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root/group/trunk/OOPSE/libmdtools/ExtendedSystem.cpp
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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 476 by gezelter, Tue Apr 8 12:50:18 2003 UTC

# Line 96 | Line 96 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
96    p_mol = p_int;
97  
98    entry_plug->getBox(oldBox);
99 –
99    volume = oldBox[0]*oldBox[1]*oldBox[2];
100  
101    ke_temp = ke * e_convert;
# Line 108 | Line 107 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
107                         (tauRelax*tauRelax * kB * targetTemp) );
108  
109  
110 <  std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " volume = " << volume << " tauRelax = " << tauRelax << "\n";
110 >  std::cerr << "dt = " << dt << " tauRelax = " << tauRelax << " kB = " << kB << "targetTemp = " << targetTemp << "\n";
111  
113 –
112    // determine the change in cell volume
113    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
114  
115 +  std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
116 +
117 +
118    newBox[0] = oldBox[0] * scale;
119    newBox[1] = oldBox[1] * scale;
120    newBox[2] = oldBox[2] * scale;
# Line 171 | Line 172 | void ExtendedSystem::AffineTransform( double oldBox[3]
172    double r[3];
173    double boxNum[3];
174    double percentScale[3];
175 +  double delta[3];
176    double rxi, ryi, rzi;
177  
178    molecules = entry_plug->molecules;
# Line 183 | Line 185 | void ExtendedSystem::AffineTransform( double oldBox[3]
185    for (i=0; i < entry_plug->n_mol; i++) {
186      
187      molecules[i].getCOM(r);
188 <    
188 >
189      // find the minimum image coordinates of the molecular centers of mass:    
190      
191      boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
# Line 204 | Line 206 | void ExtendedSystem::AffineTransform( double oldBox[3]
206      ryi += ryi*percentScale[1];
207      rzi += rzi*percentScale[2];
208  
209 <    r[0] = rxi + boxNum[0];
210 <    r[1] = ryi + boxNum[1];
211 <    r[2] = rzi + boxNum[2];
209 >    delta[0] = r[0] - (rxi + boxNum[0]);
210 >    delta[1] = r[1] - (ryi + boxNum[1]);
211 >    delta[2] = r[2] - (rzi + boxNum[2]);
212  
213 <    molecules[i].moveCOM(r);
213 >    molecules[i].moveCOM(delta);
214    }
215   }

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