| 1 |
#define _LARGEFILE_SOURCE64 |
| 2 |
#define _FILE_OFFSET_BITS 64 |
| 3 |
|
| 4 |
#include <sys/types.h> |
| 5 |
#include <sys/stat.h> |
| 6 |
|
| 7 |
#include <iostream> |
| 8 |
#include <math.h> |
| 9 |
|
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#include <stdio.h> |
| 11 |
#include <stdlib.h> |
| 12 |
#include <string.h> |
| 13 |
|
| 14 |
|
| 15 |
#include "io/ReadWrite.hpp" |
| 16 |
#include "utils/simError.h" |
| 17 |
|
| 18 |
#ifdef IS_MPI |
| 19 |
#include <mpi.h> |
| 20 |
#include "brains/mpiSimulation.hpp" |
| 21 |
#define TAKE_THIS_TAG_CHAR 0 |
| 22 |
#define TAKE_THIS_TAG_INT 1 |
| 23 |
#define TAKE_THIS_TAG_DOUBLE 2 |
| 24 |
#endif // is_mpi |
| 25 |
|
| 26 |
|
| 27 |
RestraintReader :: RestraintReader( SimInfo* the_simnfo ){ |
| 28 |
|
| 29 |
simnfo = the_simnfo; |
| 30 |
|
| 31 |
idealName = "idealCrystal.in"; |
| 32 |
|
| 33 |
isScanned = false; |
| 34 |
|
| 35 |
#ifdef IS_MPI |
| 36 |
if (worldRank == 0) { |
| 37 |
#endif |
| 38 |
|
| 39 |
inIdealFile = fopen(idealName, "r"); |
| 40 |
if(inIdealFile == NULL){ |
| 41 |
sprintf(painCave.errMsg, |
| 42 |
"Cannot open file: %s\n", idealName); |
| 43 |
painCave.isFatal = 1; |
| 44 |
simError(); |
| 45 |
} |
| 46 |
|
| 47 |
inIdealFileName = idealName; |
| 48 |
#ifdef IS_MPI |
| 49 |
} |
| 50 |
strcpy( checkPointMsg, "Restraint file opened for reading successfully." ); |
| 51 |
MPIcheckPoint(); |
| 52 |
#endif |
| 53 |
return; |
| 54 |
} |
| 55 |
|
| 56 |
RestraintReader :: ~RestraintReader( ){ |
| 57 |
#ifdef IS_MPI |
| 58 |
if (worldRank == 0) { |
| 59 |
#endif |
| 60 |
vector<fpos_t*>::iterator i; |
| 61 |
|
| 62 |
int error; |
| 63 |
error = fclose( inIdealFile ); |
| 64 |
if( error ){ |
| 65 |
sprintf( painCave.errMsg, |
| 66 |
"Error closing %s\n", inIdealFileName.c_str()); |
| 67 |
simError(); |
| 68 |
} |
| 69 |
|
| 70 |
for(i = framePos.begin(); i != framePos.end(); ++i) |
| 71 |
delete *i; |
| 72 |
framePos.clear(); |
| 73 |
|
| 74 |
#ifdef IS_MPI |
| 75 |
} |
| 76 |
strcpy( checkPointMsg, "Restraint file closed successfully." ); |
| 77 |
MPIcheckPoint(); |
| 78 |
#endif |
| 79 |
|
| 80 |
return; |
| 81 |
} |
| 82 |
|
| 83 |
|
| 84 |
void RestraintReader :: readIdealCrystal(){ |
| 85 |
|
| 86 |
int i; |
| 87 |
unsigned int j; |
| 88 |
|
| 89 |
#ifdef IS_MPI |
| 90 |
int done, which_node, which_atom; // loop counter |
| 91 |
#endif //is_mpi |
| 92 |
|
| 93 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 94 |
int nTotObjs; // the number of atoms |
| 95 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 96 |
|
| 97 |
char *eof_test; // ptr to see when we reach the end of the file |
| 98 |
char *parseErr; |
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|
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vector<StuntDouble*> integrableObjects; |
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|
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|
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#ifndef IS_MPI |
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|
| 105 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 106 |
if( eof_test == NULL ){ |
| 107 |
sprintf( painCave.errMsg, |
| 108 |
"RestraintReader error: error reading 1st line of \"%s\"\n", |
| 109 |
inIdealFileName.c_str() ); |
| 110 |
