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#include <iostream> |
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#include <cmath> |
3 |
|
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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> |
9 |
#include <sys/stat.h> |
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|
11 |
#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
14 |
#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
16 |
|
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#define TAKE_THIS_TAG 0 |
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#endif // is_mpi |
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|
20 |
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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|
25 |
c_in_file = fopen(in_name, "r"); |
26 |
if(c_in_file == NULL){ |
27 |
sprintf(painCave.errMsg, |
28 |
"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
30 |
simError(); |
31 |
} |
32 |
|
33 |
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." ); |
37 |
MPIcheckPoint(); |
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#endif |
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return; |
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} |
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|
42 |
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." ); |
56 |
MPIcheckPoint(); |
57 |
#endif |
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|
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return; |
60 |
} |
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|
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|
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void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
64 |
|
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int i; // 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 |
69 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
70 |
#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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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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|
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MPI_Status istatus[MPI_STATUS_SIZE]; |
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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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// Read Proc 0 share of the xyz file... |
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masterIndex = 0; |
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for( i=0; i <= mpiSim->getMyAtomEnd(); 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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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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} |
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|
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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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|
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for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
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procIndex++){ |
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if (worldRank == 0) { |
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|
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mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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|
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mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,TAKE_THIS_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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|
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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,TAKE_THIS_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,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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for ( i = nodeAtomsStart; i <= nodeAtomsEnd; 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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|
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sprintf(read_buffer,"ERROR"); |
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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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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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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if (sendError) MPIcheckPoint(); |
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|
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masterIndex++; |
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} |
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} |
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|
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|
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else if(worldRank == procIndex){ |
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nodeAtomsStart = mpiSim->getMyAtomStart(); |
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nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
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mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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if (sendError) MPIcheckPoint(); |
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|
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for ( i = 0; i < entry_plug->n_atoms; i++){ |
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|
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mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD, |
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istatus); |
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|
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if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint(); |
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|
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parseErr = parseDumpLine( read_buffer, i ); |
282 |
if( parseErr != NULL ){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
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|
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|
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strcpy( painCave.errMsg, parseErr ); |
288 |
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,0,TAKE_THIS_TAG,MPI_COMM_WORLD); |
293 |
} |
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} |
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sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
296 |
MPIcheckPoint(); |
297 |
} |
