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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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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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chuckv |
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entry_plug = the_entry_plug |
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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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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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mmeineke |
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if( n_atoms != entry_plug->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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} |
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mmeineke |
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chuckv |
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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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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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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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chuckv |
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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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} |
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#endif |
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} |
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char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
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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 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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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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int n_atoms; |
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#ifdef IS_MPI |
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n_atoms = entry_plug->mpiSim->getTotAtoms(); |
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#else |
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n_atoms = entry_plug->n_atoms; |
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#endi // is_mpi |
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// set the string tokenizer |
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foo = strtok(readLine, " ,;\t"); |
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// check the atom name to the current atom |
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if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
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sprintf( painCave.errMsg, |
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"Initialize from file error. Atom %s at index %d " |
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"in file %s does not" |
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" match the BASS atom %s.\n", |
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foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
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return strdup( painCave.errMsg ); |
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} |
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chuckv |
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mmeineke |
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// get the positions |
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chuckv |
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mmeineke |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading postition x from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, 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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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading postition y from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, 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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foo = strtok(NULL, " ,;\t"); |
257 |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading postition z from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, 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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// get the velocities |
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foo = strtok(NULL, " ,;\t"); |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading velocity x from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, 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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foo = strtok(NULL, " ,;\t"); |
280 |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
282 |
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"error in reading velocity y from %s\n" |
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"natoms = %d, index = %d\n", |
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c_in_name, 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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289 |
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foo = strtok(NULL, " ,;\t"); |
290 |
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if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading velocity z from %s\n" |
293 |
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"natoms = %d, index = %d\n", |
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c_in_name, n_atoms, atomIndex ); |
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return strdup( painCave.errMsg ); |
296 |
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} |
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vz = atof( foo ); |
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299 |
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300 |
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// get the quaternions |
301 |
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302 |
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if( atoms[atomIndex]->isDirectional() ){ |
303 |
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304 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
305 |
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if(foo == NULL){ |
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mmeineke |
209 |
sprintf(painCave.errMsg, |
307 |
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"error in reading quaternion 0 from %s\n" |
308 |
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"natoms = %d, index = %d\n", |
309 |
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c_in_name, n_atoms, atomIndex ); |
310 |
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return strdup( painCave.errMsg ); |
311 |
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} |
312 |
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q[0] = atof( foo ); |
313 |
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314 |
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foo = strtok(NULL, " ,;\t"); |
315 |
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if(foo == NULL){ |
316 |
chuckv |
206 |
sprintf( painCave.errMsg, |
317 |
mmeineke |
209 |
"error in reading quaternion 1 from %s\n" |
318 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
319 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
320 |
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return strdup( painCave.errMsg ); |
321 |
chuckv |
206 |
} |
322 |
mmeineke |
209 |
q[1] = atof( foo ); |
323 |
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324 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
325 |
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if(foo == NULL){ |
326 |
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sprintf( painCave.errMsg, |
327 |
mmeineke |
209 |
"error in reading quaternion 2 from %s\n" |
328 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
329 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
330 |
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return strdup( painCave.errMsg ); |
331 |
chuckv |
206 |
} |
332 |
mmeineke |
209 |
q[2] = atof( foo ); |
333 |
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334 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
335 |
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if(foo == NULL){ |
336 |
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sprintf( painCave.errMsg, |
337 |
mmeineke |
209 |
"error in reading quaternion 3 from %s\n" |
338 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
339 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
340 |
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return strdup( painCave.errMsg ); |
341 |
chuckv |
206 |
} |
342 |
mmeineke |
209 |
q[3] = atof( foo ); |
343 |
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344 |
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// get the angular velocities |
345 |
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346 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
347 |
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if(foo == NULL){ |
348 |
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sprintf( painCave.errMsg, |
349 |
mmeineke |
209 |
"error in reading angular momentum jx from %s\n" |
350 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
351 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
352 |
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return strdup( painCave.errMsg ); |
353 |
chuckv |
206 |
} |
354 |
mmeineke |
209 |
jx = atof( foo ); |
355 |
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356 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
357 |
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if(foo == NULL){ |
358 |
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sprintf( painCave.errMsg, |
359 |
mmeineke |
209 |
"error in reading angular momentum jy from %s\n" |
360 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
361 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
362 |
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return strdup( painCave.errMsg ); |
363 |
chuckv |
206 |
} |
364 |
mmeineke |
209 |
jy = atof(foo ); |
365 |
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366 |
chuckv |
206 |
foo = strtok(NULL, " ,;\t"); |
367 |
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if(foo == NULL){ |
368 |
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sprintf( painCave.errMsg, |
369 |
mmeineke |
209 |
"error in reading angular momentum jz from %s\n" |
370 |
chuckv |
206 |
"natoms = %d, index = %d\n", |
371 |
mmeineke |
209 |
c_in_name, n_atoms, atomIndex ); |
372 |
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return strdup( painCave.errMsg ); |
373 |
chuckv |
206 |
} |
374 |
mmeineke |
209 |
jz = atof( foo ); |
375 |
chuckv |
206 |
|
376 |
mmeineke |
209 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
377 |
chuckv |
206 |
|
378 |
mmeineke |
209 |
// check that the quaternion vector is normalized |
379 |
chuckv |
206 |
|
380 |
mmeineke |
209 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
381 |
chuckv |
206 |
|
382 |
mmeineke |
209 |
qLength = sqrt( qSqr ); |
383 |
|
|
q[0] = q[0] / qLength; |
384 |
|
|
q[1] = q[1] / qLength; |
385 |
|
|
q[2] = q[2] / qLength; |
386 |
|
|
q[3] = q[3] / qLength; |
387 |
chuckv |
206 |
|
388 |
mmeineke |
209 |
dAtom->setQ( q ); |
389 |
chuckv |
206 |
|
390 |
mmeineke |
209 |
// add the angular velocities |
391 |
chuckv |
206 |
|
392 |
mmeineke |
209 |
dAtom->setJx( jx ); |
393 |
|
|
dAtom->setJy( jy ); |
394 |
|
|
dAtom->setJz( jz ); |
395 |
|
|
} |
396 |
chuckv |
206 |
|
397 |
mmeineke |
209 |
// add the positions and velocities to the atom |
398 |
chuckv |
206 |
|
399 |
mmeineke |
209 |
atoms[atomIndex]->setX( rx ); |
400 |
|
|
atoms[atomIndex]->setY( ry ); |
401 |
|
|
atoms[atomIndex]->setZ( rz ); |
402 |
chuckv |
206 |
|
403 |
mmeineke |
209 |
atoms[atomIndex]->set_vx( vx ); |
404 |
|
|
atoms[atomIndex]->set_vy( vy ); |
405 |
|
|
atoms[atomIndex]->set_vz( vz ); |
406 |
|
|
|
407 |
|
|
return NULL; |
408 |
mmeineke |
10 |
} |