painCave.isFatal = 1; |
| 111 |
simError(); |
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} |
| 113 |
|
| 114 |
nTotObjs = atoi( read_buffer ); |
| 115 |
|
| 116 |
if( nTotObjs != simnfo->getTotIntegrableObjects() ){ |
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sprintf( painCave.errMsg, |
| 118 |
"RestraintReader error. %s nIntegrable, %d, " |
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"does not match the meta-data file's nIntegrable, %d.\n", |
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inIdealFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
| 121 |
painCave.isFatal = 1; |
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simError(); |
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} |
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|
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// skip over the comment line |
| 126 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 127 |
if(eof_test == NULL){ |
| 128 |
sprintf( painCave.errMsg, |
| 129 |
"error in reading commment in %s\n", inIdealFileName.c_str()); |
| 130 |
painCave.isFatal = 1; |
| 131 |
simError(); |
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} |
| 133 |
|
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// parse the ideal crystal lines |
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/* |
| 136 |
Note: we assume that there is a one-to-one correspondence between |
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integrable objects and lines in the idealCrystal.in file. Thermodynamic |
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integration is only supported for simple rigid bodies. |
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*/ |
| 140 |
for( i=0; i < simnfo->n_mol; i++){ |
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|
| 142 |
integrableObjects = (simnfo->molecules[i]).getIntegrableObjects(); |
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|
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for(j = 0; j < integrableObjects.size(); j++){ |
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|
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eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
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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" |
| 150 |
"natoms = %d; index = %d\n" |
| 151 |
"error reading the line from the file.\n", |
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inIdealFileName.c_str(), nTotObjs, i ); |
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painCave.isFatal = 1; |
| 154 |
simError(); |
| 155 |
} |
| 156 |
|
| 157 |
parseErr = parseIdealLine( read_buffer, integrableObjects[j]); |
| 158 |
if( parseErr != NULL ){ |
| 159 |
strcpy( painCave.errMsg, parseErr ); |
| 160 |
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. |
| 170 |
painCave.isEventLoop = 1; |
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|
| 172 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 173 |
int haveError; |
| 174 |
|
| 175 |
MPI_Status istatus; |
| 176 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
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int localIndex; |
| 178 |
int nCurObj; |
| 179 |
int nitems; |
| 180 |
|
