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Comparing trunk/OOPSE/libmdtools/ExtendedSystem.cpp (file contents):
Revision 454 by gezelter, Fri Apr 4 01:57:11 2003 UTC vs.
Revision 471 by gezelter, Mon Apr 7 20:51:59 2003 UTC

# Line 5 | Line 5 | ExtendedSystem::ExtendedSystem( SimInfo &info ) {
5   #include "Thermo.hpp"
6   #include "ExtendedSystem.hpp"
7  
8 < ExtendedSystem::ExtendedSystem( SimInfo &info ) {
8 > ExtendedSystem::ExtendedSystem( SimInfo* the_entry_plug ) {
9  
10    // get what information we need from the SimInfo object
11    
12 <  entry_plug = &info;
13 <  nAtoms = info.n_atoms;
14 <  atoms = info.atoms;
15 <  nMols = info.n_mol;
16 <  molecules = info.molecules;
17 <  zeta = 0;
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;
19 >  zeta = 0.0;
20 >  epsilonDot = 0.0;
21  
22   }
23  
24 < ExtendedSystem::~ExtendedSystem() {  
22 < }
24 > void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
25  
24 –
25 – void ExtendedSystem::NoseHooverNVT( double dt ){
26 –
26    // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
27    
28    int i;
29 <  double kB, keconverter, NkBT, zetaScale, ke_temp;
29 >  double NkBT, zetaScale, ke_temp;
30    double vx, vy, vz, jx, jy, jz;
31 <  
32 <  kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K
33 <  keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K
34 <  
36 <  ke_temp = getKinetic() * keconverter;
37 <  NkBT = (double)getNDF() * kB * targetTemp;
31 >  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
32 >  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
33 >                                        // amu*Ang^2*fs^-2/K
34 >  DirectionalAtom* dAtom;    
35  
36 <  // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin &
36 >  ke_temp = ke * e_convert;
37 >  NkBT = (double)ndf * kB * targetTemp;
38 >
39 >  // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
40    // qmass is set in the parameter file
41 <  zeta += dt*((ke_temp*2 - NkBT)/qmass);
41 >
42 >  zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
43 >  std::cerr << "ke_temp = " << ke_temp << "\n";
44 >
45    zetaScale = zeta * dt;
46 +  
47  
48 +
49    // perform thermostat scaling on linear velocities and angular momentum
50 <  
46 <  for(i = 0; i < n_atoms; i++){
50 >  for(i = 0; i < nAtoms; i++){
51      
52      vx = atoms[i]->get_vx();
53      vy = atoms[i]->get_vy();
54      vz = atoms[i]->get_vz();
55      
56 <    atoms[i]->set_vx(vx - zetaScale * vx);
57 <    atoms[i]->set_vy(vy - zetaScale * vy);
58 <    atoms[i]->set_vz(vz - zetaScale * vz);
56 >    atoms[i]->set_vx(vx * (1.0 - zetaScale));
57 >    atoms[i]->set_vy(vy * (1.0 - zetaScale));
58 >    atoms[i]->set_vz(vz * (1.0 - zetaScale));
59    }
60 <  if( n_oriented ){
60 >  if( nOriented ){
61      
62 <    for( i=0; i < n_atoms; i++ ){
62 >    for( i=0; i < nAtoms; i++ ){
63        
64        if( atoms[i]->isDirectional() ){
65          
# Line 65 | Line 69 | void ExtendedSystem::NoseHooverNVT( double dt ){
69          jy = dAtom->getJy();
70          jz = dAtom->getJz();
71          
72 <        dAtom->setJx( jx - zetaScale * jx);
73 <        dAtom->setJy( jy - zetaScale * jy);
74 <        dAtom->setJz( jz - zetaScale * jz);
72 >        dAtom->setJx(jx * (1.0 - zetaScale));
73 >        dAtom->setJy(jy * (1.0 - zetaScale));
74 >        dAtom->setJz(jz * (1.0 - zetaScale));
75        }
76      }  
77    }
78   }
79  
80  
81 < void ExtendedSystem::NoseHooverAndersonNPT(double pressure, double ke,
82 <                                           double dt, double temp ) {
81 > void ExtendedSystem::NoseHooverAndersonNPT( double dt,
82 >                                            double ke,
83 >                                            double p_int ) {
84  
85    // Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
86    // Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
87  
88 <  int i, j, degrees_freedom;
89 <  double pressure, dt, temp, pressure_units, epsilonScale;
90 <  double ke, kB, vxi, vyi, vzi, pressure_ext;
91 <  double boxx_old, boxy_old, boxz_old;
92 <  double keconverter, NkBT, zetaScale, ke_temp;
93 <  double jxi, jyi, jzi, scale;
88 >  double oldBox[3];
89 >  double newBox[3];
90 >  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
91 >  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
92 >  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
93 >                                        // amu*Ang^2*fs^-2/K
94  
95 <  kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K
96 <  pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
97 <  degrees_freedom = 6*nmol; // number of degrees of freedom for the system
98 <  keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K
95 >  double p_ext, zetaScale, epsilonScale, scale, NkBT, ke_temp;
96 >  double volume, p_mol;
97 >  double vx, vy, vz, jx, jy, jz;
98 >  DirectionalAtom* dAtom;
99 >  int i;
100  
101 <  pressure_ext = pressure * pressure_units;
102 <  volume = boxx*boxy*boxz;
97 <  ke_temp = ke * keconverter;
98 <  NkBT = degrees_freedom*kB*temp;
101 >  p_ext = targetPressure * p_units;
102 >  p_mol = p_int * p_units;
103  
