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#include <iostream> |
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#include <cmath> |
3 |
|
4 |
#include <stdio.h> |
5 |
#include <stdlib.h> |
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#include <string.h> |
7 |
#include <unistd.h> |
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#include <sys/types.h> |
9 |
#include <sys/stat.h> |
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|
11 |
#include "ReadWrite.hpp" |
12 |
#include "simError.h" |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
16 |
#include <mpi++.h> |
17 |
#include "mpiSimulation.hpp" |
18 |
#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
20 |
|
21 |
namespace initFile{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
24 |
} |
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|
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using namespace initFile; |
27 |
|
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#endif // is_mpi |
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|
30 |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
31 |
#ifdef IS_MPI |
32 |
if (worldRank == 0) { |
33 |
#endif |
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|
35 |
c_in_file = fopen(in_name, "r"); |
36 |
if(c_in_file == NULL){ |
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sprintf(painCave.errMsg, |
38 |
"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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|
52 |
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, |
60 |
"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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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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|
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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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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|
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haveError = 0; |
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if (worldRank == 0) { |
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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 reading 1st line of %d \n ",c_in_name); |
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haveError = 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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haveError= 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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haveError= 1; |
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simError(); |
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} |
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|
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if(haveError) nodeZeroError(); |
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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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haveError= 1; |
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simError(); |
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} |
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|
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if(haveError) nodeZeroError(); |
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|
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// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
218 |
if (which_node == 0) { |
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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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haveError = 1; |
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simError(); |
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} |
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if(haveError) nodeZeroError(); |
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} |
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|
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else { |
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|
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myStatus = 1; |
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MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
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TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR); |
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MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
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MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
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|
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if(!myStatus) nodeZeroError(); |
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} |
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} |
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myStatus = -1; |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
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MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
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TAKE_THIS_TAG_INT); |
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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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|
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MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, istatus); |
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|
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if(!myStatus) anonymousNodeDie(); |
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|
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if(myStatus < 0) break; |
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|
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MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
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TAKE_THIS_TAG_CHAR, istatus); |
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MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT, istatus); |
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|
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myStatus = 1; |
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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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myStatus = 0;; |
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simError(); |
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} |
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|
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MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
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TAKE_THIS_TAG_INT); |
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|
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} |
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} |
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|
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// last thing last, enable fatalities. |
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painCave.isEventLoop = 0; |
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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; |
