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mmeineke |
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#include <iostream> |
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#include <cmath> |
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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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mmeineke |
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#include "simError.h" |
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mmeineke |
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chuckv |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#endif // is_mpi |
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mmeineke |
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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chuckv |
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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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c_in_file = fopen(in_name, "r"); |
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if(c_in_file == NULL){ |
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mmeineke |
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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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mmeineke |
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} |
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strcpy( c_in_name, in_name); |
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chuckv |
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#ifdef IS_MPI |
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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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mmeineke |
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return; |
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} |
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InitializeFromFile :: ~InitializeFromFile( ){ |
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chuckv |
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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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int error; |
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error = fclose( c_in_file ); |
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if( error ){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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"Error closing %s\n", c_in_name ); |
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simError(); |
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mmeineke |
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} |
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chuckv |
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#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Infile closed successfully." ); |
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MPIcheckPoint(); |
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#endif |
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mmeineke |
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return; |
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} |
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chuckv |
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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mmeineke |
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int i; // loop counter |
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mmeineke |
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const int BUFFERSIZE = 2000; // size of the read buffer |
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mmeineke |
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int n_atoms; // the number of atoms |
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mmeineke |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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chuckv |
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#ifdef IS_MPI |
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mmeineke |
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char send_buffer[BUFFERSIZE]; |
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chuckv |
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#endif |
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mmeineke |
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char *eof_test; // ptr to see when we reach the end of the file |
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mmeineke |
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char *parseErr; |
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mmeineke |
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|
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chuckv |
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entry_plug = the_entry_plug; |
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chuckv |
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#ifndef IS_MPI |
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mmeineke |
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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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mmeineke |
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sprintf( painCave.errMsg, |
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"InitializeFromFile error: error reading 1st line of \"%s\"\n", |
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c_in_name ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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mmeineke |
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n_atoms = atoi( read_buffer ); |
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mmeineke |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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if( n_atoms != entry_plug->n_atoms ){ |
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mmeineke |
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sprintf( painCave.errMsg, |
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mmeineke |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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mmeineke |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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//read and toss the comment line |
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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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mmeineke |
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sprintf( painCave.errMsg, |
