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mmeineke |
377 |
#include <iostream> |
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#include <cmath> |
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#include <stdio.h> |
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#include <stdlib.h> |
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#include <string.h> |
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#include <unistd.h> |
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#include <sys/types.h> |
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#include <sys/stat.h> |
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#include "ReadWrite.hpp" |
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#include "simError.h" |
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#ifdef IS_MPI |
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gezelter |
417 |
#include <mpi.h> |
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mmeineke |
377 |
#include "mpiSimulation.hpp" |
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chuckv |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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mmeineke |
440 |
namespace initFile{ |
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void nodeZeroError( void ); |
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void anonymousNodeDie( void ); |
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} |
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chuckv |
436 |
|
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mmeineke |
440 |
using namespace initFile; |
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mmeineke |
377 |
#endif // is_mpi |
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tim |
689 |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
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mmeineke |
377 |
#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif |
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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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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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tim |
689 |
InitializeFromFile::~InitializeFromFile( ){ |
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mmeineke |
377 |
#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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return; |
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} |
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mmeineke |
641 |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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mmeineke |
377 |
|
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gezelter |
417 |
int i, j, done, which_node, which_atom; // loop counter |
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mmeineke |
377 |
|
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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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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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mmeineke |
644 |
double currTime; |
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mmeineke |
586 |
double boxMat[9]; |
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mmeineke |
590 |
double theBoxMat3[3][3]; |
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mmeineke |
377 |
|
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mmeineke |
586 |
simnfo = the_simnfo; |
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mmeineke |
377 |
|
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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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n_atoms = atoi( read_buffer ); |
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mmeineke |
586 |
Atom **atoms = simnfo->atoms; |
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mmeineke |
377 |
DirectionalAtom* dAtom; |
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mmeineke |
586 |
if( n_atoms != simnfo->n_atoms ){ |
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mmeineke |
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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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mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
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mmeineke |
377 |
painCave.isFatal = 1; |
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simError(); |
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} |
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mmeineke |
586 |
//read the box mat from the comment line |
