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root/OpenMD/trunk/src/brains/Snapshot.cpp
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Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

# Line 70 | Line 70 | namespace OpenMD {
70      frameData.torsionPotential = 0.0;  
71      frameData.inversionPotential = 0.0;
72      frameData.lrPotentials = potVec(0.0);
73 +    frameData.reciprocalPotential = 0.0;
74      frameData.excludedPotentials = potVec(0.0);
75      frameData.restraintPotential = 0.0;
76      frameData.rawPotential = 0.0;  
# Line 103 | Line 104 | namespace OpenMD {
104      frameData.torsionPotential = 0.0;  
105      frameData.inversionPotential = 0.0;
106      frameData.lrPotentials = potVec(0.0);
107 +    frameData.reciprocalPotential = 0.0;
108      frameData.excludedPotentials = potVec(0.0);
109      frameData.restraintPotential = 0.0;
110      frameData.rawPotential = 0.0;      
# Line 296 | Line 298 | namespace OpenMD {
298      hasVolume = true;
299      frameData.volume = vol;
300    }
301 +
302  
303    /** Wrap a vector according to periodic boundary conditions */
304    void Snapshot::wrapVector(Vector3d& pos) {
305      
306      if( !frameData.orthoRhombic ) {
307        Vector3d scaled = frameData.invHmat * pos;
308 <      for (int i = 0; i < 3; i++)
309 <        scaled[i] -= roundMe(scaled[i]);
308 >      for (int i = 0; i < 3; i++) {
309 >        scaled[i] -= roundMe( scaled[i] );        
310 >      }
311        // calc the wrapped real coordinates from the wrapped scaled coordinates
312        pos = frameData.hmat * scaled;
313      } else {
310 –      // calc the scaled coordinates.
314        RealType scaled;
315 <      for (int i=0; i<3; i++) {
316 <        scaled = pos[i] * frameData.invHmat(i, i);
317 <        scaled -= roundMe(scaled);
318 <        pos[i] = scaled * frameData.hmat(i, i);
315 >      for (int i=0; i<3; i++) {      
316 >        scaled = pos[i] * frameData.invHmat(i,i);
317 >        scaled -= roundMe( scaled );
318 >        pos[i] = scaled * frameData.hmat(i,i);
319        }
320      }
321    }
322  
320 –
323    /** Scaling a vector to multiples of the periodic box */
324    inline Vector3d Snapshot::scaleVector(Vector3d& pos) {  
325      
# Line 414 | Line 416 | namespace OpenMD {
416      return frameData.shortRangePotential;
417    }
418  
419 +  void Snapshot::setReciprocalPotential(RealType rp){
420 +    frameData.reciprocalPotential = rp;
421 +  }
422 +
423 +  RealType Snapshot::getReciprocalPotential() {
424 +    return frameData.reciprocalPotential;
425 +  }
426 +
427    void Snapshot::setLongRangePotential(potVec lrPot) {
428      frameData.lrPotentials = lrPot;
429    }
# Line 423 | Line 433 | namespace OpenMD {
433        for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
434          frameData.longRangePotential += frameData.lrPotentials[i];
435        }
436 +      frameData.longRangePotential += frameData.reciprocalPotential;
437        hasLongRangePotential = true;
438      }  
439      return frameData.longRangePotential;

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