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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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|
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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|
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|
15 |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
16 |
#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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|
20 |
c_in_file = fopen(in_name, "r"); |
21 |
if(c_in_file == NULL){ |
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sprintf(painCave.errMsg, |
23 |
"Cannot open file: %s\n", in_name); |
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painCave.isFatal = 1; |
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simError(); |
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} |
27 |
|
28 |
strcpy( c_in_name, in_name); |
29 |
#ifdef IS_MPI |
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} |
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strcpy( checkPointMsg, "Infile opened for reading successfully." ); |
32 |
MPIcheckPoint(); |
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#endif |
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return; |
35 |
} |
36 |
|
37 |
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; |
55 |
} |
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|
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|
58 |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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|
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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 |
64 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
65 |
#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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|
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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 != entry_plug->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 <= entry_plug->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 < entryPlug->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,MPI_ANY_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,MPI_ANY_TAG,MPI_COMM_WORLD, |
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istatus); |
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// Make sure where node 0 is reading from, matches where the receiving node |
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// expects it to be. |
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|
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if (masterIndex != nodeAtomsStart){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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sprintf(painCave.errMsg, |
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"Initialize from file error: atoms start index (%d) for " |
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"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sendError = 0; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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|
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for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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|
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sprintf(read_buffer,"ERROR"); |
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mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD); |
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|
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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,MPI_ANY_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_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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nodeAtomStart = entry_plug->mpiSim->getMyAtomStart(); |
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nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd(); |
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mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
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mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
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|
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mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_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,MPI_ANY_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 ); |
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if( parseErr != NULL ){ |
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sendError = 1; |
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mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
280 |
|
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|
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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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sendError = 0; |
287 |
mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD); |
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} |
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} |
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sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex); |
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mpiCheckPoint(); |
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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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|
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char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){ |
299 |
|
300 |
char *foo; // the pointer to the current string token |
301 |
|
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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 |
305 |
double jx, jy, jz; // angular velocity placeholders; |
306 |
double qSqr, qLength; // needed to normalize the quaternion vector. |