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mmeineke |
377 |
|
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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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mmeineke |
644 |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
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mmeineke |
586 |
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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mmeineke |
590 |
for(i=0;i<3;i++) |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
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mmeineke |
586 |
|
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mmeineke |
590 |
simnfo->setBoxM( theBoxMat3 ); |
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mmeineke |
644 |
simnfo->setTime( currTime ); |
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mmeineke |
586 |
|
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mmeineke |
590 |
|
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mmeineke |
377 |
for( i=0; i < n_atoms; i++){ |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
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if(eof_test == NULL){ |
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sprintf(painCave.errMsg, |
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"error in reading file %s\n" |
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"natoms = %d; index = %d\n" |
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"error reading the line from the file.\n", |
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c_in_name, n_atoms, i ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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mmeineke |
586 |
} |
162 |
mmeineke |
377 |
} |
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// MPI Section of code.......... |
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#else //IS_MPI |
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168 |
chuckv |
436 |
// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
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int haveError; |
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mmeineke |
447 |
MPI_Status istatus; |
175 |
gezelter |
417 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
176 |
mmeineke |
377 |
|
177 |
chuckv |
436 |
|
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haveError = 0; |
179 |
mmeineke |
377 |
if (worldRank == 0) { |
180 |
chuckv |
436 |
|
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mmeineke |
377 |
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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chuckv |
436 |
haveError = 1; |
186 |
mmeineke |
377 |
simError(); |
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} |
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n_atoms = atoi( read_buffer ); |
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mmeineke |
586 |
Atom **atoms = simnfo->atoms; |
192 |
mmeineke |
377 |
DirectionalAtom* dAtom; |
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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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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", |
201 |
mmeineke |
586 |
c_in_name, n_atoms, simnfo->n_atoms ); |
202 |
chuckv |
436 |
haveError= 1; |
203 |
mmeineke |
377 |
simError(); |
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} |
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mmeineke |
586 |
//read the boxMat from the comment line |
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mmeineke |
377 |
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
209 |
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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); |
212 |
mmeineke |
586 |
haveError = 1; |
213 |
mmeineke |
377 |
simError(); |
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} |
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mmeineke |
586 |
|
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mmeineke |
644 |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
217 |
mmeineke |
586 |
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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MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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mmeineke |
644 |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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mmeineke |
377 |
|
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chuckv |
436 |
if(haveError) nodeZeroError(); |
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gezelter |
417 |
|
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for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