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nTotObjs = simnfo->getTotIntegrableObjects(); |
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haveError = 0; |
| 183 |
if (worldRank == 0) { |
| 184 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 185 |
if( eof_test == NULL ){ |
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sprintf( painCave.errMsg, |
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"Error reading 1st line of %s \n ",inIdealFileName.c_str()); |
| 188 |
haveError = 1; |
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simError(); |
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} |
| 191 |
|
| 192 |
nitems = atoi( read_buffer ); |
| 193 |
|
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// Check to see that the number of integrable objects in the |
| 195 |
// intial configuration file is the same as derived from the |
| 196 |
// meta-data file. |
| 197 |
if( nTotObjs != nitems){ |
| 198 |
sprintf( painCave.errMsg, |
| 199 |
"RestraintReader Error. %s nIntegrable, %d, " |
| 200 |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 201 |
inIdealFileName.c_str(), nTotObjs, simnfo->getTotIntegrableObjects()); |
| 202 |
haveError= 1; |
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simError(); |
| 204 |
} |
| 205 |
|
| 206 |
// skip over the comment line |
| 207 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 208 |
if(eof_test == NULL){ |
| 209 |
sprintf( painCave.errMsg, |
| 210 |
"error in reading commment in %s\n", inIdealFileName.c_str()); |
| 211 |
haveError = 1; |
| 212 |
simError(); |
| 213 |
} |
| 214 |
|
| 215 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 216 |
which_node = MolToProcMap[i]; |
| 217 |
if(which_node == 0){ |
| 218 |
//molecules belong to master node |
| 219 |
|
| 220 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 221 |
|
| 222 |
if(localIndex == -1) { |
| 223 |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
| 224 |
haveError = 1; |
| 225 |
simError(); |
| 226 |
} |
| 227 |
|
| 228 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 229 |
for(j=0; j < integrableObjects.size(); j++){ |
| 230 |
|
| 231 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 232 |
if(eof_test == NULL){ |
| 233 |
sprintf(painCave.errMsg, |
| 234 |
"error in reading file %s\n" |
| 235 |
"natoms = %d; index = %d\n" |
| 236 |
"error reading the line from the file.\n", |
| 237 |
inIdealFileName.c_str(), nTotObjs, i ); |
| 238 |
haveError= 1; |
| 239 |
simError(); |
| 240 |
} |
| 241 |
|
| 242 |
if(haveError) nodeZeroError(); |
| 243 |
|
| 244 |
parseIdealLine(read_buffer, integrableObjects[j]); |
| 245 |
} |
| 246 |
} |
| 247 |
else{ |
| 248 |
//molecule belongs to slave nodes |
| 249 |
|
| 250 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 251 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 252 |
|
| 253 |
for(j=0; j < nCurObj; j++){ |
| 254 |
|
| 255 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inIdealFile); |
| 256 |
if(eof_test == NULL){ |
| 257 |
sprintf(painCave.errMsg, |
| 258 |
"error in reading file %s\n" |
| 259 |
"natoms = %d; index = %d\n" |
| 260 |
"error reading the line from the file.\n", |
| 261 |
inIdealFileName.c_str(), nTotObjs, i ); |
| 262 |
haveError= 1; |
| 263 |
simError(); |
| 264 |
} |
| 265 |
|