295 |
DirectionalAtom* dAtom; |
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|
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int j, n_atoms, atomIndex; |
298 |
|
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#ifdef IS_MPI |
300 |
n_atoms = mpiSim->getTotAtoms(); |
301 |
atomIndex=-1; |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
303 |
if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
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} |
305 |
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", |
309 |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
310 |
return strdup( painCave.errMsg ); |
311 |
} |
312 |
#else |
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n_atoms = entry_plug->n_atoms; |
314 |
atomIndex = globalIndex; |
315 |
#endif // is_mpi |
316 |
|
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// set the string tokenizer |
318 |
|
319 |
foo = strtok(readLine, " ,;\t"); |
320 |
|
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// check the atom name to the current atom |
322 |
|
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if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
324 |
sprintf( painCave.errMsg, |
325 |
"Initialize from file error. Atom %s at index %d " |
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"in file %s does not" |
327 |
" match the BASS atom %s.\n", |
328 |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
329 |
return strdup( painCave.errMsg ); |
330 |
} |
331 |
|
332 |
// get the positions |
333 |
|
334 |
foo = strtok(NULL, " ,;\t"); |
335 |
if(foo == NULL){ |
336 |
sprintf( painCave.errMsg, |
337 |
"error in reading postition x from %s\n" |
338 |
"natoms = %d, index = %d\n", |
339 |
c_in_name, n_atoms, atomIndex ); |
340 |
return strdup( painCave.errMsg ); |
341 |
} |
342 |
rx = atof( foo ); |
343 |
|
344 |
foo = strtok(NULL, " ,;\t"); |
345 |
if(foo == NULL){ |
346 |
sprintf( painCave.errMsg, |
347 |
"error in reading postition y from %s\n" |
348 |
"natoms = %d, index = %d\n", |
349 |
c_in_name, n_atoms, atomIndex ); |
350 |
return strdup( painCave.errMsg ); |
351 |
} |
352 |
ry = atof( foo ); |
353 |
|
354 |
foo = strtok(NULL, " ,;\t"); |
355 |
if(foo == NULL){ |
356 |
sprintf( painCave.errMsg, |
357 |
"error in reading postition z from %s\n" |
358 |
"natoms = %d, index = %d\n", |
359 |
c_in_name, n_atoms, atomIndex ); |
360 |
return strdup( painCave.errMsg ); |
361 |
} |
362 |
rz = atof( foo ); |
363 |
|
364 |
|
365 |
// get the velocities |
366 |
|
367 |
foo = strtok(NULL, " ,;\t"); |
368 |
if(foo == NULL){ |
369 |
sprintf( painCave.errMsg, |
370 |
"error in reading velocity x from %s\n" |
371 |
"natoms = %d, index = %d\n", |
372 |
c_in_name, n_atoms, atomIndex ); |
373 |
return strdup( painCave.errMsg ); |
374 |
} |
375 |
vx = atof( foo ); |
376 |
|
377 |
foo = strtok(NULL, " ,;\t"); |
378 |
if(foo == NULL){ |
379 |
sprintf( painCave.errMsg, |
380 |
"error in reading velocity y from %s\n" |
381 |
"natoms = %d, index = %d\n", |
382 |
c_in_name, n_atoms, atomIndex ); |
383 |
return strdup( painCave.errMsg ); |
384 |
} |
385 |
vy = atof( foo ); |
386 |
|
387 |
foo = strtok(NULL, " ,;\t"); |
388 |
if(foo == NULL){ |
389 |
sprintf( painCave.errMsg, |
390 |
"error in reading velocity z from %s\n" |
391 |
"natoms = %d, index = %d\n", |
392 |
c_in_name, n_atoms, atomIndex ); |
393 |
return strdup( painCave.errMsg ); |
394 |
} |
395 |
vz = atof( foo ); |
396 |
|
397 |
|
398 |
// get the quaternions |
399 |
|
400 |
if( atoms[atomIndex]->isDirectional() ){ |
401 |
|
402 |
foo = strtok(NULL, " ,;\t"); |
403 |
if(foo == NULL){ |
404 |
sprintf(painCave.errMsg, |
405 |
"error in reading quaternion 0 from %s\n" |
406 |
"natoms = %d, index = %d\n", |
407 |
c_in_name, n_atoms, atomIndex ); |
408 |
return strdup( painCave.errMsg ); |
409 |
} |
410 |
q[0] = atof( foo ); |
411 |
|
412 |
foo = strtok(NULL, " ,;\t"); |
413 |
if(foo == NULL){ |
414 |
sprintf( painCave.errMsg, |
415 |
"error in reading quaternion 1 from %s\n" |
416 |
"natoms = %d, index = %d\n", |
417 |
c_in_name, n_atoms, atomIndex ); |
418 |
return strdup( painCave.errMsg ); |
419 |
} |
420 |
q[1] = atof( foo ); |
421 |
|
422 |
foo = strtok(NULL, " ,;\t"); |
423 |
if(foo == NULL){ |
424 |
sprintf( painCave.errMsg, |
425 |
"error in reading quaternion 2 from %s\n" |
426 |
"natoms = %d, index = %d\n", |
427 |
c_in_name, n_atoms, atomIndex ); |
428 |
return strdup( painCave.errMsg ); |
429 |
} |
430 |
q[2] = atof( foo ); |
431 |
|
432 |
foo = strtok(NULL, " ,;\t"); |
433 |
if(foo == NULL){ |
434 |
sprintf( painCave.errMsg, |
435 |
"error in reading quaternion 3 from %s\n" |
436 |
"natoms = %d, index = %d\n", |
437 |
c_in_name, n_atoms, atomIndex ); |
438 |
return strdup( painCave.errMsg ); |
439 |
} |
440 |
q[3] = atof( foo ); |
441 |
|
442 |
// get the angular velocities |
443 |
|
444 |
foo = strtok(NULL, " ,;\t"); |
445 |
if(foo == NULL){ |
446 |
sprintf( painCave.errMsg, |
447 |
"error in reading angular momentum jx from %s\n" |
448 |
"natoms = %d, index = %d\n", |
449 |
c_in_name, n_atoms, atomIndex ); |
450 |
return strdup( painCave.errMsg ); |
451 |
} |
452 |
jx = atof( foo ); |
453 |
|
454 |
foo = strtok(NULL, " ,;\t"); |
455 |
if(foo == NULL){ |
456 |
sprintf( painCave.errMsg, |
457 |
"error in reading angular momentum jy from %s\n" |
458 |
"natoms = %d, index = %d\n", |
459 |
c_in_name, n_atoms, atomIndex ); |
460 |
return strdup( painCave.errMsg ); |
461 |
} |
462 |
jy = atof(foo ); |
463 |
|
464 |
foo = strtok(NULL, " ,;\t"); |
465 |
if(foo == NULL){ |
466 |
sprintf( painCave.errMsg, |
467 |
"error in reading angular momentum jz from %s\n" |
468 |
"natoms = %d, index = %d\n", |
469 |
c_in_name, n_atoms, atomIndex ); |
470 |
return strdup( painCave.errMsg ); |
471 |
} |
472 |
jz = atof( foo ); |
473 |
|
474 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
475 |
|
476 |
// check that the quaternion vector is normalized |
477 |
|
478 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
479 |
|
480 |
qLength = sqrt( qSqr ); |
481 |
q[0] = q[0] / qLength; |
482 |
q[1] = q[1] / qLength; |
483 |
q[2] = q[2] / qLength; |
484 |
q[3] = q[3] / qLength; |
485 |
|
486 |
dAtom->setQ( q ); |
487 |
|
488 |
// add the angular velocities |
489 |
|
490 |
dAtom->setJx( jx ); |
491 |
dAtom->setJy( jy ); |
492 |
dAtom->setJz( jz ); |
493 |
} |
494 |
|
495 |
// add the positions and velocities to the atom |
496 |
|
497 |
atoms[atomIndex]->setX( rx ); |
498 |
atoms[atomIndex]->setY( ry ); |
499 |
atoms[atomIndex]->setZ( rz ); |
500 |
|
501 |
atoms[atomIndex]->set_vx( vx ); |
502 |
atoms[atomIndex]->set_vy( vy ); |
503 |
atoms[atomIndex]->set_vz( vz ); |
504 |
|
505 |
return NULL; |
506 |
} |
507 |
|
508 |
|
509 |
#ifdef IS_MPI |
510 |
|
511 |
// a couple of functions to let us escape the read loop |
512 |
|
513 |
void initFile::nodeZeroError( void ){ |
514 |
int j, myStatus; |
515 |
|
516 |
myStatus = 0; |
517 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
518 |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
519 |
TAKE_THIS_TAG_INT); |
520 |
} |
521 |
|
522 |
|
523 |
MPI_Finalize(); |
524 |
exit (0); |
525 |
|
526 |
} |
527 |
|
528 |
void initFile::anonymousNodeDie( void ){ |
529 |
|
530 |
MPI_Finalize(); |
531 |
exit (0); |
532 |
} |
533 |
|
534 |
#endif //is_mpi |