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#ifdef IS_MPI |
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#include <mpi.h> |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
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#define TAKE_THIS_TAG_CHAR 0 |
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#define TAKE_THIS_TAG_INT 1 |
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|
20 |
< |
void nodeZeroError( void ); |
21 |
< |
void anonymousNodeDie( void ); |
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> |
namespace initFile{ |
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> |
void nodeZeroError( void ); |
22 |
> |
void anonymousNodeDie( void ); |
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> |
} |
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|
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+ |
using namespace initFile; |
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|
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#endif // is_mpi |
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|
29 |
< |
InitializeFromFile :: InitializeFromFile( char *in_name ){ |
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> |
InitializeFromFile::InitializeFromFile( char *in_name ){ |
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> |
|
31 |
> |
std::cerr << "Hello from Initialize from file.\n"; |
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> |
|
33 |
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#ifdef IS_MPI |
34 |
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if (worldRank == 0) { |
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#endif |
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return; |
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} |
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|
54 |
< |
InitializeFromFile :: ~InitializeFromFile( ){ |
54 |
> |
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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} |
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|
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|
75 |
< |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
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> |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
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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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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; |
89 |
+ |
double currTime; |
90 |
+ |
double boxMat[9]; |
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+ |
double theBoxMat3[3][3]; |
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|
93 |
< |
entry_plug = the_entry_plug; |
93 |
> |
simnfo = the_simnfo; |
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|
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|
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#ifndef IS_MPI |
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n_atoms = atoi( read_buffer ); |
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|
108 |
< |
Atom **atoms = entry_plug->atoms; |
108 |
> |
Atom **atoms = simnfo->atoms; |
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DirectionalAtom* dAtom; |
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|
111 |
< |
if( n_atoms != entry_plug->n_atoms ){ |
111 |
> |
if( n_atoms != simnfo->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", |
115 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
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> |
c_in_name, n_atoms, simnfo->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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//read the box mat from 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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simError(); |
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} |
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|
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parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
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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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|
137 |
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for(i=0;i<3;i++) |
138 |
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for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
139 |
+ |
|
140 |
+ |
simnfo->setBoxM( theBoxMat3 ); |
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simnfo->setTime( currTime ); |
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|
143 |