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if(haveError) nodeZeroError(); |
| 267 |
|
| 268 |
MPI_Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, |
| 269 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
| 270 |
} |
| 271 |
} |
| 272 |
} |
| 273 |
} |
| 274 |
else{ |
| 275 |
//actions taken at slave nodes |
| 276 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 277 |
which_node = MolToProcMap[i]; |
| 278 |
|
| 279 |
if(which_node == worldRank){ |
| 280 |
//molecule with global index i belongs to this processor |
| 281 |
|
| 282 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 283 |
|
| 284 |
if(localIndex == -1) { |
| 285 |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
| 286 |
haveError = 1; |
| 287 |
simError(); |
| 288 |
} |
| 289 |
|
| 290 |
integrableObjects = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 291 |
|
| 292 |
nCurObj = integrableObjects.size(); |
| 293 |
|
| 294 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 295 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 296 |
|
| 297 |
for(j = 0; j < integrableObjects.size(); j++){ |
| 298 |
|
| 299 |
MPI_Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, |
| 300 |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
| 301 |
|
| 302 |
parseErr = parseIdealLine(read_buffer, integrableObjects[j]); |
| 303 |
|
| 304 |
if( parseErr != NULL ){ |
| 305 |
strcpy( painCave.errMsg, parseErr ); |
| 306 |
simError(); |
| 307 |
} |
| 308 |
} |
| 309 |
} |
| 310 |
} |
| 311 |
} |
| 312 |
#endif |
| 313 |
} |
| 314 |
|
| 315 |
char* RestraintReader::parseIdealLine(char* readLine, StuntDouble* sd){ |
| 316 |
|
| 317 |
char *foo; // the pointer to the current string token |
| 318 |
|
| 319 |
double pos[3]; // position place holders |
| 320 |
double q[4]; // the quaternions |
| 321 |
double RfromQ[3][3]; // the rotation matrix |
| 322 |
double normalize; // to normalize the reference unit vector |
| 323 |
double uX, uY, uZ; // reference unit vector place holders |
| 324 |
|
| 325 |
// set the string tokenizer |
| 326 |
|
| 327 |
foo = strtok(readLine, " ,;\t"); |
| 328 |
|
| 329 |
// check the atom name to the current atom |
| 330 |
|
| 331 |
if( strcmp( foo, sd->getType() ) ){ |
| 332 |
sprintf( painCave.errMsg, |
| 333 |
"RestraintReader error. Does not" |
| 334 |
" match the meta-data atom %s.\n", |
| 335 |
sd->getType() ); |
| 336 |
return strdup( painCave.errMsg ); |
| 337 |
} |
| 338 |
|
| 339 |
// get the positions |
| 340 |
|
| 341 |
foo = strtok(NULL, " ,;\t"); |
| 342 |
if(foo == NULL){ |
| 343 |
sprintf( painCave.errMsg, |
| 344 |
"error in reading position x from %s\n", |
| 345 |
inIdealFileName.c_str()); |
| 346 |
return strdup( painCave.errMsg ); |
| 347 |
} |
| 348 |
pos[0] = atof( foo ); |
| 349 |
|
| 350 |
foo = strtok(NULL, " ,;\t"); |
| 351 |
if(foo == NULL){ |
| 352 |
sprintf( painCave.errMsg, |
| 353 |
"error in reading position y from %s\n", |
| 354 |
inIdealFileName.c_str()); |
| 355 |
return strdup( painCave.errMsg ); |
| 356 |
} |
| 357 |
pos[1] = atof( foo ); |
| 358 |
|
| 359 |
foo = strtok(NULL, " ,;\t"); |
| 360 |
if(foo == NULL){ |
| 361 |
sprintf( painCave.errMsg, |
| 362 |
"error in reading position z from %s\n", |
| 363 |
inIdealFileName.c_str()); |
| 364 |
return strdup( painCave.errMsg ); |
| 365 |
} |
| 366 |