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"error in reading commment in %s\n", c_in_name); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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for( i=0; i < n_atoms; i++){ |
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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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mmeineke |
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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", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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mmeineke |
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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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mmeineke |
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painCave.isFatal = 1; |
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simError(); |
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mmeineke |
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} |
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mmeineke |
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} |
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chuckv |
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// MPI Section of code.......... |
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#else //IS_MPI |
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chuckv |
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int masterIndex; |
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int nodeAtomsStart; |
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int nodeAtomsEnd; |
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int mpiErr; |
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int sendError; |
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chuckv |
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|
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chuckv |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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chuckv |
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if (worldRank == 0) { |
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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mmeineke |
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n_atoms = atoi( read_buffer ); |
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chuckv |
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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chuckv |
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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. |
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chuckv |
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|
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chuckv |
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if( n_atoms != mpiSim->getTotAtoms() ){ |
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chuckv |
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sprintf( painCave.errMsg, |
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"Initialize from File error. %s n_atoms, %d, " |
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"does not match the BASS file's n_atoms, %d.\n", |
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c_in_name, n_atoms, entry_plug->n_atoms ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//read and toss the comment line |
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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 in reading commment in %s\n", c_in_name); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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chuckv |
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// Read Proc 0 share of the xyz file... |
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masterIndex = 0; |
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chuckv |
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for( i=0; i <= mpiSim->getMyAtomEnd(); i++){ |
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chuckv |
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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 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", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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masterIndex++; |
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} |
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chuckv |
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} |
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mmeineke |
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chuckv |
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sprintf(checkPointMsg, |
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"Node 0 has successfully read positions from input file."); |
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mpiCheckPoint(); |
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for (procIndex = 1; procIndex < entryPlug->mpiSim->getNumberProcessors(); |
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procIndex++){ |
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if (worldRank == 0) { |
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mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD, |
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istatus); |
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD, |
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istatus); |
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// Make sure where node 0 is reading from, matches where the receiving node |
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// expects it to be. |
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if (masterIndex != nodeAtomsStart){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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sprintf(painCave.errMsg, |
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"Initialize from file error: atoms start index (%d) for " |
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"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){ |
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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(read_buffer,"ERROR"); |
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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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", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
251 |
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD, |
254 |
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istatus); |
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if (sendError) mpiCheckpoint(); |
256 |
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masterIndex++; |