307 |
|
308 |
Atom **atoms = entry_plug->atoms; |
309 |
DirectionalAtom* dAtom; |
310 |
|
311 |
int n_atoms; |
312 |
|
313 |
#ifdef IS_MPI |
314 |
n_atoms = entry_plug->mpiSim->getTotAtoms(); |
315 |
#else |
316 |
n_atoms = entry_plug->n_atoms; |
317 |
#endi // is_mpi |
318 |
|
319 |
|
320 |
// set the string tokenizer |
321 |
|
322 |
foo = strtok(readLine, " ,;\t"); |
323 |
|
324 |
// check the atom name to the current atom |
325 |
|
326 |
if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
327 |
sprintf( painCave.errMsg, |
328 |
"Initialize from file error. Atom %s at index %d " |
329 |
"in file %s does not" |
330 |
" match the BASS atom %s.\n", |
331 |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
332 |
return strdup( painCave.errMsg ); |
333 |
} |
334 |
|
335 |
// get the positions |
336 |
|
337 |
foo = strtok(NULL, " ,;\t"); |
338 |
if(foo == NULL){ |
339 |
sprintf( painCave.errMsg, |
340 |
"error in reading postition x from %s\n" |
341 |
"natoms = %d, index = %d\n", |
342 |
c_in_name, n_atoms, atomIndex ); |
343 |
return strdup( painCave.errMsg ); |
344 |
} |
345 |
rx = atof( foo ); |
346 |
|
347 |
foo = strtok(NULL, " ,;\t"); |
348 |
if(foo == NULL){ |
349 |
sprintf( painCave.errMsg, |
350 |
"error in reading postition y from %s\n" |
351 |
"natoms = %d, index = %d\n", |
352 |
c_in_name, n_atoms, atomIndex ); |
353 |
return strdup( painCave.errMsg ); |
354 |
} |
355 |
ry = atof( foo ); |
356 |
|
357 |
foo = strtok(NULL, " ,;\t"); |
358 |
if(foo == NULL){ |
359 |
sprintf( painCave.errMsg, |
360 |
"error in reading postition z from %s\n" |
361 |
"natoms = %d, index = %d\n", |
362 |
c_in_name, n_atoms, atomIndex ); |
363 |
return strdup( painCave.errMsg ); |
364 |
} |
365 |
rz = atof( foo ); |
366 |
|
367 |
|
368 |
// get the velocities |
369 |
|
370 |
foo = strtok(NULL, " ,;\t"); |
371 |
if(foo == NULL){ |
372 |
sprintf( painCave.errMsg, |
373 |
"error in reading velocity x from %s\n" |
374 |
"natoms = %d, index = %d\n", |
375 |
c_in_name, n_atoms, atomIndex ); |
376 |
return strdup( painCave.errMsg ); |
377 |
} |
378 |
vx = atof( foo ); |
379 |
|
380 |
foo = strtok(NULL, " ,;\t"); |
381 |
if(foo == NULL){ |
382 |
sprintf( painCave.errMsg, |
383 |
"error in reading velocity y from %s\n" |
384 |
"natoms = %d, index = %d\n", |
385 |
c_in_name, n_atoms, atomIndex ); |
386 |
return strdup( painCave.errMsg ); |
387 |
} |
388 |
vy = atof( foo ); |
389 |
|
390 |
foo = strtok(NULL, " ,;\t"); |
391 |
if(foo == NULL){ |
392 |
sprintf( painCave.errMsg, |
393 |
"error in reading velocity z from %s\n" |
394 |
"natoms = %d, index = %d\n", |
395 |
c_in_name, n_atoms, atomIndex ); |
396 |
return strdup( painCave.errMsg ); |
397 |
} |
398 |
vz = atof( foo ); |
399 |
|
400 |
|
401 |
// get the quaternions |
402 |
|
403 |
if( atoms[atomIndex]->isDirectional() ){ |
404 |
|
405 |
foo = strtok(NULL, " ,;\t"); |
406 |
if(foo == NULL){ |
407 |
sprintf(painCave.errMsg, |
408 |
"error in reading quaternion 0 from %s\n" |
409 |
"natoms = %d, index = %d\n", |
410 |
c_in_name, n_atoms, atomIndex ); |
411 |
return strdup( painCave.errMsg ); |
412 |
} |
413 |
q[0] = atof( foo ); |
414 |
|
415 |
foo = strtok(NULL, " ,;\t"); |
416 |
if(foo == NULL){ |
417 |
sprintf( painCave.errMsg, |
418 |
"error in reading quaternion 1 from %s\n" |
419 |
"natoms = %d, index = %d\n", |
420 |
c_in_name, n_atoms, atomIndex ); |
421 |
return strdup( painCave.errMsg ); |
422 |
} |
423 |
q[1] = atof( foo ); |
424 |
|
425 |
foo = strtok(NULL, " ,;\t"); |
426 |
if(foo == NULL){ |
427 |
sprintf( painCave.errMsg, |
428 |
"error in reading quaternion 2 from %s\n" |
429 |
"natoms = %d, index = %d\n", |
430 |
c_in_name, n_atoms, atomIndex ); |
431 |
return strdup( painCave.errMsg ); |
432 |
} |
433 |
q[2] = atof( foo ); |
434 |
|
435 |
foo = strtok(NULL, " ,;\t"); |
436 |
if(foo == NULL){ |
437 |
sprintf( painCave.errMsg, |
438 |
"error in reading quaternion 3 from %s\n" |
439 |
"natoms = %d, index = %d\n", |
440 |
c_in_name, n_atoms, atomIndex ); |
441 |
return strdup( painCave.errMsg ); |
442 |
} |
443 |
q[3] = atof( foo ); |
444 |
|
445 |
// get the angular velocities |
446 |
|
447 |
foo = strtok(NULL, " ,;\t"); |
448 |
if(foo == NULL){ |
449 |
sprintf( painCave.errMsg, |
450 |
"error in reading angular momentum jx from %s\n" |
451 |
"natoms = %d, index = %d\n", |
452 |
c_in_name, n_atoms, atomIndex ); |
453 |
return strdup( painCave.errMsg ); |
454 |
} |
455 |
jx = atof( foo ); |
456 |
|
457 |
foo = strtok(NULL, " ,;\t"); |
458 |
if(foo == NULL){ |
459 |
sprintf( painCave.errMsg, |
460 |
"error in reading angular momentum jy from %s\n" |
461 |
"natoms = %d, index = %d\n", |
462 |
c_in_name, n_atoms, atomIndex ); |
463 |
return strdup( painCave.errMsg ); |
464 |
} |
465 |
jy = atof(foo ); |
466 |
|
467 |
foo = strtok(NULL, " ,;\t"); |
468 |
if(foo == NULL){ |
469 |
sprintf( painCave.errMsg, |
470 |
"error in reading angular momentum jz from %s\n" |
471 |
"natoms = %d, index = %d\n", |
472 |
c_in_name, n_atoms, atomIndex ); |
473 |
return strdup( painCave.errMsg ); |
474 |
} |
475 |
jz = atof( foo ); |
476 |
|
477 |
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
478 |
|
479 |
// check that the quaternion vector is normalized |
480 |
|
481 |
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
482 |
|
483 |
qLength = sqrt( qSqr ); |
484 |
q[0] = q[0] / qLength; |
485 |
q[1] = q[1] / qLength; |
486 |
q[2] = q[2] / qLength; |
487 |
q[3] = q[3] / qLength; |
488 |
|
489 |
dAtom->setQ( q ); |
490 |
|
491 |
// add the angular velocities |
492 |
|
493 |
dAtom->setJx( jx ); |
494 |
dAtom->setJy( jy ); |
495 |
dAtom->setJz( jz ); |
496 |
} |
497 |
|
498 |
// add the positions and velocities to the atom |
499 |
|
500 |
atoms[atomIndex]->setX( rx ); |
501 |
atoms[atomIndex]->setY( ry ); |
502 |
atoms[atomIndex]->setZ( rz ); |
503 |
|
504 |
atoms[atomIndex]->set_vx( vx ); |
505 |
atoms[atomIndex]->set_vy( vy ); |
506 |
atoms[atomIndex]->set_vz( vz ); |
507 |
|
508 |
return NULL; |
509 |
} |