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#include <iostream> |
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#include <cmath> |
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|
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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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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG 0 |
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#endif // is_mpi |
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|
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InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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|
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c_in_file = fopen(in_name, "r"); |
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if(c_in_file == NULL){ |
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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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} |
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|
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strcpy( c_in_name, in_name); |
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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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return; |
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} |
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|
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InitializeFromFile :: ~InitializeFromFile( ){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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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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sprintf( painCave.errMsg, |
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"Error closing %s\n", c_in_name ); |
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simError(); |
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} |
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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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|
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return; |
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} |
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|
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|
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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|
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int i, j, done, which_node, which_atom; // loop counter |
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|
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const int BUFFERSIZE = 2000; // size of the read buffer |
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int n_atoms; // the number of atoms |
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char read_buffer[BUFFERSIZE]; //the line buffer for reading |
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#ifdef IS_MPI |
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char send_buffer[BUFFERSIZE]; |
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#endif |
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|
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char *eof_test; // ptr to see when we reach the end of the file |
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char *parseErr; |
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int procIndex; |
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|
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entry_plug = the_entry_plug; |
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|
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|
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#ifndef IS_MPI |
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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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"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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} |
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|
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n_atoms = atoi( read_buffer ); |
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|
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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|
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if( n_atoms != entry_plug->n_atoms ){ |
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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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|
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//read and toss the comment line |
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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 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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for( i=0; i < n_atoms; i++){ |
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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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|
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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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} |
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|
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|
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// MPI Section of code.......... |
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#else //IS_MPI |
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|
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MPI::Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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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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|
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n_atoms = atoi( read_buffer ); |
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|
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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|
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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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|
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if( n_atoms != mpiSim->getTotAtoms() ){ |
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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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|
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//read and toss the comment line |
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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 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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|
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
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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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|
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
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if (which_node == mpiSim->getMyNode()) { |
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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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} else { |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
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} |
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} |
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sprintf(read_buffer, "GAMEOVER"); |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, |
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TAKE_THIS_TAG); |
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} |
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|
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} else { |
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|
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done = 0; |
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while (!done) { |
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MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG, istatus); |
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if (strcmp(read_buffer, "GAMEOVER")) { |
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done = 1; |
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continue; |
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} else { |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG, istatus); |
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|
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parseErr = parseDumpLine( read_buffer, which_atom ); |
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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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} |
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} |
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} |
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|
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#endif |
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} |
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|
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char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
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|
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char *foo; // the pointer to the current string token |
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|
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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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|
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Atom **atoms = entry_plug->atoms; |
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DirectionalAtom* dAtom; |
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|
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int j, n_atoms, atomIndex; |
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|
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#ifdef IS_MPI |
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n_atoms = mpiSim->getTotAtoms(); |
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atomIndex=-1; |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
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if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
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} |
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if (atomIndex == -1) { |
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sprintf( painCave.errMsg, |
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"Initialize from file error. Atom at index %d " |
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"in file %s does not exist on processor %d .\n", |
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globalIndex, c_in_name, mpiSim->getMyNode() ); |
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return strdup( painCave.errMsg ); |
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} |
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#else |
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n_atoms = entry_plug->n_atoms; |
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atomIndex = globalIndex; |
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#endif // is_mpi |
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|
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// set the string tokenizer |
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|
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foo = strtok(readLine, " ,;\t"); |
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|
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// check the atom name to the current atom |
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|
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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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|
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// get the positions |
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|
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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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|
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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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|
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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 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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|
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|
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// get the velocities |
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|
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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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|
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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 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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|
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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 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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vz = atof( foo ); |
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|
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|
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// get the quaternions |
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|
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if( atoms[atomIndex]->isDirectional() ){ |
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|
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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 quaternion 0 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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q[0] = atof( foo ); |
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|
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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 quaternion 1 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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q[1] = atof( foo ); |
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|
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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 quaternion 2 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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q[2] = atof( foo ); |
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|
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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 quaternion 3 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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q[3] = atof( foo ); |
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|
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// get the angular velocities |
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|
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foo = strtok(NULL, " ,;\t"); |
403 |
if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jx 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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jx = atof( foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
413 |
if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jy 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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jy = atof(foo ); |
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|
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foo = strtok(NULL, " ,;\t"); |
423 |
if(foo == NULL){ |
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sprintf( painCave.errMsg, |
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"error in reading angular momentum jz from %s\n" |
426 |
"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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jz = atof( foo ); |
431 |
|
432 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
433 |
|
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// check that the quaternion vector is normalized |
435 |
|
436 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
437 |
|
438 |
qLength = sqrt( qSqr ); |
439 |
q[0] = q[0] / qLength; |
440 |
q[1] = q[1] / qLength; |
441 |
q[2] = q[2] / qLength; |
442 |
q[3] = q[3] / qLength; |
443 |
|
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dAtom->setQ( q ); |
445 |
|
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// add the angular velocities |
447 |
|
448 |
dAtom->setJx( jx ); |
449 |
dAtom->setJy( jy ); |
450 |
dAtom->setJz( jz ); |
451 |
} |
452 |
|
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// add the positions and velocities to the atom |
454 |
|
455 |
atoms[atomIndex]->setX( rx ); |
456 |
atoms[atomIndex]->setY( ry ); |
457 |
atoms[atomIndex]->setZ( rz ); |
458 |
|
459 |
atoms[atomIndex]->set_vx( vx ); |
460 |
atoms[atomIndex]->set_vy( vy ); |
461 |
atoms[atomIndex]->set_vz( vz ); |
462 |
|
463 |
return NULL; |
464 |
} |