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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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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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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; |
176 |
> |
MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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n_atoms = atoi( read_buffer ); |
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193 |
< |
Atom **atoms = entry_plug->atoms; |
193 |
> |
Atom **atoms = simnfo->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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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", |
203 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
203 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
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haveError= 1; |
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simError(); |
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} |
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< |
//read and toss the comment line |
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//read the boxMat from the comment line |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
211 |
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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; |
214 |
> |
haveError = 1; |
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simError(); |
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} |
217 |
+ |
|
218 |
+ |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
219 |
+ |
if( parseErr != NULL ){ |
220 |
+ |
strcpy( painCave.errMsg, parseErr ); |
221 |
+ |
haveError = 1; |
222 |
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simError(); |
223 |
+ |
} |
224 |
+ |
|
225 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
226 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
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|
228 |
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if(haveError) nodeZeroError(); |
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else { |
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|
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myStatus = 1; |
260 |
< |
MPI::COMM_WORLD.Send(&myStatus, 1, MPI_INT, which_node, |
261 |
< |
TAKE_THIS_TAG_INT); |
262 |
< |
MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
263 |
< |
TAKE_THIS_TAG_CHAR); |
264 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT); |
265 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, istatus); |
260 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
261 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
262 |
> |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
263 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
264 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
265 |
> |
MPI_COMM_WORLD); |
266 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
267 |
> |
MPI_COMM_WORLD, &istatus); |
268 |
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|
269 |
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if(!myStatus) nodeZeroError(); |
270 |
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} |
271 |
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} |
272 |
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myStatus = -1; |
273 |
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for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
274 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
275 |
< |
TAKE_THIS_TAG_INT); |
274 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
275 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
276 |
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} |
277 |
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|
278 |
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} else { |
279 |
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|
280 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
281 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
282 |
+ |
|
283 |
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done = 0; |
284 |
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while (!done) { |
285 |
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|
286 |
< |
MPI::COMM_WORLD.Recv(&myStatus, 1, MPI_INT, 0, |
287 |
< |
TAKE_THIS_TAG_INT, istatus); |
286 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
287 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
288 |
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|
289 |
|
if(!myStatus) anonymousNodeDie(); |
290 |