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mmeineke |
377 |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
231 |
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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 ); |
237 |
chuckv |
436 |
haveError= 1; |
238 |
mmeineke |
377 |
simError(); |
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} |
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241 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
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gezelter |
417 |
// Get the Node number which wants this atom: |
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which_node = AtomToProcMap[i]; |
245 |
chuckv |
436 |
if (which_node == 0) { |
246 |
gezelter |
417 |
parseErr = parseDumpLine( read_buffer, i ); |
247 |
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if( parseErr != NULL ){ |
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strcpy( painCave.errMsg, parseErr ); |
249 |
chuckv |
436 |
haveError = 1; |
250 |
gezelter |
417 |
simError(); |
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} |
252 |
chuckv |
436 |
if(haveError) nodeZeroError(); |
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} |
254 |
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255 |
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else { |
256 |
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257 |
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myStatus = 1; |
258 |
mmeineke |
447 |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
259 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
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MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
262 |
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MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
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MPI_COMM_WORLD); |
264 |
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MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
265 |
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MPI_COMM_WORLD, &istatus); |
266 |
chuckv |
436 |
|
267 |
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if(!myStatus) nodeZeroError(); |
268 |
mmeineke |
377 |
} |
269 |
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} |
270 |
chuckv |
436 |
myStatus = -1; |
271 |
gezelter |
417 |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
272 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
273 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
274 |
gezelter |
417 |
} |
275 |
gezelter |
419 |
|
276 |
gezelter |
417 |
} else { |
277 |
gezelter |
419 |
|
278 |
mmeineke |
586 |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
279 |
mmeineke |
644 |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
280 |
mmeineke |
586 |
|
281 |
gezelter |
417 |
done = 0; |
282 |
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while (!done) { |
283 |
chuckv |
436 |
|
284 |
mmeineke |
447 |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
285 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
286 |
chuckv |
436 |
|
287 |
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if(!myStatus) anonymousNodeDie(); |
288 |
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289 |
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if(myStatus < 0) break; |
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291 |
mmeineke |
447 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
292 |
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TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
293 |
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MPI_Recv(&which_atom, 1, MPI_INT, 0, |
294 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
295 |
chuckv |
436 |
|
296 |
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myStatus = 1; |
297 |
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parseErr = parseDumpLine( read_buffer, which_atom ); |
298 |
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if( parseErr != NULL ){ |
299 |
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strcpy( painCave.errMsg, parseErr ); |
300 |
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myStatus = 0;; |
301 |
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simError(); |
302 |
mmeineke |
377 |
} |
303 |
chuckv |
436 |
|
304 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
305 |
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TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
306 |
chuckv |
436 |
|
307 |
mmeineke |
377 |
} |
308 |
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} |
309 |
chuckv |
436 |
|
310 |
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// last thing last, enable fatalities. |
311 |