104 +  entry_plug->getBox(oldBox);
105 +
106 +  volume = oldBox[0]*oldBox[1]*oldBox[2];
107 +
108 +  ke_temp = ke * e_convert;
109 +  NkBT = (double)ndf * kB * targetTemp;
110 +
111    // propogate the strain rate
112  
113 <  epsilon_dot +=  dt * ( (p_mol - pressure_ext)*volume
114 <                         / (tau_relax*tau_relax * kB * targetTemp) );
113 >  epsilonDot +=  dt * ((p_mol - p_ext) * volume /
114 >                       (tauRelax*tauRelax * kB * targetTemp) );
115  
116    // determine the change in cell volume
117 <  scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0));
117 >  scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
118  
119 <  volume = volume * pow(scale, 3.0);
119 >  newBox[0] = oldBox[0] * scale;
120 >  newBox[1] = oldBox[1] * scale;
121 >  newBox[2] = oldBox[2] * scale;
122 >  volume = newBox[0]*newBox[1]*newBox[2];
123  
124 +  entry_plug->setBox(newBox);
125 +
126    // perform affine transform to update positions with volume fluctuations
127 <  affine_transform( scale );
127 >  this->AffineTransform( oldBox, newBox );
128  
113 –  // save old lengths and update box size
114 –  boxx_old = boxx;
115 –  boxy_old = boxy;
116 –  boxz_old = boxz;
117 –
118 –  boxx = boxx_old*scale;
119 –  boxy = boxy_old*scale;
120 –  boxz = boxz_old*scale;
121 –
129    epsilonScale = epsilonDot * dt;
130  
131    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
132    // qmass is set in the parameter file
133 <  zeta += dt * ( (ke_temp*2 - NkBT) / qmass );
133 >
134 >  zeta += dt * ( (ke_temp*2.0 - NkBT) / qmass );
135    zetaScale = zeta * dt;
136    
137    // apply barostating and thermostating to velocities and angular momenta
138 <  for(i = 0; i < n_atoms; i++){
138 >  for(i = 0; i < nAtoms; i++){
139      
140      vx = atoms[i]->get_vx();
141      vy = atoms[i]->get_vy();
142      vz = atoms[i]->get_vz();
143      
144 <    atoms[i]->set_vx(vx * (1.0 - zetaScale * epsilonScale));
145 <    atoms[i]->set_vy(vy * (1.0 - zetaScale * epsilonScale));
146 <    atoms[i]->set_vz(vz * (1.0 - zetaScale * epsilonScale));
144 >    atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
145 >    atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
146 >    atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
147    }
148 <  if( n_oriented ){
148 >  if( nOriented ){
149      
150 <    for( i=0; i < n_atoms; i++ ){
150 >    for( i=0; i < nAtoms; i++ ){
151        
152        if( atoms[i]->isDirectional() ){
153          
# Line 157 | Line 165 | void ExtendedSystem::AffineTransform( double scale ){
165    }
166   }
167  
168 < void ExtendedSystem::AffineTransform( double scale ){
168 > void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
169  
170    int i;
171 <  double boxx_old, boxy_old, boxz_old, percentScale;
172 <  double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi;
173 <  double[3] r;
171 >  double r[3];
172 >  double boxNum[3];
173 >  double percentScale[3];
174 >  double rxi, ryi, rzi;
175      
176    // first determine the scaling factor from the box size change
177 <  percentScale = (boxx - boxx_old)/boxx_old;
177 >  percentScale[0] = (newBox[0] - oldBox[0]) / oldBox[0];
178 >  percentScale[1] = (newBox[1] - oldBox[1]) / oldBox[1];
179 >  percentScale[2] = (newBox[2] - oldBox[2]) / oldBox[2];
180    
170 –
181    for (i=0; i < nMols; i++) {
182      
183 <    molecules[i]->getCOM(r);
183 >    molecules[i].getCOM(r);
184      
185 <    // find the minimum image coordinates of the molecular centers of mass:
185 >    // find the minimum image coordinates of the molecular centers of mass:    
186      
187 <    
188 <    boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5);
187 >    boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
188 >      (double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
189  
190 <    boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0);
191 <    boxy_num = boxy_old*dsign(1.0d0,ry(i))*int(abs(ry(i)/boxy_old)+0.5d0);
182 <    boxz_num = boxz_old*dsign(1.0d0,rz(i))*int(abs(rz(i)/boxz_old)+0.5d0);
190 >    boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
191 >      (double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
192  
193 <    rxi = rx(i) - boxx_num;
194 <    ryi = ry(i) - boxy_num;
186 <    rzi = rz(i) - boxz_num;
193 >    boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
194 >      (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
195  
196 +    rxi = r[0] - boxNum[0];
197 +    ryi = r[1] - boxNum[1];
198 +    rzi = r[2] - boxNum[2];
199 +
200      // update the minimum image coordinates using the scaling factor
201 <    rxi = rxi + rxi*percentScale;
202 <    ryi = ryi + ryi*percentScale;
203 <    rzi = rzi + rzi*percentScale;
201 >    rxi += rxi*percentScale[0];
202 >    ryi += ryi*percentScale[1];
203 >    rzi += rzi*percentScale[2];
204  
205 <    rx(i) = rxi + boxx_num;
206 <    ry(i) = ryi + boxy_num;
207 <    rz(i) = rzi + boxz_num;
205 >    r[0] = rxi + boxNum[0];
206 >    r[1] = ryi + boxNum[1];
207 >    r[2] = rzi + boxNum[2];
208 >
209 >    molecules[i].moveCOM(r);
210    }
211   }

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