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|
291 |
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if(myStatus < 0) break; |
292 |
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|
293 |
< |
MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
294 |
< |
TAKE_THIS_TAG_CHAR, istatus); |
295 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
296 |
< |
TAKE_THIS_TAG_INT, istatus); |
293 |
> |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
294 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
295 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
296 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
297 |
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|
298 |
|
myStatus = 1; |
299 |
|
parseErr = parseDumpLine( read_buffer, which_atom ); |
303 |
|
simError(); |
304 |
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} |
305 |
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|
306 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, 0, |
307 |
< |
TAKE_THIS_TAG_INT); |
306 |
> |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
307 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
308 |
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|
309 |
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} |
310 |
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} |
311 |
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|
312 |
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// last thing last, enable fatalities. |
313 |
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painCave.isEventLoop = 0; |
314 |
+ |
|
315 |
+ |
for(i=0;i<3;i++) |
316 |
+ |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
317 |
+ |
|
318 |
+ |
simnfo->setBoxM( theBoxMat3 ); |
319 |
+ |
simnfo->setTime( currTime ); |
320 |
+ |
|
321 |
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|
322 |
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#endif |
323 |
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} |
326 |
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|
327 |
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char *foo; // the pointer to the current string token |
328 |
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|
329 |
< |
double rx, ry, rz; // position place holders |
330 |
< |
double vx, vy, vz; // velocity placeholders |
329 |
> |
double pos[3]; // position place holders |
330 |
> |
double vel[3]; // velocity placeholders |
331 |
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double q[4]; // the quaternions |
332 |
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double jx, jy, jz; // angular velocity placeholders; |
333 |
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double qSqr, qLength; // needed to normalize the quaternion vector. |
334 |
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|
335 |
< |
Atom **atoms = entry_plug->atoms; |
335 |
> |
Atom **atoms = simnfo->atoms; |
336 |
|
DirectionalAtom* dAtom; |
337 |
|
|
338 |
|
int j, n_atoms, atomIndex; |
351 |
|
return strdup( painCave.errMsg ); |
352 |
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} |
353 |
|
#else |
354 |
< |
n_atoms = entry_plug->n_atoms; |
354 |
> |
n_atoms = simnfo->n_atoms; |
355 |
|
atomIndex = globalIndex; |
356 |
|
#endif // is_mpi |
357 |
|
|
380 |
|
c_in_name, n_atoms, atomIndex ); |
381 |
|
return strdup( painCave.errMsg ); |
382 |
|
} |
383 |
< |
rx = atof( foo ); |
383 |
> |
pos[0] = atof( foo ); |
384 |
|
|
385 |
|
foo = strtok(NULL, " ,;\t"); |
386 |
|
if(foo == NULL){ |
390 |
|
c_in_name, n_atoms, atomIndex ); |
391 |
|
return strdup( painCave.errMsg ); |
392 |
|
} |
393 |
< |
ry = atof( foo ); |
393 |
> |
pos[1] = atof( foo ); |
394 |
|
|
395 |
|
foo = strtok(NULL, " ,;\t"); |
396 |
|
if(foo == NULL){ |
400 |
|
c_in_name, n_atoms, atomIndex ); |
401 |
|
return strdup( painCave.errMsg ); |
402 |
|
} |
403 |
< |
rz = atof( foo ); |
403 |
> |
pos[2] = atof( foo ); |
404 |
|
|
405 |
|
|
406 |
|
// get the velocities |
413 |
|
c_in_name, n_atoms, atomIndex ); |
414 |
|
return strdup( painCave.errMsg ); |
415 |
|
} |
416 |
< |
vx = atof( foo ); |
416 |
> |
vel[0] = atof( foo ); |
417 |
|
|
418 |
|
foo = strtok(NULL, " ,;\t"); |
419 |
|
if(foo == NULL){ |
423 |
|
c_in_name, n_atoms, atomIndex ); |
424 |
|
return strdup( painCave.errMsg ); |
425 |
|
} |
426 |
< |
vy = atof( foo ); |
426 |
> |
vel[1] = atof( foo ); |
427 |
|
|
428 |
|
foo = strtok(NULL, " ,;\t"); |
429 |
|
if(foo == NULL){ |
433 |
|
c_in_name, n_atoms, atomIndex ); |
434 |
|
return strdup( painCave.errMsg ); |
435 |
|
} |
436 |
< |
vz = atof( foo ); |
436 |
> |
vel[2] = atof( foo ); |
437 |
|
|
438 |
|
|
439 |