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painCave.isEventLoop = 0; |
312 |
mmeineke |
586 |
|
313 |
mmeineke |
590 |
for(i=0;i<3;i++) |
314 |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
315 |
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316 |
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simnfo->setBoxM( theBoxMat3 ); |
317 |
mmeineke |
644 |
simnfo->setTime( currTime ); |
318 |
mmeineke |
590 |
|
319 |
chuckv |
436 |
|
320 |
mmeineke |
377 |
#endif |
321 |
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} |
322 |
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323 |
gezelter |
419 |
char* InitializeFromFile::parseDumpLine(char* readLine, int globalIndex){ |
324 |
mmeineke |
377 |
|
325 |
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char *foo; // the pointer to the current string token |
326 |
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|
327 |
mmeineke |
670 |
double pos[3]; // position place holders |
328 |
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double vel[3]; // velocity placeholders |
329 |
mmeineke |
377 |
double q[4]; // the quaternions |
330 |
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double jx, jy, jz; // angular velocity placeholders; |
331 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
332 |
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333 |
mmeineke |
586 |
Atom **atoms = simnfo->atoms; |
334 |
mmeineke |
377 |
DirectionalAtom* dAtom; |
335 |
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|
336 |
gezelter |
419 |
int j, n_atoms, atomIndex; |
337 |
mmeineke |
377 |
|
338 |
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#ifdef IS_MPI |
339 |
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n_atoms = mpiSim->getTotAtoms(); |
340 |
gezelter |
419 |
atomIndex=-1; |
341 |
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for (j=0; j < mpiSim->getMyNlocal(); j++) { |
342 |
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if (atoms[j]->getGlobalIndex() == globalIndex) atomIndex = j; |
343 |
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} |
344 |
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if (atomIndex == -1) { |
345 |
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sprintf( painCave.errMsg, |
346 |
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"Initialize from file error. Atom at index %d " |
347 |
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"in file %s does not exist on processor %d .\n", |
348 |
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globalIndex, c_in_name, mpiSim->getMyNode() ); |
349 |
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return strdup( painCave.errMsg ); |
350 |
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} |
351 |
mmeineke |
377 |
#else |
352 |
mmeineke |
586 |
n_atoms = simnfo->n_atoms; |
353 |
gezelter |
419 |
atomIndex = globalIndex; |
354 |
mmeineke |
377 |
#endif // is_mpi |
355 |
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|
356 |
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// set the string tokenizer |
357 |
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358 |
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foo = strtok(readLine, " ,;\t"); |
359 |
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360 |
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// check the atom name to the current atom |
361 |
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362 |
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if( strcmp( foo, atoms[atomIndex]->getType() ) ){ |
363 |
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sprintf( painCave.errMsg, |
364 |
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"Initialize from file error. Atom %s at index %d " |
365 |
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"in file %s does not" |
366 |
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" match the BASS atom %s.\n", |
367 |
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foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
368 |
|
|
return strdup( painCave.errMsg ); |
369 |
|
|
} |
370 |
|
|
|
371 |
|
|
// get the positions |
372 |
|
|
|
373 |
|
|
foo = strtok(NULL, " ,;\t"); |
374 |
|
|
if(foo == NULL){ |
375 |
|
|
sprintf( painCave.errMsg, |
376 |
|
|
"error in reading postition x from %s\n" |
377 |
|
|
"natoms = %d, index = %d\n", |
378 |
|
|
c_in_name, n_atoms, atomIndex ); |
379 |
|
|
return strdup( painCave.errMsg ); |
380 |
|
|
} |
381 |
mmeineke |
670 |
pos[0] = atof( foo ); |
382 |
mmeineke |
377 |
|
383 |
|
|
foo = strtok(NULL, " ,;\t"); |
384 |
|
|
if(foo == NULL){ |
385 |
|
|
sprintf( painCave.errMsg, |
386 |
|
|
"error in reading postition y from %s\n" |
387 |
|
|
"natoms = %d, index = %d\n", |
388 |
|
|
c_in_name, n_atoms, atomIndex ); |