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|
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#endif |
300 |
} |
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|
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|
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char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
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|
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char *foo; // the pointer to the current string token |
306 |
|
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double rx, ry, rz; // position place holders |
308 |
double vx, vy, vz; // velocity placeholders |
309 |
double q[4]; // the quaternions |
310 |
double jx, jy, jz; // angular velocity placeholders; |
311 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
312 |
|
313 |
Atom **atoms = entry_plug->atoms; |
314 |
DirectionalAtom* dAtom; |
315 |
|
316 |
int n_atoms; |
317 |
|
318 |
#ifdef IS_MPI |
319 |
n_atoms = mpiSim->getTotAtoms(); |
320 |
#else |
321 |
n_atoms = entry_plug->n_atoms; |
322 |
#endif // is_mpi |
323 |
|
324 |
|
325 |
// set the string tokenizer |
326 |
|
327 |
foo = strtok(readLine, " ,;\t"); |
328 |
|
329 |
// check the atom name to the current atom |
330 |
|
331 |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
332 |
sprintf( painCave.errMsg, |
333 |
"Initialize from file error. Atom %s at index %d " |
334 |
"in file %s does not" |
335 |
" match the BASS atom %s.\n", |
336 |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
337 |
return strdup( painCave.errMsg ); |
338 |
} |
339 |
|
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// get the positions |
341 |
|
342 |
foo = strtok(NULL, " ,;\t"); |
343 |
if(foo == NULL){ |
344 |
sprintf( painCave.errMsg, |
345 |
"error in reading postition x from %s\n" |
346 |
"natoms = %d, index = %d\n", |
347 |
c_in_name, n_atoms, atomIndex ); |
348 |
return strdup( painCave.errMsg ); |
349 |
} |
350 |
rx = atof( foo ); |
351 |
|
352 |
foo = strtok(NULL, " ,;\t"); |
353 |
if(foo == NULL){ |
354 |
sprintf( painCave.errMsg, |
355 |
"error in reading postition y from %s\n" |
356 |
"natoms = %d, index = %d\n", |
357 |
c_in_name, n_atoms, atomIndex ); |
358 |
return strdup( painCave.errMsg ); |
359 |
} |
360 |
ry = atof( foo ); |
361 |
|
362 |
foo = strtok(NULL, " ,;\t"); |
363 |
if(foo == NULL){ |
364 |
sprintf( painCave.errMsg, |
365 |
"error in reading postition z from %s\n" |
366 |
"natoms = %d, index = %d\n", |
367 |
c_in_name, n_atoms, atomIndex ); |
368 |
return strdup( painCave.errMsg ); |
369 |
} |
370 |
rz = atof( foo ); |
371 |
|
372 |
|
373 |
// get the velocities |
374 |
|
375 |
foo = strtok(NULL, " ,;\t"); |
376 |
if(foo == NULL){ |
377 |
sprintf( painCave.errMsg, |
378 |
"error in reading velocity x from %s\n" |
379 |
"natoms = %d, index = %d\n", |
380 |
c_in_name, n_atoms, atomIndex ); |
381 |
return strdup( painCave.errMsg ); |
382 |
} |
383 |
vx = atof( foo ); |
384 |
|
385 |
foo = strtok(NULL, " ,;\t"); |
386 |
if(foo == NULL){ |
387 |
sprintf( painCave.errMsg, |
388 |
"error in reading velocity y from %s\n" |
389 |
"natoms = %d, index = %d\n", |
390 |
c_in_name, n_atoms, atomIndex ); |
391 |
return strdup( painCave.errMsg ); |
392 |
} |
393 |
vy = atof( foo ); |
394 |
|
395 |
foo = strtok(NULL, " ,;\t"); |
396 |
if(foo == NULL){ |
397 |
sprintf( painCave.errMsg, |
398 |
"error in reading velocity z from %s\n" |
399 |
"natoms = %d, index = %d\n", |
400 |
c_in_name, n_atoms, atomIndex ); |
401 |
return strdup( painCave.errMsg ); |
402 |
} |
403 |
vz = atof( foo ); |
404 |
|
405 |
|
406 |
// get the quaternions |
407 |
|
408 |
if( atoms[atomIndex]->isDirectional() ){ |
409 |
|
410 |
foo = strtok(NULL, " ,;\t"); |
411 |
if(foo == NULL){ |
412 |
sprintf(painCave.errMsg, |
413 |
"error in reading quaternion 0 from %s\n" |
414 |
"natoms = %d, index = %d\n", |
415 |
c_in_name, n_atoms, atomIndex ); |
416 |
return strdup( painCave.errMsg ); |
417 |
} |
418 |
q[0] = atof( foo ); |
419 |
|
420 |
foo = strtok(NULL, " ,;\t"); |
421 |
if(foo == NULL){ |
422 |
sprintf( painCave.errMsg, |
423 |
"error in reading quaternion 1 from %s\n" |
424 |
"natoms = %d, index = %d\n", |
425 |
c_in_name, n_atoms, atomIndex ); |
426 |
return strdup( painCave.errMsg ); |
427 |
} |
428 |
q[1] = atof( foo ); |
429 |
|
430 |
foo = strtok(NULL, " ,;\t"); |
431 |
if(foo == NULL){ |
432 |
sprintf( painCave.errMsg, |
433 |
"error in reading quaternion 2 from %s\n" |
434 |
"natoms = %d, index = %d\n", |
435 |
c_in_name, n_atoms, atomIndex ); |
436 |
return strdup( painCave.errMsg ); |
437 |
} |
438 |
q[2] = atof( foo ); |
439 |
|
440 |
foo = strtok(NULL, " ,;\t"); |
441 |
if(foo == NULL){ |
442 |
sprintf( painCave.errMsg, |
443 |
"error in reading quaternion 3 from %s\n" |
444 |
"natoms = %d, index = %d\n", |
445 |
c_in_name, n_atoms, atomIndex ); |
446 |
return strdup( painCave.errMsg ); |
447 |
} |
448 |
q[3] = atof( foo ); |
449 |
|
450 |
// get the angular velocities |
451 |
|
452 |
foo = strtok(NULL, " ,;\t"); |
453 |
if(foo == NULL){ |
454 |
sprintf( painCave.errMsg, |
455 |
"error in reading angular momentum jx from %s\n" |
456 |
"natoms = %d, index = %d\n", |
457 |
c_in_name, n_atoms, atomIndex ); |
458 |
return strdup( painCave.errMsg ); |
459 |
} |
460 |
jx = atof( foo ); |
461 |
|
462 |
foo = strtok(NULL, " ,;\t"); |
463 |
if(foo == NULL){ |
464 |
sprintf( painCave.errMsg, |
465 |
"error in reading angular momentum jy from %s\n" |
466 |
"natoms = %d, index = %d\n", |
467 |
c_in_name, n_atoms, atomIndex ); |
468 |
return strdup( painCave.errMsg ); |
469 |
} |
470 |
jy = atof(foo ); |
471 |
|
472 |
foo = strtok(NULL, " ,;\t"); |
473 |
if(foo == NULL){ |
474 |
sprintf( painCave.errMsg, |
475 |
"error in reading angular momentum jz from %s\n" |
476 |
"natoms = %d, index = %d\n", |
477 |
c_in_name, n_atoms, atomIndex ); |
478 |
return strdup( painCave.errMsg ); |
479 |
} |
480 |
jz = atof( foo ); |
481 |
|
482 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
483 |
|
484 |
// check that the quaternion vector is normalized |
485 |
|
486 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
487 |
|
488 |
qLength = sqrt( qSqr ); |
489 |
q[0] = q[0] / qLength; |
490 |
q[1] = q[1] / qLength; |
491 |
q[2] = q[2] / qLength; |
492 |
q[3] = q[3] / qLength; |
493 |
|
494 |
dAtom->setQ( q ); |
495 |
|
496 |
// add the angular velocities |
497 |
|
498 |
dAtom->setJx( jx ); |
499 |
dAtom->setJy( jy ); |
500 |
dAtom->setJz( jz ); |
501 |
} |
502 |
|
503 |
// add the positions and velocities to the atom |
504 |
|
505 |
atoms[atomIndex]->setX( rx ); |
506 |
atoms[atomIndex]->setY( ry ); |
507 |
atoms[atomIndex]->setZ( rz ); |
508 |
|
509 |
atoms[atomIndex]->set_vx( vx ); |
510 |
atoms[atomIndex]->set_vy( vy ); |
511 |
atoms[atomIndex]->set_vz( vz ); |
512 |
|
513 |
return NULL; |
514 |
} |