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root/OpenMD/branches/development/src/io/RestReader.cpp
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Comparing branches/development/src/io/RestReader.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
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 279 | Line 280 | namespace OpenMD {
280  
281      int index = tokenizer.nextTokenAsInt();
282  
283 <    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
283 >    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
284  
285 <    if (integrableObject == NULL) {
285 >    if (sd == NULL) {
286        return;
287      }
288    
# Line 309 | Line 310 | namespace OpenMD {
310        }
311  
312        case 'q' : {
313 <        if (integrableObject->isDirectional()) {
313 >        if (sd->isDirectional()) {
314            
315            q[0] = tokenizer.nextTokenAsDouble();
316            q[1] = tokenizer.nextTokenAsDouble();
# Line 331 | Line 332 | namespace OpenMD {
332        }  
333        case 'j' : {
334          Vector3d ji;
335 <        if (integrableObject->isDirectional()) {
335 >        if (sd->isDirectional()) {
336            ji[0] = tokenizer.nextTokenAsDouble();
337            ji[1] = tokenizer.nextTokenAsDouble();
338            ji[2] = tokenizer.nextTokenAsDouble();
# Line 365 | Line 366 | namespace OpenMD {
366        all_pos_[index] = pos;      
367          
368        // is this io restrained?
369 <      GenericData* data = integrableObject->getPropertyByName("Restraint");
369 >      GenericData* data = sd->getPropertyByName("Restraint");
370        ObjectRestraint* oRest;
371        
372        if (data != NULL) {
# Line 376 | Line 377 | namespace OpenMD {
377              // an ObjectRestraint:
378            oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
379            if (oRest != NULL) {          
380 <            if (integrableObject->isDirectional()) {
380 >            if (sd->isDirectional()) {
381                oRest->setReferenceStructure(pos, q.toRotationMatrix3());
382              } else {                          
383                oRest->setReferenceStructure(pos);

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