--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp 2003/03/28 21:45:03 436 +++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp 2004/04/12 20:32:20 1097 @@ -1,5 +1,6 @@ +#define _FILE_OFFSET_BITS 64 #include -#include +#include #include #include @@ -10,20 +11,25 @@ #include "ReadWrite.hpp" #include "simError.h" +#include "GenericData.hpp" #ifdef IS_MPI #include -#include #include "mpiSimulation.hpp" #define TAKE_THIS_TAG_CHAR 0 #define TAKE_THIS_TAG_INT 1 -void nodeZeroError( void ); -void anonymousNodeDie( void ); +namespace initFile{ + void nodeZeroError( void ); + void anonymousNodeDie( void ); +} +using namespace initFile; + #endif // is_mpi -InitializeFromFile :: InitializeFromFile( char *in_name ){ +InitializeFromFile::InitializeFromFile( char *in_name ){ + #ifdef IS_MPI if (worldRank == 0) { #endif @@ -35,17 +41,21 @@ InitializeFromFile :: InitializeFromFile( char *in_nam painCave.isFatal = 1; simError(); } - + strcpy( c_in_name, in_name); #ifdef IS_MPI } - strcpy( checkPointMsg, "Infile opened for reading successfully." ); + else{ + sprintf( c_in_name, "mpiNodeParser_%d", worldRank ); + } + + strcpy( checkPointMsg, "Infile opened for reading successfully." ); MPIcheckPoint(); #endif - return; + return; } -InitializeFromFile :: ~InitializeFromFile( ){ +InitializeFromFile::~InitializeFromFile( ){ #ifdef IS_MPI if (worldRank == 0) { #endif @@ -66,22 +76,22 @@ InitializeFromFile :: ~InitializeFromFile( ){ } -void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ +void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ - int i, j, done, which_node, which_atom; // loop counter + int i, j; +#ifdef IS_MPI + int done, which_node, which_atom; // loop counter +#endif //is_mpi + const int BUFFERSIZE = 2000; // size of the read buffer int n_atoms; // the number of atoms - char read_buffer[BUFFERSIZE]; //the line buffer for reading -#ifdef IS_MPI - char send_buffer[BUFFERSIZE]; -#endif + char read_buffer[BUFFERSIZE]; //the line buffer for reading - char *eof_test; // ptr to see when we reach the end of the file + char *eof_test; // ptr to see when we reach the end of the file char *parseErr; - int procIndex; - entry_plug = the_entry_plug; + simnfo = the_simnfo; #ifndef IS_MPI @@ -96,20 +106,17 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr n_atoms = atoi( read_buffer ); - Atom **atoms = entry_plug->atoms; - DirectionalAtom* dAtom; - - if( n_atoms != entry_plug->n_atoms ){ + if( n_atoms != simnfo->n_atoms ){ sprintf( painCave.errMsg, "Initialize from File error. %s n_atoms, %d, " "does not match the BASS file's n_atoms, %d.\n", - c_in_name, n_atoms, entry_plug->n_atoms ); + c_in_name, n_atoms, simnfo->n_atoms ); painCave.isFatal = 1; simError(); } - - //read and toss the comment line - + + //read the box mat from the comment line + eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); if(eof_test == NULL){ sprintf( painCave.errMsg, @@ -118,8 +125,19 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr simError(); } + + + parseErr = parseCommentLine( read_buffer, simnfo); + if( parseErr != NULL ){ + strcpy( painCave.errMsg, parseErr ); + painCave.isFatal = 1; + simError(); + } + + //parse dump lines + for( i=0; i < n_atoms; i++){ - + eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); if(eof_test == NULL){ sprintf(painCave.errMsg, @@ -131,13 +149,13 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr simError(); } - + parseErr = parseDumpLine( read_buffer, i ); if( parseErr != NULL ){ strcpy( painCave.errMsg, parseErr ); painCave.isFatal = 1; simError(); - } + } } @@ -149,53 +167,63 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone int haveError; - - MPI::Status istatus; + + MPI_Status istatus; int *AtomToProcMap = mpiSim->getAtomToProcMap(); - + haveError = 0; if (worldRank == 0) { eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); if( eof_test == NULL ){ sprintf( painCave.errMsg, - "Error reading 1st line of %d \n ",c_in_name); + "Error reading 1st line of %s \n ",c_in_name); haveError = 1; simError(); } - + n_atoms = atoi( read_buffer ); - - Atom **atoms = entry_plug->atoms; - DirectionalAtom* dAtom; - + // Check to see that the number of atoms in the intial configuration file is the // same as declared in simBass. - + if( n_atoms != mpiSim->getTotAtoms() ){ sprintf( painCave.errMsg, "Initialize from File error. %s n_atoms, %d, " "does not match the BASS file's n_atoms, %d.\n", - c_in_name, n_atoms, entry_plug->n_atoms ); + c_in_name, n_atoms, simnfo->n_atoms ); haveError= 1; simError(); } - - //read and toss the comment line - + + //read the boxMat from the comment line + eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); if(eof_test == NULL){ sprintf( painCave.errMsg, "error in reading commment in %s\n", c_in_name); - haveError= 1; + haveError = 1; simError(); } - - if(haveError) nodeZeroError(); + //Every single processor will parse the comment line by itself + //By using this way, we might lose some efficiency, but if we want to add + //more parameters into comment line, we only need to modify function + //parseCommentLine + + MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); + + parseErr = parseCommentLine( read_buffer, simnfo); + + if( parseErr != NULL ){ + strcpy( painCave.errMsg, parseErr ); + haveError = 1; + simError(); + } + for (i=0 ; i < mpiSim->getTotAtoms(); i++) { - + eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); if(eof_test == NULL){ sprintf(painCave.errMsg, @@ -206,57 +234,70 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr haveError= 1; simError(); } - + if(haveError) nodeZeroError(); // Get the Node number which wants this atom: - which_node = AtomToProcMap[i]; + which_node = AtomToProcMap[i]; if (which_node == 0) { parseErr = parseDumpLine( read_buffer, i ); if( parseErr != NULL ){ strcpy( painCave.errMsg, parseErr ); haveError = 1; simError(); - } + } if(haveError) nodeZeroError(); - } - + } + else { - + myStatus = 1; - MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, - TAKE_THIS_TAG_INT); - MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, - TAKE_THIS_TAG_CHAR); - MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); - MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); - + MPI_Send(&myStatus, 1, MPI_INT, which_node, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); + MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD); + MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, + MPI_COMM_WORLD, &istatus); + if(!myStatus) nodeZeroError(); } } myStatus = -1; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT); + for (j = 1; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send( &myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } - + } else { - + + MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD); + + parseErr = parseCommentLine( read_buffer, simnfo); + + if( parseErr != NULL ){ + strcpy( painCave.errMsg, parseErr ); + haveError = 1; + simError(); + } + + done = 0; while (!done) { - MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, istatus); - + MPI_Recv(&myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + if(!myStatus) anonymousNodeDie(); - + if(myStatus < 0) break; - MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, - TAKE_THIS_TAG_CHAR, istatus); - MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT, istatus); - + MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, + TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); + MPI_Recv(&which_atom, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); + myStatus = 1; parseErr = parseDumpLine( read_buffer, which_atom ); if( parseErr != NULL ){ @@ -264,37 +305,41 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr myStatus = 0;; simError(); } - - MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, - TAKE_THIS_TAG_INT); - + + MPI_Send( &myStatus, 1, MPI_INT, 0, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + } } - + // last thing last, enable fatalities. painCave.isEventLoop = 0; - + + + #endif } char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ - char *foo; // the pointer to the current string token - - double rx, ry, rz; // position place holders - double vx, vy, vz; // velocity placeholders + char *foo; // the pointer to the current string token + + double pos[3]; // position place holders + double vel[3]; // velocity placeholders double q[4]; // the quaternions - double jx, jy, jz; // angular velocity placeholders; + double ji[3]; // angular velocity placeholders; double qSqr, qLength; // needed to normalize the quaternion vector. - - Atom **atoms = entry_plug->atoms; + + Atom **atoms = simnfo->atoms; DirectionalAtom* dAtom; - - int j, n_atoms, atomIndex; + int n_atoms, atomIndex; + #ifdef IS_MPI + int j; + n_atoms = mpiSim->getTotAtoms(); - atomIndex=-1; + atomIndex=-1; for (j=0; j < mpiSim->getMyNlocal(); j++) { if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; } @@ -304,18 +349,18 @@ char* InitializeFromFile::parseDumpLine(char* readLine "in file %s does not exist on processor %d .\n", globalIndex, c_in_name, mpiSim->getMyNode() ); return strdup( painCave.errMsg ); - } + } #else - n_atoms = entry_plug->n_atoms; + n_atoms = simnfo->n_atoms; atomIndex = globalIndex; #endif // is_mpi // set the string tokenizer - + foo = strtok(readLine, " ,;\t"); - + // check the atom name to the current atom - + if( strcmp( foo, atoms[atomIndex]->getType() ) ){ sprintf( painCave.errMsg, "Initialize from file error. Atom %s at index %d " @@ -324,7 +369,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); return strdup( painCave.errMsg ); } - + // get the positions foo = strtok(NULL, " ,;\t"); @@ -335,8 +380,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - rx = atof( foo ); - + pos[0] = atof( foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -345,8 +390,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - ry = atof( foo ); - + pos[1] = atof( foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -355,7 +400,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - rz = atof( foo ); + pos[2] = atof( foo ); // get the velocities @@ -368,8 +413,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - vx = atof( foo ); - + vel[0] = atof( foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -378,8 +423,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - vy = atof( foo ); - + vel[1] = atof( foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -388,13 +433,13 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - vz = atof( foo ); - - + vel[2] = atof( foo ); + + // get the