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} |
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chuckv |
206 |
} |
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chuckv |
212 |
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else if(worldRank == procIndex){ |
263 |
chuckv |
215 |
nodeAtomStart = mpiSim->getMyAtomStart(); |
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nodeAtomEnd = mpiSim->getMyAtomEnd(); |
265 |
chuckv |
212 |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
267 |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD, |
269 |
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istatus); |
270 |
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if (sendError) mpiCheckpoint(); |
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272 |
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for ( i = 0; i < entry_plug->n_atoms, i++){ |
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mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD, |
275 |
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istatus); |
276 |
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277 |
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if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint(); |
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279 |
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parseErr = parseDumpLine( read_buffer, i ); |
280 |
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if( parseErr != NULL ){ |
281 |
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sendError = 1; |
282 |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
283 |
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284 |
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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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} |
289 |
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sendError = 0; |
290 |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
291 |
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} |
292 |
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} |
293 |
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sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
294 |
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mpiCheckPoint(); |
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mmeineke |
209 |
} |
296 |
chuckv |
212 |
|
297 |
mmeineke |
209 |
#endif |
298 |
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} |
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300 |
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301 |
chuckv |
249 |
char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
302 |
mmeineke |
209 |
|
303 |
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char *foo; // the pointer to the current string token |
304 |
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305 |
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double rx, ry, rz; // position place holders |
306 |
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double vx, vy, vz; // velocity placeholders |
307 |
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double q[4]; // the quaternions |
308 |
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double jx, jy, jz; // angular velocity placeholders; |
309 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
310 |
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311 |
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Atom **atoms = entry_plug->atoms; |
312 |
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DirectionalAtom* dAtom; |
313 |
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314 |
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int n_atoms; |
315 |
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316 |
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#ifdef IS_MPI |
317 |
chuckv |
215 |
n_atoms = mpiSim->getTotAtoms(); |
318 |
mmeineke |
209 |
#else |
319 |
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n_atoms = entry_plug->n_atoms; |
320 |
chuckv |
249 |
#endif // is_mpi |
321 |
mmeineke |
209 |
|
322 |
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323 |
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// set the string tokenizer |
324 |
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325 |
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foo = strtok(readLine, " ,;\t"); |
326 |
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327 |
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// check the atom name to the current atom |
328 |
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329 |
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if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
330 |
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sprintf( painCave.errMsg, |
331 |
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"Initialize from file error. Atom %s at index %d " |
332 |
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"in file %s does not" |
333 |
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" match the BASS atom %s.\n", |
334 |
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foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
335 |
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return strdup( painCave.errMsg ); |
336 |
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} |
337 |
chuckv |
206 |
|
338 |
mmeineke |
209 |
// get the positions |
339 |
chuckv |
206 |
|
340 |
mmeineke |
209 |
foo = strtok(NULL, " ,;\t"); |
341 |
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if(foo == NULL){ |
342 |
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sprintf( painCave.errMsg, |
343 |
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"error in reading postition x from %s\n" |
344 |
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"natoms = %d, index = %d\n", |
345 |
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c_in_name, n_atoms, atomIndex ); |
346 |
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return strdup( painCave.errMsg ); |
347 |
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} |
348 |
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rx = atof( foo ); |
349 |
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350 |
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foo = strtok(NULL, " ,;\t"); |
351 |
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if(foo == NULL){ |
352 |
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sprintf( painCave.errMsg, |
353 |
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"error in reading postition y from %s\n" |
354 |
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"natoms = %d, index = %d\n", |
355 |