pos[2] = atof( foo ); |
| 367 |
|
| 368 |
// store the positions in the stuntdouble as generic data doubles |
| 369 |
DoubleGenericData* refPosX = new DoubleGenericData(); |
| 370 |
refPosX->setID("refPosX"); |
| 371 |
refPosX->setData(pos[0]); |
| 372 |
sd->addProperty(refPosX); |
| 373 |
|
| 374 |
DoubleGenericData* refPosY = new DoubleGenericData(); |
| 375 |
refPosY->setID("refPosY"); |
| 376 |
refPosY->setData(pos[1]); |
| 377 |
sd->addProperty(refPosY); |
| 378 |
|
| 379 |
DoubleGenericData* refPosZ = new DoubleGenericData(); |
| 380 |
refPosZ->setID("refPosZ"); |
| 381 |
refPosZ->setData(pos[2]); |
| 382 |
sd->addProperty(refPosZ); |
| 383 |
|
| 384 |
// we don't need the velocities |
| 385 |
foo = strtok(NULL, " ,;\t"); |
| 386 |
foo = strtok(NULL, " ,;\t"); |
| 387 |
foo = strtok(NULL, " ,;\t"); |
| 388 |
|
| 389 |
if (!sd->isDirectional()) |
| 390 |
return NULL; |
| 391 |
|
| 392 |
// get the quaternions |
| 393 |
if( sd->isDirectional() ){ |
| 394 |
|
| 395 |
foo = strtok(NULL, " ,;\t"); |
| 396 |
if(foo == NULL){ |
| 397 |
sprintf( painCave.errMsg, |
| 398 |
"error in reading quaternion 0 from %s\n", |
| 399 |
inIdealFileName.c_str() ); |
| 400 |
return strdup( painCave.errMsg ); |
| 401 |
} |
| 402 |
q[0] = atof( foo ); |
| 403 |
|
| 404 |
foo = strtok(NULL, " ,;\t"); |
| 405 |
if(foo == NULL){ |
| 406 |
sprintf( painCave.errMsg, |
| 407 |
"error in reading quaternion 1 from %s\n", |
| 408 |
inIdealFileName.c_str() ); |
| 409 |
return strdup( painCave.errMsg ); |
| 410 |
} |
| 411 |
q[1] = atof( foo ); |
| 412 |
|
| 413 |
foo = strtok(NULL, " ,;\t"); |
| 414 |
if(foo == NULL){ |
| 415 |
sprintf( painCave.errMsg, |
| 416 |
"error in reading quaternion 2 from %s\n", |
| 417 |
inIdealFileName.c_str() ); |
| 418 |
return strdup( painCave.errMsg ); |
| 419 |
} |
| 420 |
q[2] = atof( foo ); |
| 421 |
|
| 422 |
foo = strtok(NULL, " ,;\t"); |
| 423 |
if(foo == NULL){ |
| 424 |
sprintf( painCave.errMsg, |
| 425 |
"error in reading quaternion 3 from %s\n", |
| 426 |
inIdealFileName.c_str() ); |
| 427 |
return strdup( painCave.errMsg ); |
| 428 |
} |
| 429 |
q[3] = atof( foo ); |
| 430 |
|
| 431 |
// now build the rotation matrix and find the unit vectors |
| 432 |
RfromQ[0][0] = q[0]*q[0] + q[1]*q[1] - q[2]*q[2] - q[3]*q[3]; |
| 433 |
RfromQ[0][1] = 2*(q[1]*q[2] + q[0]*q[3]); |
| 434 |
RfromQ[0][2] = 2*(q[1]*q[3] - q[0]*q[2]); |
| 435 |
RfromQ[1][0] = 2*(q[1]*q[2] - q[0]*q[3]); |
| 436 |
RfromQ[1][1] = q[0]*q[0] - q[1]*q[1] + q[2]*q[2] - q[3]*q[3]; |
| 437 |
RfromQ[1][2] = 2*(q[2]*q[3] + q[0]*q[1]); |
| 438 |
RfromQ[2][0] = 2*(q[1]*q[3] + q[0]*q[2]); |
| 439 |
RfromQ[2][1] = 2*(q[2]*q[3] - q[0]*q[1]); |
| 440 |
RfromQ[2][2] = q[0]*q[0] - q[1]*q[1] - q[2]*q[2] + q[3]*q[3]; |
| 441 |
|
| 442 |
normalize = sqrt(RfromQ[2][0]*RfromQ[2][0] + RfromQ[2][1]*RfromQ[2][1] |
| 443 |
+ RfromQ[2][2]*RfromQ[2][2]); |
| 444 |
uX = RfromQ[2][0]/normalize; |
| 445 |
uY = RfromQ[2][1]/normalize; |
| 446 |
uZ = RfromQ[2][2]/normalize; |
| 447 |
|
| 448 |
// store reference unit vectors as generic data in the stuntdouble |
| 449 |
DoubleGenericData* refVectorX = new DoubleGenericData(); |
| 450 |
refVectorX->setID("refVectorX"); |
| 451 |
refVectorX->setData(uX); |
| 452 |
sd->addProperty(refVectorX); |
| 453 |
|
| 454 |
