--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp 2003/03/28 21:45:03 436 +++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp 2003/08/12 19:56:49 689 @@ -13,17 +13,23 @@ #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 ){ + + std::cerr << "Hello from Initialize from file.\n"; + #ifdef IS_MPI if (worldRank == 0) { #endif @@ -45,7 +51,7 @@ InitializeFromFile :: InitializeFromFile( char *in_nam return; } -InitializeFromFile :: ~InitializeFromFile( ){ +InitializeFromFile::~InitializeFromFile( ){ #ifdef IS_MPI if (worldRank == 0) { #endif @@ -66,7 +72,7 @@ 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 @@ -80,8 +86,11 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr char *eof_test; // ptr to see when we reach the end of the file char *parseErr; int procIndex; + double currTime; + double boxMat[9]; + double theBoxMat3[3][3]; - entry_plug = the_entry_plug; + simnfo = the_simnfo; #ifndef IS_MPI @@ -96,19 +105,19 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr n_atoms = atoi( read_buffer ); - Atom **atoms = entry_plug->atoms; + Atom **atoms = simnfo->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){ @@ -118,6 +127,20 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr simError(); } + parseErr = parseBoxLine( read_buffer, boxMat, currTime ); + if( parseErr != NULL ){ + strcpy( painCave.errMsg, parseErr ); + painCave.isFatal = 1; + simError(); + } + + for(i=0;i<3;i++) + for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; + + simnfo->setBoxM( theBoxMat3 ); + simnfo->setTime( currTime ); + + for( i=0; i < n_atoms; i++){ eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); @@ -137,7 +160,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr strcpy( painCave.errMsg, parseErr ); painCave.isFatal = 1; simError(); - } + } } @@ -150,7 +173,7 @@ 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(); @@ -167,7 +190,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr n_atoms = atoi( read_buffer ); - Atom **atoms = entry_plug->atoms; + Atom **atoms = simnfo->atoms; DirectionalAtom* dAtom; // Check to see that the number of atoms in the intial configuration file is the @@ -177,20 +200,30 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr 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(); } + + parseErr = parseBoxLine( read_buffer, boxMat, currTime ); + if( parseErr != NULL ){ + strcpy( painCave.errMsg, parseErr ); + haveError = 1; + simError(); + } + + MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); + MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); if(haveError) nodeZeroError(); @@ -224,38 +257,43 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr 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); + MPI_Send( &myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } } else { + MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); + MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); + 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 ); @@ -265,14 +303,21 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr 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; + + for(i=0;i<3;i++) + for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; + + simnfo->setBoxM( theBoxMat3 ); + simnfo->setTime( currTime ); + #endif } @@ -281,13 +326,13 @@ char* InitializeFromFile::parseDumpLine(char* readLine char *foo; // the pointer to the current string token - double rx, ry, rz; // position place holders - double vx, vy, vz; // velocity placeholders + double pos[3]; // position place holders + double vel[3]; // velocity placeholders double q[4]; // the quaternions double jx, jy, jz; // 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; @@ -306,7 +351,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine return strdup( painCave.errMsg ); } #else - n_atoms = entry_plug->n_atoms; + n_atoms = simnfo->n_atoms; atomIndex = globalIndex; #endif // is_mpi @@ -335,7 +380,7 @@ 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){ @@ -345,7 +390,7 @@ 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){ @@ -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 @@ -368,7 +413,7 @@ 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){ @@ -378,7 +423,7 @@ 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){ @@ -388,7 +433,7 @@ 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 @@ -490,29 +535,134 @@ char* InitializeFromFile::parseDumpLine(char* readLine // 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; } +char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], + double &time ){ + + char *foo; // the pointer to the current string token + int j; + + // 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 ); + } + time = atof( foo ); + + // get the Hx vector + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hx[0] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[0] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hx[1] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[1] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hx[2] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[2] = atof( foo ); + + // get the Hy vector + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hy[0] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[3] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hy[1] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[4] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hy[2] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[5] = atof( foo ); + + // get the Hz vector + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hz[0] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[6] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hz[1] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[7] = atof( foo ); + + foo = strtok(NULL, " ,;\t"); + if(foo == NULL){ + sprintf( painCave.errMsg, + "error in reading Hz[2] from %s\n", + c_in_name ); + return strdup( painCave.errMsg ); + } + boxMat[8] = atof( foo ); + + return NULL; +} + + #ifdef IS_MPI // a couple of functions to let us escape the read loop -void nodeZeroError( void ){ +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); + MPI_Send( &myStatus, 1, MPI_INT, j, + TAKE_THIS_TAG_INT, MPI_COMM_WORLD); } @@ -521,7 +671,7 @@ void nodeZeroError( void ){ } -void anonymousNodeDie( void ){ +void initFile::anonymousNodeDie( void ){ MPI_Finalize(); exit (0);