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c_in_name, n_atoms, atomIndex ); |
356 |
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return strdup( painCave.errMsg ); |
357 |
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} |
358 |
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ry = atof( foo ); |
359 |
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360 |
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foo = strtok(NULL, " ,;\t"); |
361 |
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if(foo == NULL){ |
362 |
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sprintf( painCave.errMsg, |
363 |
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"error in reading postition z from %s\n" |
364 |
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"natoms = %d, index = %d\n", |
365 |
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c_in_name, n_atoms, atomIndex ); |
366 |
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return strdup( painCave.errMsg ); |
367 |
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} |
368 |
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rz = atof( foo ); |
369 |
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370 |
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371 |
|
|
// get the velocities |
372 |
|
|
|
373 |
|
|
foo = strtok(NULL, " ,;\t"); |
374 |
|
|
if(foo == NULL){ |
375 |
|
|
sprintf( painCave.errMsg, |
376 |
|
|
"error in reading velocity x from %s\n" |
377 |
|
|
"natoms = %d, index = %d\n", |
378 |
|
|
c_in_name, n_atoms, atomIndex ); |
379 |
|
|
return strdup( painCave.errMsg ); |
380 |
|
|
} |
381 |
|
|
vx = atof( foo ); |
382 |
|
|
|
383 |
|
|
foo = strtok(NULL, " ,;\t"); |
384 |
|
|
if(foo == NULL){ |
385 |
|
|
sprintf( painCave.errMsg, |
386 |
|
|
"error in reading velocity y from %s\n" |
387 |
|
|
"natoms = %d, index = %d\n", |
388 |
|
|
c_in_name, n_atoms, atomIndex ); |
389 |
|
|
return strdup( painCave.errMsg ); |
390 |
|
|
} |
391 |
|
|
vy = atof( foo ); |
392 |
|
|
|
393 |
|
|
foo = strtok(NULL, " ,;\t"); |
394 |
|
|
if(foo == NULL){ |
395 |
|
|
sprintf( painCave.errMsg, |
396 |
|
|
"error in reading velocity z from %s\n" |
397 |
|
|
"natoms = %d, index = %d\n", |
398 |
|
|
c_in_name, n_atoms, atomIndex ); |
399 |
|
|
return strdup( painCave.errMsg ); |
400 |
|
|
} |
401 |
|
|
vz = atof( foo ); |
402 |
|
|
|
403 |
|
|
|
404 |
|
|
// get the quaternions |
405 |
|
|
|
406 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
407 |
|
|
|
408 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
409 |
|
|
if(foo == NULL){ |
410 |
mmeineke |
209 |
sprintf(painCave.errMsg, |
411 |
|
|
"error in reading quaternion 0 from %s\n" |
412 |
|
|
"natoms = %d, index = %d\n", |
413 |
|
|
c_in_name, n_atoms, atomIndex ); |
414 |
|
|
return strdup( painCave.errMsg ); |
415 |
|
|
} |
416 |
|
|
q[0] = atof( foo ); |
417 |
|
|
|
418 |
|
|
foo = strtok(NULL, " ,;\t"); |
419 |
|
|
if(foo == NULL){ |
420 |
chuckv |
206 |
sprintf( painCave.errMsg, |
421 |
mmeineke |
209 |
"error in reading quaternion 1 from %s\n" |
422 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
423 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
424 |
|
|
return strdup( painCave.errMsg ); |
425 |
chuckv |
206 |
} |
426 |
mmeineke |
209 |
q[1] = atof( foo ); |
427 |
|
|
|
428 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
429 |
|
|
if(foo == NULL){ |
430 |
|
|
sprintf( painCave.errMsg, |
431 |
mmeineke |
209 |
"error in reading quaternion 2 from %s\n" |
432 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
433 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
434 |
|
|
return strdup( painCave.errMsg ); |
435 |
chuckv |
206 |
} |
436 |
mmeineke |
209 |
q[2] = atof( foo ); |
437 |
|
|
|
438 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
439 |
|
|
if(foo == NULL){ |
440 |
|
|
sprintf( painCave.errMsg, |
441 |
mmeineke |
209 |
"error in reading quaternion 3 from %s\n" |
442 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
443 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
444 |
|
|
return strdup( painCave.errMsg ); |
445 |
chuckv |
206 |
} |
446 |
mmeineke |
209 |
q[3] = atof( foo ); |
447 |
|
|
|
448 |
|
|
// get the angular velocities |
449 |
|
|
|
450 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
451 |
|
|
if(foo == NULL){ |
452 |
|
|
sprintf( painCave.errMsg, |
453 |
mmeineke |
209 |
"error in reading angular momentum jx from %s\n" |
454 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
455 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
456 |
|
|
return strdup( painCave.errMsg ); |
457 |
chuckv |
206 |
} |
458 |
mmeineke |
209 |
jx = atof( foo ); |
459 |
|
|
|
460 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
461 |
|
|
if(foo == NULL){ |
462 |
|
|
sprintf( painCave.errMsg, |
463 |
mmeineke |
209 |
"error in reading angular momentum jy from %s\n" |
464 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
465 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
466 |
|
|
return strdup( painCave.errMsg ); |
467 |
chuckv |
206 |
} |
468 |
mmeineke |
209 |
jy = atof(foo ); |
469 |
|
|
|
470 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
471 |
|
|
if(foo == NULL){ |
472 |
|
|
sprintf( painCave.errMsg, |
473 |
mmeineke |
209 |
"error in reading angular momentum jz from %s\n" |
474 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
475 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
476 |
|
|
return strdup( painCave.errMsg ); |
477 |
chuckv |
206 |
} |
478 |
mmeineke |
209 |
jz = atof( foo ); |
479 |
chuckv |
206 |
|
480 |
mmeineke |
209 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
481 |
chuckv |
206 |
|
482 |
mmeineke |
209 |
// check that the quaternion vector is normalized |
483 |
chuckv |
206 |
|
484 |
mmeineke |
209 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
485 |
chuckv |
206 |
|
486 |
mmeineke |
209 |
qLength = sqrt( qSqr ); |
487 |
|
|
q[0] = q[0] / qLength; |
488 |
|
|
q[1] = q[1] / qLength; |
489 |
|
|
q[2] = q[2] / qLength; |
490 |
|
|
q[3] = q[3] / qLength; |
491 |
chuckv |
206 |
|
492 |
mmeineke |
209 |
dAtom->setQ( q ); |
493 |
chuckv |
206 |
|
494 |
mmeineke |
209 |
// add the angular velocities |
495 |
chuckv |
206 |
|
496 |
mmeineke |
209 |
dAtom->setJx( jx ); |
497 |
|
|
dAtom->setJy( jy ); |
498 |
|
|
dAtom->setJz( jz ); |
499 |
|
|
} |
500 |
chuckv |
206 |
|
501 |
mmeineke |
209 |
// add the positions and velocities to the atom |
502 |
chuckv |
206 |
|
503 |
mmeineke |
209 |
atoms[atomIndex]->setX( rx ); |
504 |
|
|
atoms[atomIndex]->setY( ry ); |
505 |
|
|
atoms[atomIndex]->setZ( rz ); |
506 |
chuckv |
206 |
|
507 |
mmeineke |
209 |
atoms[atomIndex]->set_vx( vx ); |
508 |
|
|
atoms[atomIndex]->set_vy( vy ); |
509 |
|
|
atoms[atomIndex]->set_vz( vz ); |
510 |
|
|
|
511 |
|
|
return NULL; |
512 |
mmeineke |
10 |
} |