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#define _FILE_OFFSET_BITS 64 |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include <iostream> |
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#include <cmath> |
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#include <vector> |
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#include <math.h> |
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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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void anonymousNodeDie( void ); |
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#endif // is_mpi |
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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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private: |
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fpos_t *myPos |
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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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vector<FilePos> frameStart; |
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} |
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using namespace dumpRead; |
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DumpReader :: DumpReader( char *in_name ){ |
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isScanned = false; |
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headFP = new FilePos; |
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#ifdef IS_MPI |
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if (worldRank == 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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double time; |
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FilePos *currFP; |
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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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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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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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if( feof( inFile ) ){ |
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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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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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nFrames = 0; |
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while( !feof( inFile ) ){ |
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headFP->add( currPos ); |
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nFrames++; |
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i = atoi(readBuffer); |
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fgets( readBuffer, sizeof( readBuffer ), in_file ); |
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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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if( feof( inFile ) ){ |
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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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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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// 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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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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lineNum++; |
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if( feof( in_file ) ){ |
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if( feof( inFile ) ){ |
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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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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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fgets( readBuffer, sizeof( readBuffer ), inFile ); |
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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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frameStart = new FilePos*[nFrames]; |
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currFP = headFP; |
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for(i=0; i<nFrames; i++){ |
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currFP = currFP->getNext(); |
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if( currFP == NULL ){ |
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sprintf( painCave.errMsg, |
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"DumpReader error: scanFile FilePos mismatch at " |
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"nFrames = %d\n", |
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i ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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frameStart[i] = currFP; |
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} |
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isScanned = true; |
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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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void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
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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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double time; |
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fpos_t *framePos; |
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#ifndef IS_MPI |
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framePos = startFrame[whichFrame].getPos(); |
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framePos = frameStart[whichFrame]->getPos(); |
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simError(); |
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} |
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MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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} else { |
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MPI_Bcast(time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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MPI_Bcast(&time, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
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done = 0; |
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char *foo; // the pointer to the current string token |
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double rx, ry, rz; // position place holders |
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double vx, vy, vz; // velocity placeholders |
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double pos[3]; // position place holders |
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double vel[3]; // velocity placeholders |
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double q[4]; // the quaternions |
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double jx, jy, jz; // angular velocity placeholders; |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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rx = atof( foo ); |
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pos[0] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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ry = atof( foo ); |
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pos[1] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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rz = atof( foo ); |
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pos[2] = atof( foo ); |
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// get the velocities |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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vx = atof( foo ); |
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vel[0] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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vy = atof( foo ); |
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vel[1] = atof( foo ); |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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inName, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
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} |
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vz = atof( foo ); |
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vel[2] = atof( foo ); |
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// get the quaternions |
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} |
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// add the positions and velocities to the atom |
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atoms[atomIndex]->setX( rx ); |
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atoms[atomIndex]->setY( ry ); |
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atoms[atomIndex]->setZ( rz ); |
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|
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atoms[atomIndex]->set_vx( vx ); |
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atoms[atomIndex]->set_vy( vy ); |
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atoms[atomIndex]->set_vz( vz ); |
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atoms[atomIndex]->setPos( pos ); |
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atoms[atomIndex]->setVel( vel ); |
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return NULL; |
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} |
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char* DumpReader::parseCommentLine(char* readLine, double time, |
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char* DumpReader::parseCommentLine(char* readLine, double &time, |
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double boxMat[9]){ |
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char *foo; // the pointer to the current string token |
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// a couple of functions to let us escape the read loop |
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void initFile::nodeZeroError( void ){ |
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void dumpRead::nodeZeroError( void ){ |
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int j, myStatus; |
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myStatus = 0; |
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} |
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void initFile::anonymousNodeDie( void ){ |
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void dumpRead::anonymousNodeDie( void ){ |
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MPI_Finalize(); |
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exit (0); |