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root/group/trunk/OOPSE/libmdtools/ExtendedSystem.cpp
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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 477 by gezelter, Tue Apr 8 14:34:30 2003 UTC

# Line 10 | Line 10 | ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plu
10    // get what information we need from the SimInfo object
11    
12    entry_plug = the_entry_plug;
13 –  nAtoms = entry_plug->n_atoms;
14 –  atoms = entry_plug->atoms;
15 –  nMols = entry_plug->n_mol;
16 –  molecules = entry_plug->molecules;
17 –  nOriented = entry_plug->n_oriented;
18 –  ndf = entry_plug->ndf;
13    zeta = 0.0;
14    epsilonDot = 0.0;
21 –
15   }
16  
17   void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
# Line 32 | Line 25 | void ExtendedSystem::NoseHooverNVT( double dt, double
25    const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
26                                          // amu*Ang^2*fs^-2/K
27    DirectionalAtom* dAtom;    
28 +  atoms = entry_plug->atoms;
29  
36 –
30    ke_temp = ke * e_convert;
31 <  NkBT = (double)ndf * kB * targetTemp;
31 >  NkBT = (double)entry_plug->ndf * kB * targetTemp;
32  
33    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
34    // qmass is set in the parameter file
35  
36    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
37 +
38    zetaScale = zeta * dt;
39 +  
40 +  std::cerr << "zetaScale = " << zetaScale << "\n";
41  
42    // perform thermostat scaling on linear velocities and angular momentum
43 <  for(i = 0; i < nAtoms; i++){
43 >  for(i = 0; i < entry_plug->n_atoms; i++){
44      
45      vx = atoms[i]->get_vx();
46      vy = atoms[i]->get_vy();
47      vz = atoms[i]->get_vz();
48 <    
48 >
49      atoms[i]->set_vx(vx * (1.0 - zetaScale));
50      atoms[i]->set_vy(vy * (1.0 - zetaScale));
51      atoms[i]->set_vz(vz * (1.0 - zetaScale));
52    }
53 <  if( nOriented ){
53 >  if( entry_plug->n_oriented ){
54      
55 <    for( i=0; i < nAtoms; i++ ){
55 >    for( i=0; i < entry_plug->n_atoms; i++ ){
56        
57        if( atoms[i]->isDirectional() ){
58          
# Line 89 | Line 85 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
85    const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
86                                          // amu*Ang^2*fs^-2/K
87  
88 +  int i;
89    double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
90    double volume, p_mol;
91    double vx, vy, vz, jx, jy, jz;
92    DirectionalAtom* dAtom;
93 <  int i;
93 >  atoms = entry_plug->atoms;
94  
95    p_ext = targetPressure * p_units;
96    p_mol = p_int * p_units;
97  
98    entry_plug->getBox(oldBox);
102 –
99    volume = oldBox[0]*oldBox[1]*oldBox[2];
100  
101    ke_temp = ke * e_convert;
102 <  NkBT = (double)ndf * kB * targetTemp;
102 >  NkBT = (double)entry_plug->ndf * kB * targetTemp;
103  
104    // propogate the strain rate
105  
# Line 130 | Line 126 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
126  
127    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
128    zetaScale = zeta * dt;
129 +
130 +  std::cerr << "zetaScale = " << zetaScale << " epsilonScale = " << epsilonScale <<  "\n";
131    
132    // apply barostating and thermostating to velocities and angular momenta
133 <  for(i = 0; i < nAtoms; i++){
133 >  for(i = 0; i < entry_plug->n_atoms; i++){
134      
135      vx = atoms[i]->get_vx();
136      vy = atoms[i]->get_vy();
# Line 142 | Line 140 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
140      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
141      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
142    }
143 <  if( nOriented ){
143 >  if( entry_plug->n_oriented ){
144      
145 <    for( i=0; i < nAtoms; i++ ){
145 >    for( i=0; i < entry_plug->n_atoms; i++ ){
146        
147        if( atoms[i]->isDirectional() ){
148          
# Line 168 | 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;
173      
174    // first determine the scaling factor from the box size change
175    percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
176    percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
177    percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
178    
179 <  for (i=0; i < nMols; i++) {
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 199 | 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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