quaternions - + if( atoms[atomIndex]->isDirectional() ){ - + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf(painCave.errMsg, @@ -404,7 +449,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine return strdup( painCave.errMsg ); } q[0] = atof( foo ); - + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -414,7 +459,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine return strdup( painCave.errMsg ); } q[1] = atof( foo ); - + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -424,7 +469,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine return strdup( painCave.errMsg ); } q[2] = atof( foo ); - + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -434,9 +479,9 @@ char* InitializeFromFile::parseDumpLine(char* readLine return strdup( painCave.errMsg ); } q[3] = atof( foo ); - + // get the angular velocities - + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -445,8 +490,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - jx = atof( foo ); - + ji[0] = atof( foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -455,8 +500,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - jy = atof(foo ); - + ji[1] = atof(foo ); + foo = strtok(NULL, " ,;\t"); if(foo == NULL){ sprintf( painCave.errMsg, @@ -465,63 +510,161 @@ char* InitializeFromFile::parseDumpLine(char* readLine c_in_name, n_atoms, atomIndex ); return strdup( painCave.errMsg ); } - jz = atof( foo ); - + ji[2] = atof( foo ); + dAtom = ( DirectionalAtom* )atoms[atomIndex]; // check that the quaternion vector is normalized qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); - + qLength = sqrt( qSqr ); q[0] = q[0] / qLength; q[1] = q[1] / qLength; q[2] = q[2] / qLength; q[3] = q[3] / qLength; - + dAtom->setQ( q ); - + // add the angular velocities - dAtom->setJx( jx ); - dAtom->setJy( jy ); - dAtom->setJz( jz ); + dAtom->setJ( ji ); } - + // add the positions and velocities to the atom - - atoms[atomIndex]->setX( rx ); - atoms[atomIndex]->setY( ry ); - atoms[atomIndex]->setZ( rz ); - - atoms[atomIndex]->set_vx( vx ); - atoms[atomIndex]->set_vy( vy ); - atoms[atomIndex]->set_vz( vz ); + atoms[atomIndex]->setPos( pos ); + atoms[atomIndex]->setVel( vel ); + return NULL; } -#ifdef IS_MPI +char* InitializeFromFile::parseCommentLine(char* readLine, SimInfo* entry_plug){ -// a couple of functions to let us escape the read loop + double currTime; + double boxMat[9]; + double theBoxMat3[3][3]; + double chi; + double integralOfChidt; + double eta[9]; -void nodeZeroError( void ){ - int j, myStatus; + char *foo; // the pointer to the current string token + + // set the string tokenizer + + foo = strtok(readLine, " ,;\t"); + // set the timeToken. + + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Time from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + + currTime = atof( foo ); + entry_plug->setTime( currTime ); + + //get H-Matrix + + for(int i = 0 ; i < 9; i++){ + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading H[%d] from %s\n", i, c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[i] = atof( foo ); + } + + for(int i=0;i<3;i++) + for(int j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; + + //set H-Matrix + entry_plug->setBoxM( theBoxMat3 ); + + //get chi and integralOfChidt, they should appear by pair + + if( entry_plug->useInitXSstate ){ + foo = strtok(NULL, " ,;\t\n"); + if(foo != NULL){ + chi = atof(foo); + + foo = strtok(NULL, " ,;\t\n"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "chi and integralOfChidt should appear by pair in %s\n", c_in_name ); + return strdup( painCave.errMsg ); + } + integralOfChidt = atof( foo ); + + //push chi and integralOfChidt into SimInfo::properties which can be + //retrieved by integrator later + DoubleData* chiValue = new DoubleData(); + chiValue->setID(CHIVALUE_ID); + chiValue->setData(chi); + entry_plug->addProperty(chiValue); + + DoubleData* integralOfChidtValue = new DoubleData(); + integralOfChidtValue->setID(INTEGRALOFCHIDT_ID); + integralOfChidtValue->setData(integralOfChidt); + entry_plug->addProperty(integralOfChidtValue); + + } + else + return NULL; + + //get eta + foo = strtok(NULL, " ,;\t\n"); + if(foo != NULL ){ + for(int i = 0 ; i < 9; i++){ + + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading eta[%d] from %s\n", i, c_in_name ); + return strdup( painCave.errMsg ); + } + eta[i] = atof( foo ); + foo = strtok(NULL, " ,;\t\n"); + } + } + else + return NULL; + + //push eta into SimInfo::properties which can be + //retrieved by integrator later + //entry_plug->setBoxM( theBoxMat3 ); + DoubleArrayData* etaValue = new DoubleArrayData(); + etaValue->setID(ETAVALUE_ID); + etaValue->setData(eta, 9); + entry_plug->addProperty(etaValue); + } + + return NULL; +} + +#ifdef IS_MPI + +// a couple of functions to let us escape the read loop + +void initFile::nodeZeroError( void ){ + int j, myStatus; + myStatus = 0; - for (j = 0; j < mpiSim->getNumberProcessors(); j++) { - MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, - TAKE_THIS_TAG_INT); - } - + for (j = 0; j < mpiSim->getNumberProcessors(); j++) { + MPI_Send( &myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); + } + MPI_Finalize(); exit (0); - + } -void anonymousNodeDie( void ){ +void initFile::anonymousNodeDie( void ){ MPI_Finalize(); exit (0);