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root/group/trunk/OOPSE/libmdtools/ExtendedSystem.cpp
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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 475 by gezelter, Tue Apr 8 12:44:18 2003 UTC vs.
Revision 477 by gezelter, Tue Apr 8 14:34:30 2003 UTC

# Line 93 | Line 93 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
93    atoms = entry_plug->atoms;
94  
95    p_ext = targetPressure * p_units;
96 <  p_mol = p_int;
96 >  p_mol = p_int * p_units;
97  
98    entry_plug->getBox(oldBox);
99    volume = oldBox[0]*oldBox[1]*oldBox[2];
# Line 106 | Line 106 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
106    epsilonDot +=  dt * ((p_mol - p_ext) * volume /
107                         (tauRelax*tauRelax * kB * targetTemp) );
108  
109 –
110 –  std::cerr << "dt = " << dt << " tauRelax = " << tauRelax << " kB = " << kB << "targetTemp = " << targetTemp << "\n";
111 –
109    // determine the change in cell volume
110    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
111  
115 –  std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " scale = " << scale << "\n";
116 –
117 –
112    newBox[0] = oldBox[0] * scale;
113    newBox[1] = oldBox[1] * scale;
114    newBox[2] = oldBox[2] * scale;
# Line 133 | Line 127 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
127    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
128    zetaScale = zeta * dt;
129  
130 <  std::cerr << "zetaScale = " << zetaScale << "epsilonScale = " << epsilonScale <<  "\n";
130 >  std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
131    
132    // apply barostating and thermostating to velocities and angular momenta
133    for(i = 0; i < entry_plug->n_atoms; i++){
# Line 172 | Line 166 | void ExtendedSystem::AffineTransform( double oldBox[3]
166    double r[3];
167    double boxNum[3];
168    double percentScale[3];
169 +  double delta[3];
170    double rxi, ryi, rzi;
171  
172    molecules = entry_plug->molecules;
# Line 181 | Line 176 | void ExtendedSystem::AffineTransform( double oldBox[3]
176    percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
177    percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
178    
184 –  std::cerr << "ps = " << percentScale[0] <<" " << percentScale[1] << " " << percentScale[2] << "\n";
185 –
186 –
179    for (i=0; i < entry_plug->n_mol; i++) {
180      
181      molecules[i].getCOM(r);
# Line 199 | Line 191 | void ExtendedSystem::AffineTransform( double oldBox[3]
191      boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
192        (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
193  
202 –
203 –    std::cerr << "boxNum = " << boxNum[0] << " " << boxNum[1] << " " << boxNum[2] << "\n";
204 –
194      rxi = r[0] - boxNum[0];
195      ryi = r[1] - boxNum[1];
196      rzi = r[2] - boxNum[2];
# Line 211 | Line 200 | void ExtendedSystem::AffineTransform( double oldBox[3]
200      ryi += ryi*percentScale[1];
201      rzi += rzi*percentScale[2];
202  
203 <    r[0] = rxi + boxNum[0];
204 <    r[1] = ryi + boxNum[1];
205 <    r[2] = rzi + boxNum[2];
203 >    delta[0] = r[0] - (rxi + boxNum[0]);
204 >    delta[1] = r[1] - (ryi + boxNum[1]);
205 >    delta[2] = r[2] - (rzi + boxNum[2]);
206  
207 <    molecules[i].moveCOM(r);
207 >    molecules[i].moveCOM(delta);
208    }
209   }

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