|
// get the quaternions |
535 |
|
|
536 |
|
// add the positions and velocities to the atom |
537 |
|
|
538 |
< |
atoms[atomIndex]->setX( rx ); |
539 |
< |
atoms[atomIndex]->setY( ry ); |
495 |
< |
atoms[atomIndex]->setZ( rz ); |
496 |
< |
|
497 |
< |
atoms[atomIndex]->set_vx( vx ); |
498 |
< |
atoms[atomIndex]->set_vy( vy ); |
499 |
< |
atoms[atomIndex]->set_vz( vz ); |
538 |
> |
atoms[atomIndex]->setPos( pos ); |
539 |
> |
atoms[atomIndex]->setVel( vel ); |
540 |
|
|
541 |
|
return NULL; |
542 |
|
} |
543 |
|
|
544 |
|
|
545 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
546 |
+ |
double &time ){ |
547 |
+ |
|
548 |
+ |
char *foo; // the pointer to the current string token |
549 |
+ |
int j; |
550 |
+ |
|
551 |
+ |
// set the string tokenizer |
552 |
+ |
|
553 |
+ |
foo = strtok(readLine, " ,;\t"); |
554 |
+ |
// set the timeToken. |
555 |
+ |
|
556 |
+ |
if(foo == NULL){ |
557 |
+ |
sprintf( painCave.errMsg, |
558 |
+ |
"error in reading Time from %s\n", |
559 |
+ |
c_in_name ); |
560 |
+ |
return strdup( painCave.errMsg ); |
561 |
+ |
} |
562 |
+ |
time = atof( foo ); |
563 |
+ |
|
564 |
+ |
// get the Hx vector |
565 |
+ |
|
566 |
+ |
foo = strtok(NULL, " ,;\t"); |
567 |
+ |
if(foo == NULL){ |
568 |
+ |
sprintf( painCave.errMsg, |
569 |
+ |
"error in reading Hx[0] from %s\n", |
570 |
+ |
c_in_name ); |
571 |
+ |
return strdup( painCave.errMsg ); |
572 |
+ |
} |
573 |
+ |
boxMat[0] = atof( foo ); |
574 |
+ |
|
575 |
+ |
foo = strtok(NULL, " ,;\t"); |
576 |
+ |
if(foo == NULL){ |
577 |
+ |
sprintf( painCave.errMsg, |
578 |
+ |
"error in reading Hx[1] from %s\n", |
579 |
+ |
c_in_name ); |
580 |
+ |
return strdup( painCave.errMsg ); |
581 |
+ |
} |
582 |
+ |
boxMat[1] = atof( foo ); |
583 |
+ |
|
584 |
+ |
foo = strtok(NULL, " ,;\t"); |
585 |
+ |
if(foo == NULL){ |
586 |
+ |
sprintf( painCave.errMsg, |
587 |
+ |
"error in reading Hx[2] from %s\n", |
588 |
+ |
c_in_name ); |
589 |
+ |
return strdup( painCave.errMsg ); |
590 |
+ |
} |
591 |
+ |
boxMat[2] = atof( foo ); |
592 |
+ |
|
593 |
+ |
// get the Hy vector |
594 |
+ |
|
595 |
+ |
foo = strtok(NULL, " ,;\t"); |
596 |
+ |
if(foo == NULL){ |
597 |
+ |
sprintf( painCave.errMsg, |
598 |
+ |
"error in reading Hy[0] from %s\n", |
599 |
+ |
c_in_name ); |
600 |
+ |
return strdup( painCave.errMsg ); |
601 |
+ |
} |
602 |
+ |
boxMat[3] = atof( foo ); |
603 |
+ |
|
604 |
+ |
foo = strtok(NULL, " ,;\t"); |
605 |
+ |
if(foo == NULL){ |
606 |
+ |
sprintf( painCave.errMsg, |
607 |
+ |
"error in reading Hy[1] from %s\n", |
608 |
+ |
c_in_name ); |
609 |
+ |
return strdup( painCave.errMsg ); |
610 |
+ |
} |
611 |
+ |
boxMat[4] = atof( foo ); |
612 |
+ |
|
613 |
+ |
foo = strtok(NULL, " ,;\t"); |
614 |
+ |
if(foo == NULL){ |
615 |
+ |
sprintf( painCave.errMsg, |
616 |
+ |
"error in reading Hy[2] from %s\n", |
617 |
+ |
c_in_name ); |
618 |
+ |
return strdup( painCave.errMsg ); |
619 |
+ |
} |
620 |
+ |
boxMat[5] = atof( foo ); |
621 |
+ |
|
622 |
+ |
// get the Hz vector |
623 |
+ |
|
624 |
+ |
foo = strtok(NULL, " ,;\t"); |
625 |
+ |
if(foo == NULL){ |
626 |
+ |
sprintf( painCave.errMsg, |
627 |
+ |
"error in reading Hz[0] from %s\n", |
628 |
+ |
c_in_name ); |
629 |
+ |
return strdup( painCave.errMsg ); |
630 |
+ |
} |
631 |
+ |
boxMat[6] = atof( foo ); |
632 |
+ |
|
633 |
+ |
foo = strtok(NULL, " ,;\t"); |
634 |
+ |
if(foo == NULL){ |
635 |
+ |
sprintf( painCave.errMsg, |
636 |
+ |
"error in reading Hz[1] from %s\n", |
637 |
+ |
c_in_name ); |
638 |
+ |
return strdup( painCave.errMsg ); |
639 |
+ |
} |
640 |
+ |
boxMat[7] = atof( foo ); |
641 |
+ |
|
642 |
+ |
foo = strtok(NULL, " ,;\t"); |
643 |
+ |
if(foo == NULL){ |
644 |
+ |
sprintf( painCave.errMsg, |
645 |
+ |
"error in reading Hz[2] from %s\n", |
646 |
+ |
c_in_name ); |
647 |
+ |
return strdup( painCave.errMsg ); |
648 |
+ |
} |
649 |
+ |
boxMat[8] = atof( foo ); |
650 |
+ |
|
651 |
+ |
return NULL; |
652 |
+ |
} |
653 |
+ |
|
654 |
+ |
|
655 |
|
#ifdef IS_MPI |
656 |
|
|
657 |
|
// a couple of functions to let us escape the read loop |
658 |
|
|
659 |
< |
void nodeZeroError( void ){ |
659 |
> |
void initFile::nodeZeroError( void ){ |
660 |
|
int j, myStatus; |
661 |
|
|
662 |
|
myStatus = 0; |
663 |
|
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
664 |
< |
MPI::COMM_WORLD.Send( &myStatus, 1, MPI_INT, j, |
665 |
< |
TAKE_THIS_TAG_INT); |
664 |
> |
MPI_Send( &myStatus, 1, MPI_INT, j, |
665 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
666 |
|
} |
667 |
|
|
668 |
|
|
671 |
|
|
672 |
|
} |
673 |
|
|
674 |
< |
void anonymousNodeDie( void ){ |
674 |
> |
void initFile::anonymousNodeDie( void ){ |
675 |
|
|
676 |
|
MPI_Finalize(); |
677 |
|
exit (0); |