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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 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 –
99    volume = oldBox[0]*oldBox[1]*oldBox[2];
100  
101    ke_temp = ke * e_convert;
# Line 107 | Line 106 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
106    epsilonDot +=  dt * ((p_mol - p_ext) * volume /
107                         (tauRelax*tauRelax * kB * targetTemp) );
108  
110 –
111 –  std::cerr << "p_mol = " << p_mol << " p_ext = " << p_ext << " volume = " << volume << " tauRelax = " << tauRelax << "\n";
112 –
113 –
109    // determine the change in cell volume
110    scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
111  
# Line 132 | 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 171 | 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 183 | Line 179 | void ExtendedSystem::AffineTransform( double oldBox[3]
179    for (i=0; i < entry_plug->n_mol; i++) {
180      
181      molecules[i].getCOM(r);
182 <    
182 >
183      // find the minimum image coordinates of the molecular centers of mass:    
184      
185      boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
# Line 204 | 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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