389 |
|
|
return strdup( painCave.errMsg ); |
390 |
|
|
} |
391 |
mmeineke |
670 |
pos[1] = atof( foo ); |
392 |
mmeineke |
377 |
|
393 |
|
|
foo = strtok(NULL, " ,;\t"); |
394 |
|
|
if(foo == NULL){ |
395 |
|
|
sprintf( painCave.errMsg, |
396 |
|
|
"error in reading postition z from %s\n" |
397 |
|
|
"natoms = %d, index = %d\n", |
398 |
|
|
c_in_name, n_atoms, atomIndex ); |
399 |
|
|
return strdup( painCave.errMsg ); |
400 |
|
|
} |
401 |
mmeineke |
670 |
pos[2] = atof( foo ); |
402 |
mmeineke |
377 |
|
403 |
|
|
|
404 |
|
|
// get the velocities |
405 |
|
|
|
406 |
|
|
foo = strtok(NULL, " ,;\t"); |
407 |
|
|
if(foo == NULL){ |
408 |
|
|
sprintf( painCave.errMsg, |
409 |
|
|
"error in reading velocity x from %s\n" |
410 |
|
|
"natoms = %d, index = %d\n", |
411 |
|
|
c_in_name, n_atoms, atomIndex ); |
412 |
|
|
return strdup( painCave.errMsg ); |
413 |
|
|
} |
414 |
mmeineke |
670 |
vel[0] = atof( foo ); |
415 |
mmeineke |
377 |
|
416 |
|
|
foo = strtok(NULL, " ,;\t"); |
417 |
|
|
if(foo == NULL){ |
418 |
|
|
sprintf( painCave.errMsg, |
419 |
|
|
"error in reading velocity y from %s\n" |
420 |
|
|
"natoms = %d, index = %d\n", |
421 |
|
|
c_in_name, n_atoms, atomIndex ); |
422 |
|
|
return strdup( painCave.errMsg ); |
423 |
|
|
} |
424 |
mmeineke |
670 |
vel[1] = atof( foo ); |
425 |
mmeineke |
377 |
|
426 |
|
|
foo = strtok(NULL, " ,;\t"); |
427 |
|
|
if(foo == NULL){ |
428 |
|
|
sprintf( painCave.errMsg, |
429 |
|
|
"error in reading velocity z from %s\n" |
430 |
|
|
"natoms = %d, index = %d\n", |
431 |
|
|
c_in_name, n_atoms, atomIndex ); |
432 |
|
|
return strdup( painCave.errMsg ); |
433 |
|
|
} |
434 |
mmeineke |
670 |
vel[2] = atof( foo ); |
435 |
mmeineke |
377 |
|
436 |
|
|
|
437 |
|
|
// get the quaternions |
438 |
|
|
|
439 |
|
|
if( atoms[atomIndex]->isDirectional() ){ |
440 |
|
|
|
441 |
|
|
foo = strtok(NULL, " ,;\t"); |
442 |
|
|
if(foo == NULL){ |
443 |
|
|
sprintf(painCave.errMsg, |
444 |
|
|
"error in reading quaternion 0 from %s\n" |
445 |
|
|
"natoms = %d, index = %d\n", |
446 |
|
|
c_in_name, n_atoms, atomIndex ); |
447 |
|
|
return strdup( painCave.errMsg ); |
448 |
|
|
} |
449 |
|
|
q[0] = atof( foo ); |
450 |
|
|
|
451 |
|
|
foo = strtok(NULL, " ,;\t"); |
452 |
|
|
if(foo == NULL){ |
453 |
|
|
sprintf( painCave.errMsg, |
454 |
|
|
"error in reading quaternion 1 from %s\n" |
455 |
|
|
"natoms = %d, index = %d\n", |
456 |
|
|
c_in_name, n_atoms, atomIndex ); |
457 |
|
|
return strdup( painCave.errMsg ); |
458 |
|
|
} |
459 |
|
|
q[1] = atof( foo ); |
460 |
|
|
|
461 |
|
|
foo = strtok(NULL, " ,;\t"); |
462 |
|
|
if(foo == NULL){ |
463 |
|
|
sprintf( painCave.errMsg, |
464 |
|
|
"error in reading quaternion 2 from %s\n" |
465 |
|
|
"natoms = %d, index = %d\n", |
466 |
|
|
c_in_name, n_atoms, atomIndex ); |
467 |
|
|
return strdup( painCave.errMsg ); |
468 |
|
|
} |
469 |
|
|
q[2] = atof( foo ); |
470 |
|
|
|
471 |
|
|
foo = strtok(NULL, " ,;\t"); |
472 |
|
|
if(foo == NULL){ |
473 |
|
|
sprintf( painCave.errMsg, |
474 |
|
|
"error in reading quaternion 3 from %s\n" |
475 |
|
|
"natoms = %d, index = %d\n", |
476 |
|
|
c_in_name, n_atoms, atomIndex ); |
477 |
|
|
return strdup( painCave.errMsg ); |
478 |
|
|
} |
479 |
|
|
q[3] = atof( foo ); |
480 |
|
|
|
481 |
|
|
// get the angular velocities |
482 |
|
|
|
483 |
|
|
foo = strtok(NULL, " ,;\t"); |
484 |
|
|
if(foo == NULL){ |
485 |
|
|
sprintf( painCave.errMsg, |
486 |
|
|
"error in reading angular momentum jx from %s\n" |
487 |
|
|
"natoms = %d, index = %d\n", |
488 |
|
|
c_in_name, n_atoms, atomIndex ); |
489 |
|
|
return strdup( painCave.errMsg ); |
490 |
|
|
} |
491 |
|
|
jx = atof( foo ); |
492 |
|
|
|
493 |
|
|
foo = strtok(NULL, " ,;\t"); |
494 |
|
|
if(foo == NULL){ |
495 |
|
|
sprintf( painCave.errMsg, |
496 |
|
|
"error in reading angular momentum jy from %s\n" |
497 |
|
|
"natoms = %d, index = %d\n", |
498 |
|
|
c_in_name, n_atoms, atomIndex ); |
499 |
|
|
return strdup( painCave.errMsg ); |
500 |
|
|
} |
501 |
|
|
jy = atof(foo ); |
502 |
|
|
|
503 |
|
|
foo = strtok(NULL, " ,;\t"); |
504 |
|
|
if(foo == NULL){ |
505 |
|
|
sprintf( painCave.errMsg, |
506 |
|
|
"error in reading angular momentum jz from %s\n" |
507 |
|
|
"natoms = %d, index = %d\n", |
508 |
|
|
c_in_name, n_atoms, atomIndex ); |
509 |
|
|
return strdup( painCave.errMsg ); |
510 |
|
|
} |
511 |
|
|
jz = atof( foo ); |
512 |
|
|
|
513 |
|
|
dAtom = ( DirectionalAtom* )atoms[atomIndex]; |
514 |
|
|
|
515 |
|
|
// check that the quaternion vector is normalized |
516 |
|
|
|
517 |
|
|
qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]); |
518 |
|
|
|
519 |
|
|
qLength = sqrt( qSqr ); |
520 |
|
|
q[0] = q[0] / qLength; |
521 |
|
|
q[1] = q[1] / qLength; |
522 |
|
|
q[2] = q[2] / qLength; |
523 |
|
|
q[3] = q[3] / qLength; |
524 |
|