DoubleGenericData* refVectorY = new DoubleGenericData(); |
| 455 |
refVectorY->setID("refVectorY"); |
| 456 |
refVectorY->setData(uY); |
| 457 |
sd->addProperty(refVectorY); |
| 458 |
|
| 459 |
DoubleGenericData* refVectorZ = new DoubleGenericData(); |
| 460 |
refVectorZ->setID("refVectorZ"); |
| 461 |
refVectorZ->setData(uZ); |
| 462 |
sd->addProperty(refVectorZ); |
| 463 |
} |
| 464 |
|
| 465 |
// we don't need the angular velocities, so let's exit the line |
| 466 |
return NULL; |
| 467 |
} |
| 468 |
|
| 469 |
#ifdef IS_MPI |
| 470 |
void RestraintReader::nodeZeroError( void ){ |
| 471 |
int j, myStatus; |
| 472 |
|
| 473 |
myStatus = 0; |
| 474 |
for (j = 0; j < mpiSim->getNProcessors(); j++) { |
| 475 |
MPI_Send( &myStatus, 1, MPI_INT, j, |
| 476 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 477 |
} |
| 478 |
|
| 479 |
|
| 480 |
MPI_Finalize(); |
| 481 |
exit (0); |
| 482 |
|
| 483 |
} |
| 484 |
|
| 485 |
void RestraintReader::anonymousNodeDie( void ){ |
| 486 |
|
| 487 |
MPI_Finalize(); |
| 488 |
exit (0); |
| 489 |
} |
| 490 |
#endif |
| 491 |
|
| 492 |
void RestraintReader::readZangle( const char *in_name ){ |
| 493 |
|
| 494 |
int i; |
| 495 |
unsigned int j; |
| 496 |
|
| 497 |
#ifdef IS_MPI |
| 498 |
int done, which_node, which_atom; // loop counter |
| 499 |
|
| 500 |
int *potatoes; |
| 501 |
int myPotato; |
| 502 |
|
| 503 |
int nProc; |
| 504 |
#endif //is_mpi |
| 505 |
|
| 506 |
const int BUFFERSIZE = 2000; // size of the read buffer |
| 507 |
int nTotObjs; // the number of atoms |
| 508 |
char read_buffer[BUFFERSIZE]; //the line buffer for reading |
| 509 |
|
| 510 |
char *eof_test; // ptr to see when we reach the end of the file |
| 511 |
char *parseErr; |
| 512 |
|
| 513 |
vector<StuntDouble*> vecParticles; |
| 514 |
vector<double> tempZangs; |
| 515 |
|
| 516 |
// open the omega value file for reading |
| 517 |
#ifdef IS_MPI |
| 518 |
if (worldRank == 0) { |
| 519 |
#endif |
| 520 |
|
| 521 |
inAngFile = fopen(in_name, "r"); |
| 522 |
if(!inAngFile){ |
| 523 |
sprintf(painCave.errMsg, |
| 524 |
"Restraints Warning: %s file is not present\n" |
| 525 |
"\tAll omega values will be initialized to zero. If the\n" |
| 526 |
"\tsimulation is starting from the idealCrystal.in reference\n" |
| 527 |
"\tconfiguration, this is the desired action. If this is not\n" |
| 528 |
"\tthe case, the energy calculations will be incorrect.\n", |
| 529 |
in_name); |
| 530 |
painCave.severity = OOPSE_WARNING; |
| 531 |
painCave.isFatal = 0; |
| 532 |
simError(); |
| 533 |
return; |
| 534 |
} |
| 535 |
|
| 536 |
inAngFileName = in_name; |
| 537 |
#ifdef IS_MPI |
| 538 |
} |
| 539 |
strcpy( checkPointMsg, "zAngle file opened successfully for reading." ); |
| 540 |
MPIcheckPoint(); |
| 541 |
#endif |
| 542 |
|
| 543 |
#ifndef IS_MPI |
| 544 |
|
| 545 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 546 |
if( eof_test == NULL ){ |
| 547 |
sprintf( painCave.errMsg, |
| 548 |
"RestraintReader error: error reading 1st line of \"%s\"\n", |
| 549 |
inAngFileName.c_str() ); |
| 550 |
painCave.isFatal = 1; |
| 551 |
simError(); |
| 552 |
} |
| 553 |
|
| 554 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 555 |
while ( eof_test != NULL ) { |
| 556 |
// check for and ignore blank lines |
| 557 |
if ( read_buffer != NULL ) |
| 558 |
