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root/OpenMD/branches/development/src/io/RestReader.cpp

Comparing:
trunk/src/io/RestReader.cpp (file contents), Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC vs.
branches/development/src/io/RestReader.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43
#	Line 191 | Line 192 | namespace OpenMD {
192
193		scanFile();
194
194	–
195		readSet();
196
197
#	Line 280 | Line 280 | namespace OpenMD {
280
281		int index = tokenizer.nextTokenAsInt();
282
283	+	StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284	+
285	+	if (sd == NULL) {
286	+	return;
287	+	}
288
289	<	if (index < 1116){
290	<	std::string type = tokenizer.nextToken();
291	<
292	<	Vector3d pos;
293	<
294	<	pos[0] = tokenizer.nextTokenAsDouble();
295	<	pos[1] = tokenizer.nextTokenAsDouble();
296	<	pos[2] = tokenizer.nextTokenAsDouble();
297	<
298	<	all_pos_[index] = pos;
294	<	}else{
295	<
296	<	bool exist = false;
297	<	int indexCount = 0;
298	<
299	<	while ( (!exist) && (indexCount < stuntDoubleIndex_.size())){
300	<	if (index == stuntDoubleIndex_[indexCount])
301	<	exist = true;
302	<	indexCount++;
303	<	}
304	<
305	<	StuntDouble* integrableObject;
306	<
307	<	if (exist){
308	<
309	<	integrableObject = info_->getIOIndexToIntegrableObject(index);
310	<
311	<	int compareindex = integrableObject->getGlobalIntegrableObjectIndex();
312	<
313	<	if (integrableObject == NULL) {
314	<	return;
315	<	}
316	<
317	<	std::string type = tokenizer.nextToken();
318	<
319	<	Vector3d pos;
320	<
289	>	std::string type = tokenizer.nextToken();
290	>	int size = type.size();
291	>
292	>	Vector3d pos;
293	>	Quat4d q;
294	>
295	>	for(int i = 0; i < size; ++i) {
296	>	switch(type[i]) {
297	>
298	>	case 'p': {
299		pos[0] = tokenizer.nextTokenAsDouble();
300		pos[1] = tokenizer.nextTokenAsDouble();
301		pos[2] = tokenizer.nextTokenAsDouble();
302	<
302	>	break;
303	>	}
304	>	case 'v' : {
305		Vector3d vel;
306		vel[0] = tokenizer.nextTokenAsDouble();
307		vel[1] = tokenizer.nextTokenAsDouble();
308		vel[2] = tokenizer.nextTokenAsDouble();
309	<
310	<
311	<	Quat4d q;
312	<	if (integrableObject->isDirectional()) {
309	>	break;
310	>	}
311	>
312	>	case 'q' : {
313	>	if (sd->isDirectional()) {
314
315		q[0] = tokenizer.nextTokenAsDouble();
316		q[1] = tokenizer.nextTokenAsDouble();
317		q[2] = tokenizer.nextTokenAsDouble();
318		q[3] = tokenizer.nextTokenAsDouble();
319	<	}
320	<	// keep the position in case we need it for a molecular restraint:
321	<
322	<	all_pos_[index] = pos;
323	<
324	<	// is this io restrained?
325	<	GenericData* data = integrableObject->getPropertyByName("Restraint");
326	<	ObjectRestraint* oRest;
319	>
320	>	RealType qlen = q.length();
321	>	if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
322	>
323	>	sprintf(painCave.errMsg,
324	>	"RestReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
325	>	painCave.isFatal = 1;
326	>	simError();
327	>	}
328	>
329	>	q.normalize();
330	>	}
331	>	break;
332	>	}
333	>	case 'j' : {
334	>	Vector3d ji;
335	>	if (sd->isDirectional()) {
336	>	ji[0] = tokenizer.nextTokenAsDouble();
337	>	ji[1] = tokenizer.nextTokenAsDouble();
338	>	ji[2] = tokenizer.nextTokenAsDouble();
339	>	}
340	>	break;
341	>	}
342	>	case 'f': {
343	>	Vector3d force;
344	>	force[0] = tokenizer.nextTokenAsDouble();
345	>	force[1] = tokenizer.nextTokenAsDouble();
346	>	force[2] = tokenizer.nextTokenAsDouble();
347	>	break;
348	>	}
349	>	case 't' : {
350	>	Vector3d torque;
351	>	torque[0] = tokenizer.nextTokenAsDouble();
352	>	torque[1] = tokenizer.nextTokenAsDouble();
353	>	torque[2] = tokenizer.nextTokenAsDouble();
354	>	break;
355	>	}
356	>	default: {
357	>	sprintf(painCave.errMsg,
358	>	"RestReader Error: %s is an unrecognized type\n", type.c_str());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	break;
362	>	}
363	>	}
364	>	// keep the position in case we need it for a molecular restraint:
365	>
366	>	all_pos_[index] = pos;
367
368	<	if (data != NULL) {
369	<	// make sure we can reinterpret the generic data as restraint data:
370	<	RestraintData* restData= dynamic_cast<RestraintData*>(data);
371	<	if (restData != NULL) {
372	<	// make sure we can reinterpet the restraint data as a pointer to
368	>	// is this io restrained?
369	>	GenericData* data = sd->getPropertyByName("Restraint");
370	>	ObjectRestraint* oRest;
371	>
372	>	if (data != NULL) {
373	>	// make sure we can reinterpret the generic data as restraint data:
374	>	RestraintData* restData= dynamic_cast<RestraintData*>(data);
375	>	if (restData != NULL) {
376	>	// make sure we can reinterpet the restraint data as a pointer to
377		// an ObjectRestraint:
378	<	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
379	<	if (oRest != NULL) {
380	<	if (integrableObject->isDirectional()) {
381	<	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
382	<	} else {
383	<	oRest->setReferenceStructure(pos);
359	<	}
378	>	oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
379	>	if (oRest != NULL) {
380	>	if (sd->isDirectional()) {
381	>	oRest->setReferenceStructure(pos, q.toRotationMatrix3());
382	>	} else {
383	>	oRest->setReferenceStructure(pos);
384		}
385		}
386		}

Comparing:
trunk/src/io/RestReader.cpp (property svn:keywords), Revision 1407 by cli2, Wed Jan 20 16:04:40 2010 UTC vs.
branches/development/src/io/RestReader.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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