617 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
618 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
619 |
|
|
} |
620 |
|
|
jx = atof( foo ); |
621 |
|
|
|
622 |
|
|
foo = strtok(NULL, " ,;\t"); |
623 |
|
|
if(foo == NULL){ |
624 |
|
|
sprintf( painCave.errMsg, |
625 |
|
|
"error in reading angular momentum jy from %s\n" |
626 |
|
|
"natoms = %d, index = %d\n", |
627 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
628 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
629 |
|
|
} |
630 |
|
|
jy = atof(foo ); |
631 |
|
|
|
632 |
|
|
foo = strtok(NULL, " ,;\t"); |
633 |
|
|
if(foo == NULL){ |
634 |
|
|
sprintf( painCave.errMsg, |
635 |
|
|
"error in reading angular momentum jz from %s\n" |
636 |
|
|
"natoms = %d, index = %d\n", |
637 |
mmeineke |
647 |
inName, n_atoms, atomIndex ); |
638 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
639 |
|
|
} |
640 |
|
|
jz = atof( foo ); |
641 |
|
|
|
642 |
|
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
643 |
|
|
|
644 |
|
|
// check that the quaternion vector is normalized |
645 |
|
|
|
646 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
647 |
|
|
|
648 |
|
|
qLength = sqrt( qSqr ); |
649 |
|
|
q[0] = q[0] / qLength; |
650 |
|
|
q[1] = q[1] / qLength; |
651 |
|
|
q[2] = q[2] / qLength; |
652 |
|
|
q[3] = q[3] / qLength; |
653 |
|
|
|
654 |
|
|
dAtom->setQ( q ); |
655 |
|
|
|
656 |
|
|
// add the angular velocities |
657 |
|
|
|
658 |
|
|
dAtom->setJx( jx ); |
659 |
|
|
dAtom->setJy( jy ); |
660 |
|
|
dAtom->setJz( jz ); |
661 |
|
|
} |
662 |
|
|
|
663 |
|
|
// add the positions and velocities to the atom |
664 |
|
|
|
665 |
|
|
atoms[atomIndex]->setX( rx ); |
666 |
|
|
atoms[atomIndex]->setY( ry ); |
667 |
|
|
atoms[atomIndex]->setZ( rz ); |
668 |
|
|
|
669 |
|
|
atoms[atomIndex]->set_vx( vx ); |
670 |
|
|
atoms[atomIndex]->set_vy( vy ); |
671 |
|
|
atoms[atomIndex]->set_vz( vz ); |
672 |
|
|
|
673 |
|
|
return NULL; |
674 |
|
|
} |
675 |
|
|
|
676 |
|
|
|
677 |
|
|
char* DumpReader::parseCommentLine(char* readLine, double time, |
678 |
|
|
double boxMat[9]){ |
679 |
|
|
|
680 |
|
|
char *foo; // the pointer to the current string token |
681 |
|
|
int j; |
682 |
|
|
|
683 |
|
|
// set the string tokenizer |
684 |
|
|
|
685 |
|
|
foo = strtok(readLine, " ,;\t"); |
686 |
|
|
if(foo == NULL){ |
687 |
|
|
sprintf( painCave.errMsg, |
688 |
|
|
"error in reading time from %s\n", |
689 |
mmeineke |
647 |
inName ); |
690 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
691 |
|
|
} |
692 |
|
|
time = atof( foo ); |
693 |
|
|
|
694 |
|
|
// get the Hx vector |
695 |
|
|
|
696 |
|
|
foo = strtok(NULL, " ,;\t"); |
697 |
|
|
if(foo == NULL){ |
698 |
|
|
sprintf( painCave.errMsg, |
699 |
|
|
"error in reading Hx[0] from %s\n", |
700 |
mmeineke |
647 |
inName ); |
701 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
702 |
|
|
} |
703 |
|
|
boxMat[0] = atof( foo ); |
704 |
|
|
|
705 |
|
|
foo = strtok(NULL, " ,;\t"); |
706 |
|
|
if(foo == NULL){ |
707 |
|
|
sprintf( painCave.errMsg, |
708 |
|
|
"error in reading Hx[1] from %s\n", |
709 |
mmeineke |
647 |
inName ); |