tempZangs.push_back( atof(read_buffer) ); |
| 559 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 560 |
} |
| 561 |
|
| 562 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
| 563 |
|
| 564 |
if( nTotObjs != tempZangs.size() ){ |
| 565 |
sprintf( painCave.errMsg, |
| 566 |
"RestraintReader zAngle reading error. %s nIntegrable, %d, " |
| 567 |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 568 |
inAngFileName.c_str(), tempZangs.size(), nTotObjs ); |
| 569 |
painCave.isFatal = 1; |
| 570 |
simError(); |
| 571 |
} |
| 572 |
|
| 573 |
// load the zAngles into the integrable objects |
| 574 |
vecParticles = simnfo->integrableObjects; |
| 575 |
|
| 576 |
for ( i=0; i<vecParticles.size(); i++ ) { |
| 577 |
vecParticles[i]->setZangle(tempZangs[i]); |
| 578 |
} |
| 579 |
|
| 580 |
// MPI Section of code.......... |
| 581 |
#else //IS_MPI |
| 582 |
|
| 583 |
// first thing first, suspend fatalities. |
| 584 |
painCave.isEventLoop = 1; |
| 585 |
|
| 586 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 587 |
int haveError, index; |
| 588 |
|
| 589 |
MPI_Status istatus; |
| 590 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
| 591 |
int localIndex; |
| 592 |
int nCurObj; |
| 593 |
double angleTranfer; |
| 594 |
|
| 595 |
nTotObjs = simnfo->getTotIntegrableObjects(); |
| 596 |
haveError = 0; |
| 597 |
if (worldRank == 0) { |
| 598 |
|
| 599 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 600 |
if( eof_test == NULL ){ |
| 601 |
sprintf( painCave.errMsg, |
| 602 |
"Error reading 1st line of %s \n ",inAngFileName.c_str()); |
| 603 |
haveError = 1; |
| 604 |
simError(); |
| 605 |
} |
| 606 |
|
| 607 |
// let node 0 load the temporary angle vector |
| 608 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 609 |
while ( eof_test != NULL ) { |
| 610 |
// check for and ignore blank lines |
| 611 |
if ( read_buffer != NULL ) |
| 612 |
tempZangs.push_back( atof(read_buffer) ); |
| 613 |
eof_test = fgets(read_buffer, sizeof(read_buffer), inAngFile); |
| 614 |
} |
| 615 |
|
| 616 |
// Check to see that the number of integrable objects in the |
| 617 |
// intial configuration file is the same as derived from the |
| 618 |
// meta-data file. |
| 619 |
if( nTotObjs != tempZangs.size() ){ |
| 620 |
sprintf( painCave.errMsg, |
| 621 |
"RestraintReader zAngle reading Error. %s nIntegrable, %d, " |
| 622 |
"does not match the meta-data file's nIntegrable, %d.\n", |
| 623 |
inAngFileName.c_str(), tempZangs.size(), nTotObjs); |
| 624 |
haveError= 1; |
| 625 |
simError(); |
| 626 |
} |
| 627 |
|
| 628 |
} |
| 629 |
// At this point, node 0 has a tempZangs vector completed, and |
| 630 |
// everyone else has nada |
| 631 |
index = 0; |
| 632 |
|
| 633 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 634 |
// Get the Node number which has this atom |
| 635 |
which_node = MolToProcMap[i]; |
| 636 |
|
| 637 |
if (worldRank == 0) { |
| 638 |
if (which_node == 0) { |
| 639 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 640 |
|
| 641 |
if(localIndex == -1) { |
| 642 |
strcpy(painCave.errMsg, "Molecule not found on node 0!"); |
| 643 |
haveError = 1; |
| 644 |
simError(); |
| 645 |
} |
| 646 |
|
| 647 |
vecParticles = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 648 |
for(j = 0; j < vecParticles.size(); j++){ |
| 649 |