|
|
525 |
|
|
dAtom->setQ( q ); |
526 |
|
|
|
527 |
|
|
// add the angular velocities |
528 |
|
|
|
529 |
|
|
dAtom->setJx( jx ); |
530 |
|
|
dAtom->setJy( jy ); |
531 |
|
|
dAtom->setJz( jz ); |
532 |
|
|
} |
533 |
|
|
|
534 |
|
|
// add the positions and velocities to the atom |
535 |
|
|
|
536 |
mmeineke |
670 |
atoms[atomIndex]->setPos( pos ); |
537 |
|
|
atoms[atomIndex]->setVel( vel ); |
538 |
mmeineke |
377 |
|
539 |
|
|
return NULL; |
540 |
|
|
} |
541 |
chuckv |
436 |
|
542 |
|
|
|
543 |
mmeineke |
644 |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
544 |
|
|
double &time ){ |
545 |
mmeineke |
586 |
|
546 |
|
|
char *foo; // the pointer to the current string token |
547 |
|
|
int j; |
548 |
|
|
|
549 |
|
|
// set the string tokenizer |
550 |
|
|
|
551 |
|
|
foo = strtok(readLine, " ,;\t"); |
552 |
mmeineke |
641 |
// set the timeToken. |
553 |
mmeineke |
586 |
|
554 |
mmeineke |
641 |
if(foo == NULL){ |
555 |
|
|
sprintf( painCave.errMsg, |
556 |
|
|
"error in reading Time from %s\n", |
557 |
|
|
c_in_name ); |
558 |
|
|
return strdup( painCave.errMsg ); |
559 |
|
|
} |
560 |
mmeineke |
644 |
time = atof( foo ); |
561 |
mmeineke |
586 |
|
562 |
|
|
// get the Hx vector |
563 |
|
|
|
564 |
|
|
foo = strtok(NULL, " ,;\t"); |
565 |
|
|
if(foo == NULL){ |
566 |
|
|
sprintf( painCave.errMsg, |
567 |
|
|
"error in reading Hx[0] from %s\n", |
568 |
|
|
c_in_name ); |
569 |
|
|
return strdup( painCave.errMsg ); |
570 |
|
|
} |
571 |
|
|
boxMat[0] = atof( foo ); |
572 |
|
|
|
573 |
|
|
foo = strtok(NULL, " ,;\t"); |
574 |
|
|
if(foo == NULL){ |
575 |
|
|
sprintf( painCave.errMsg, |
576 |
|
|
"error in reading Hx[1] from %s\n", |
577 |
|
|
c_in_name ); |
578 |
|
|
return strdup( painCave.errMsg ); |
579 |
|
|
} |
580 |
|
|
boxMat[1] = atof( foo ); |
581 |
|
|
|
582 |
|
|
foo = strtok(NULL, " ,;\t"); |
583 |
|
|
if(foo == NULL){ |
584 |
|
|
sprintf( painCave.errMsg, |
585 |
|
|
"error in reading Hx[2] from %s\n", |
586 |
|
|
c_in_name ); |
587 |
|
|
return strdup( painCave.errMsg ); |
588 |
|
|
} |
589 |
|
|
boxMat[2] = atof( foo ); |
590 |
|
|
|
591 |
|
|
// get the Hy vector |
592 |
|
|
|
593 |
|
|
foo = strtok(NULL, " ,;\t"); |
594 |
|
|
if(foo == NULL){ |
595 |
|
|
sprintf( painCave.errMsg, |
596 |
|
|
"error in reading Hy[0] from %s\n", |
597 |
|
|
c_in_name ); |
598 |
|
|
return strdup( painCave.errMsg ); |
599 |
|
|
} |
600 |
|
|
boxMat[3] = atof( foo ); |
601 |
|
|
|
602 |
|
|
foo = strtok(NULL, " ,;\t"); |
603 |
|
|
if(foo == NULL){ |
604 |
|
|
sprintf( painCave.errMsg, |
605 |
|
|
"error in reading Hy[1] from %s\n", |
606 |
|
|
c_in_name ); |
607 |
|
|
return strdup( painCave.errMsg ); |
608 |
|
|
} |
609 |
|
|
boxMat[4] = atof( foo ); |
610 |
|
|
|
611 |
|
|
foo = strtok(NULL, " ,;\t"); |
612 |
|
|
if(foo == NULL){ |
613 |
|
|
sprintf( painCave.errMsg, |
614 |
|
|
"error in reading Hy[2] from %s\n", |
615 |
|
|
c_in_name ); |
616 |
|
|
return strdup( painCave.errMsg ); |
617 |
|
|
} |
618 |
|
|
boxMat[5] = atof( foo ); |
619 |
|
|
|
620 |
|
|
// get the Hz vector |
621 |
|
|
|
622 |
|
|
foo = strtok(NULL, " ,;\t"); |
623 |
|
|
if(foo == NULL){ |
624 |
|
|
sprintf( painCave.errMsg, |
625 |
|
|
"error in reading Hz[0] from %s\n", |
626 |
|
|
c_in_name ); |
627 |
|
|
return strdup( painCave.errMsg ); |
628 |
|
|
} |
629 |
|
|
boxMat[6] = atof( foo ); |
630 |
|
|
|
631 |
|
|
foo = strtok(NULL, " ,;\t"); |
632 |
|
|
if(foo == NULL){ |
633 |
|
|
sprintf( painCave.errMsg, |
634 |
|
|
"error in reading Hz[1] from %s\n", |
635 |
|
|
c_in_name ); |
636 |
|
|
return strdup( painCave.errMsg ); |
637 |
|
|
} |
638 |
|
|
boxMat[7] = atof( foo ); |
639 |
|
|
|
640 |
|
|
foo = strtok(NULL, " ,;\t"); |
641 |
|
|
if(foo == NULL){ |
642 |
|
|
sprintf( painCave.errMsg, |
643 |
|
|
"error in reading Hz[2] from %s\n", |
644 |
|
|
c_in_name ); |
645 |
|
|
return strdup( painCave.errMsg ); |
646 |
|
|
} |
647 |
|
|
boxMat[8] = atof( foo ); |
648 |
|
|
|
649 |
|
|
return NULL; |
650 |
|
|
} |
651 |
|
|
|
652 |
|
|
|
653 |
chuckv |
436 |
#ifdef IS_MPI |
654 |
|
|
|
655 |
|
|
// a couple of functions to let us escape the read loop |
656 |
|
|
|
657 |
mmeineke |
440 |
void initFile::nodeZeroError( void ){ |
658 |
chuckv |
436 |
int j, myStatus; |
659 |
|
|
|
660 |
|
|
myStatus = 0; |
661 |
|
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
662 |
mmeineke |
447 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
663 |
|
|
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
664 |
chuckv |
436 |
} |
665 |
|
|
|
666 |
|
|
|
667 |
|
|
MPI_Finalize(); |
668 |
|
|
exit (0); |
669 |
|
|
|
670 |
|
|
} |
671 |
|
|
|
672 |
mmeineke |
440 |
void initFile::anonymousNodeDie( void ){ |
673 |
chuckv |
436 |
|
674 |
|
|
MPI_Finalize(); |
675 |
|
|
exit (0); |
676 |
|
|
} |
677 |
|
|
|
678 |
|
|
#endif //is_mpi |