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root/group/trunk/OOPSE/libmdtools/ExtendedSystem.cpp
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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 468 by gezelter, Mon Apr 7 16:56:38 2003 UTC vs.
Revision 476 by gezelter, Tue Apr 8 12:50:18 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  
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 88 | 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;
96 >  p_mol = p_int;
97  
98    entry_plug->getBox(oldBox);
101 –
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  
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 +
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 129 | Line 132 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
132  
133    zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
134    zetaScale = zeta * dt;
135 +
136 +  std::cerr << "zetaScale = " << zetaScale << "epsilonScale = " << epsilonScale <<  "\n";
137    
138    // apply barostating and thermostating to velocities and angular momenta
139 <  for(i = 0; i < nAtoms; i++){
139 >  for(i = 0; i < entry_plug->n_atoms; i++){
140      
141      vx = atoms[i]->get_vx();
142      vy = atoms[i]->get_vy();
# Line 141 | Line 146 | void ExtendedSystem::NoseHooverAndersonNPT( double dt,
146      atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
147      atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
148    }
149 <  if( nOriented ){
149 >  if( entry_plug->n_oriented ){
150      
151 <    for( i=0; i < nAtoms; i++ ){
151 >    for( i=0; i < entry_plug->n_atoms; i++ ){
152        
153        if( atoms[i]->isDirectional() ){
154          
# Line 167 | 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;
179      
180    // first determine the scaling factor from the box size change
181    percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
182    percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
183    percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
184    
185 <  for (i=0; i < nMols; i++) {
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 198 | 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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