vecParticles[j]->setZangle(tempZangs[index]); |
| 650 |
index++; |
| 651 |
} |
| 652 |
|
| 653 |
// restraints is limited to a single zAngle per molecule |
| 654 |
vecParticles = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 655 |
for(j=0; j < vecParticles.size(); j++) |
| 656 |
vecParticles[j]->setZangle(tempZangs[i]); |
| 657 |
|
| 658 |
} else { |
| 659 |
// I am MASTER OF THE UNIVERSE, but I don't own this molecule |
| 660 |
|
| 661 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 662 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
| 663 |
|
| 664 |
for(j=0; j < nCurObj; j++){ |
| 665 |
angleTransfer = tempZangs[index]; |
| 666 |
MPI_Send(&angleTransfer, 1, MPI_DOUBLE, which_node, |
| 667 |
TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD); |
| 668 |
index++; |
| 669 |
} |
| 670 |
|
| 671 |
} |
| 672 |
|
| 673 |
} else { |
| 674 |
// I am SLAVE TO THE MASTER |
| 675 |
|
| 676 |
if (which_node == worldRank) { |
| 677 |
|
| 678 |
// BUT I OWN THIS MOLECULE!!! |
| 679 |
|
| 680 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 681 |
vecParticles = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 682 |
nCurObj = vecParticles.size(); |
| 683 |
|
| 684 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 685 |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 686 |
|
| 687 |
for(j = 0; j < vecParticles.size(); j++){ |
| 688 |
|
| 689 |
MPI_Recv(&angleTransfer, 1, MPI_DOUBLE, 0, |
| 690 |
TAKE_THIS_TAG_DOUBLE, MPI_COMM_WORLD, &istatus); |
| 691 |
vecParticles[j]->setZangle(angleTransfer); |
| 692 |
} |
| 693 |
} |
| 694 |
} |
| 695 |
} |
| 696 |
#endif |
| 697 |
} |
| 698 |
|
| 699 |
void RestraintReader :: zeroZangle(){ |
| 700 |
|
| 701 |
int i; |
| 702 |
unsigned int j; |
| 703 |
|
| 704 |
vector<StuntDouble*> vecParticles; |
| 705 |
|
| 706 |
#ifndef IS_MPI |
| 707 |
// set all zAngles to 0.0 |
| 708 |
vecParticles = simnfo->integrableObjects; |
| 709 |
|
| 710 |
for ( i=0; i<vecParticles.size(); i++ ) { |
| 711 |
vecParticles[i]->setZangle( 0.0 ); |
| 712 |
} |
| 713 |
|
| 714 |
// MPI Section of code.......... |
| 715 |
#else //IS_MPI |
| 716 |
|
| 717 |
// first thing first, suspend fatalities. |
| 718 |
painCave.isEventLoop = 1; |
| 719 |
|
| 720 |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
| 721 |
int haveError; |
| 722 |
|
| 723 |
MPI_Status istatus; |
| 724 |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
| 725 |
int localIndex; |
| 726 |
int which_node; |
| 727 |
|
| 728 |
haveError = 0; |
| 729 |
|
| 730 |
for (i=0 ; i < mpiSim->getNMolGlobal(); i++) { |
| 731 |
which_node = MolToProcMap[i]; |
| 732 |
|
| 733 |
if(which_node == worldRank){ |
| 734 |
//molecule with global index i belongs to this processor |
| 735 |
|
| 736 |
localIndex = mpiSim->getGlobalToLocalMol(i); |
| 737 |
|
| 738 |
if(localIndex == -1) { |
| 739 |
sprintf(painCave.errMsg, "Molecule not found on node %d\n", worldRank); |
| 740 |
haveError = 1; |
| 741 |
simError(); |
| 742 |
} |
| 743 |
|
| 744 |
vecParticles = (simnfo->molecules[localIndex]).getIntegrableObjects(); |
| 745 |
|
| 746 |
// set zAngle to 0.0 for all integrable objects |
| 747 |
for(j = 0; j < vecParticles.size(); j++){ |
| 748 |
vecParticles[j]->setZangle( 0.0 ); |
| 749 |
} |
| 750 |
} |
| 751 |
} |
| 752 |
#endif |
| 753 |
} |