710 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
711 |
|
|
} |
712 |
|
|
boxMat[1] = atof( foo ); |
713 |
|
|
|
714 |
|
|
foo = strtok(NULL, " ,;\t"); |
715 |
|
|
if(foo == NULL){ |
716 |
|
|
sprintf( painCave.errMsg, |
717 |
|
|
"error in reading Hx[2] from %s\n", |
718 |
mmeineke |
647 |
inName ); |
719 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
720 |
|
|
} |
721 |
|
|
boxMat[2] = atof( foo ); |
722 |
|
|
|
723 |
|
|
// get the Hy vector |
724 |
|
|
|
725 |
|
|
foo = strtok(NULL, " ,;\t"); |
726 |
|
|
if(foo == NULL){ |
727 |
|
|
sprintf( painCave.errMsg, |
728 |
|
|
"error in reading Hy[0] from %s\n", |
729 |
mmeineke |
647 |
inName ); |
730 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
731 |
|
|
} |
732 |
|
|
boxMat[3] = atof( foo ); |
733 |
|
|
|
734 |
|
|
foo = strtok(NULL, " ,;\t"); |
735 |
|
|
if(foo == NULL){ |
736 |
|
|
sprintf( painCave.errMsg, |
737 |
|
|
"error in reading Hy[1] from %s\n", |
738 |
mmeineke |
647 |
inName ); |
739 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
740 |
|
|
} |
741 |
|
|
boxMat[4] = atof( foo ); |
742 |
|
|
|
743 |
|
|
foo = strtok(NULL, " ,;\t"); |
744 |
|
|
if(foo == NULL){ |
745 |
|
|
sprintf( painCave.errMsg, |
746 |
|
|
"error in reading Hy[2] from %s\n", |
747 |
mmeineke |
647 |
inName ); |
748 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
749 |
|
|
} |
750 |
|
|
boxMat[5] = atof( foo ); |
751 |
|
|
|
752 |
|
|
// get the Hz vector |
753 |
|
|
|
754 |
|
|
foo = strtok(NULL, " ,;\t"); |
755 |
|
|
if(foo == NULL){ |
756 |
|
|
sprintf( painCave.errMsg, |
757 |
|
|
"error in reading Hz[0] from %s\n", |
758 |
mmeineke |
647 |
inName ); |
759 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
760 |
|
|
} |
761 |
|
|
boxMat[6] = atof( foo ); |
762 |
|
|
|
763 |
|
|
foo = strtok(NULL, " ,;\t"); |
764 |
|
|
if(foo == NULL){ |
765 |
|
|
sprintf( painCave.errMsg, |
766 |
|
|
"error in reading Hz[1] from %s\n", |
767 |
mmeineke |
647 |
inName ); |
768 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
769 |
|
|
} |
770 |
|
|
boxMat[7] = atof( foo ); |
771 |
|
|
|
772 |
|
|
foo = strtok(NULL, " ,;\t"); |
773 |
|
|
if(foo == NULL){ |
774 |
|
|
sprintf( painCave.errMsg, |
775 |
|
|
"error in reading Hz[2] from %s\n", |
776 |
mmeineke |
647 |
inName ); |
777 |
gezelter |
637 |
return strdup( painCave.errMsg ); |
778 |
|
|
} |
779 |
|
|
boxMat[8] = atof( foo ); |
780 |
|
|
|
781 |
|
|
return NULL; |
782 |
|
|
} |
783 |
|
|
|
784 |
|
|
|
785 |
|
|
#ifdef IS_MPI |
786 |
|
|
|
787 |
|
|
// a couple of functions to let us escape the read loop |
788 |
|
|
|
789 |
|
|
void initFile::nodeZeroError( void ){ |
790 |
|
|
int j, myStatus; |
791 |
|
|
|
792 |
|
|
myStatus = 0; |
793 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
794 |
|
|
MPI_Send( &myStatus, 1, MPI_INT, j, |
795 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
796 |
|
|
} |
797 |
|
|
|
798 |
|
|
|
799 |
|
|
MPI_Finalize(); |
800 |
|
|
exit (0); |
801 |
|
|
|
802 |
|
|
} |
803 |
|
|
|
804 |
|
|
void initFile::anonymousNodeDie( void ){ |
805 |
|
|
|
806 |
|
|
MPI_Finalize(); |
807 |
|
|
exit (0); |
808 |
|
|
} |
809 |
|
|
|
810 |
|
|
#endif //is_mpi |