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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 475 by gezelter, Tue Apr 8 12:44:18 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 180 | Line 181 | void ExtendedSystem::AffineTransform( double oldBox[3]
181    percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
182    percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
183    
184 +  std::cerr << "ps = " << percentScale[0] <<" " << percentScale[1] << " " << percentScale[2] << "\n";
185 +
186 +
187    for (i=0; i < entry_plug->n_mol; i++) {
188      
189      molecules[i].getCOM(r);
190 <    
190 >
191      // find the minimum image coordinates of the molecular centers of mass:    
192      
193      boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
# Line 195 | Line 199 | void ExtendedSystem::AffineTransform( double oldBox[3]
199      boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
200        (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
201  
202 +
203 +    std::cerr << "boxNum = " << boxNum[0] << " " << boxNum[1] << " " << boxNum[2] << "\n";
204 +
205      rxi = r[0] - boxNum[0];
206      ryi = r[1] - boxNum[1];
207      rzi = r[2] - boxNum[2];

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