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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 477 by gezelter, Tue Apr 8 14:34:30 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;
18 <
12 >  entry_plug = the_entry_plug;
13 >  zeta = 0.0;
14 >  epsilonDot = 0.0;
15   }
16  
17 < ExtendedSystem::~ExtendedSystem() {  
22 < }
17 > void ExtendedSystem::NoseHooverNVT( double dt, double ke ){
18  
24 –
25 – void ExtendedSystem::NoseHooverNVT( double dt ){
26 –
19    // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
20    
21    int i;
22 <  double kB, keconverter, NkBT, zetaScale, ke_temp;
22 >  double NkBT, zetaScale, ke_temp;
23    double vx, vy, vz, jx, jy, jz;
24 <  
25 <  kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K
26 <  keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2 / K
27 <  
28 <  ke_temp = getKinetic() * keconverter;
37 <  NkBT = (double)getNDF() * kB * targetTemp;
24 >  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
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 <  // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin &
30 >  ke_temp = ke * e_convert;
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 <  zeta += dt*((ke_temp*2 - NkBT)/qmass);
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 <  
46 <  for(i = 0; i < n_atoms; 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 <    
49 <    atoms[i]->set_vx(vx - zetaScale * vx);
50 <    atoms[i]->set_vy(vy - zetaScale * vy);
51 <    atoms[i]->set_vz(vz - zetaScale * vz);
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( n_oriented ){
53 >  if( entry_plug->n_oriented ){
54      
55 <    for( i=0; i < n_atoms; i++ ){
55 >    for( i=0; i < entry_plug->n_atoms; i++ ){
56        
57        if( atoms[i]->isDirectional() ){
58          
# Line 65 | Line 62 | void ExtendedSystem::NoseHooverNVT( double dt ){
62          jy = dAtom->getJy();
63          jz = dAtom->getJz();
64          
65 <        dAtom->setJx( jx - zetaScale * jx);
66 <        dAtom->setJy( jy - zetaScale * jy);
67 <        dAtom->setJz( jz - zetaScale * jz);
65 >        dAtom->setJx(jx * (1.0 - zetaScale));
66 >        dAtom->setJy(jy * (1.0 - zetaScale));
67 >        dAtom->setJz(jz * (1.0 - zetaScale));
68        }
69      }  
70    }
71   }
72  
73  
74 < void ExtendedSystem::NoseHooverAndersonNPT(double pressure, double ke,
75 <                                           double dt, double temp ) {
74 > void ExtendedSystem::NoseHooverAndersonNPT( double dt,
75 >                                            double ke,
76 >                                            double p_int ) {
77  
78    // Basic barostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
79    // Hoover, Phys.Rev.A, 1986, Vol.34 (3) 2499-2500
80  
81 <  int i, j, degrees_freedom;
82 <  double pressure, dt, temp, pressure_units, epsilonScale;
83 <  double ke, kB, vxi, vyi, vzi, pressure_ext;
84 <  double boxx_old, boxy_old, boxz_old;
85 <  double keconverter, NkBT, zetaScale, ke_temp;
86 <  double jxi, jyi, jzi, scale;
81 >  double oldBox[3];
82 >  double newBox[3];
83 >  const double kB = 8.31451e-7;     // boltzmann constant in amu*Ang^2*fs^-2/K
84 >  const double p_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
85 >  const double e_convert = 4.184e-4;    // to convert ke from kcal/mol to
86 >                                        // amu*Ang^2*fs^-2/K
87  
88 <  kB = 8.31451e-7; // boltzmann constant in amu*Ang^2*fs^-2/K
89 <  pressure_units = 6.10192996e-9; // converts atm to amu*fs^-2*Ang^-1
90 <  degrees_freedom = 6*nmol; // number of degrees of freedom for the system
91 <  keconverter = 4.184e-4; // to convert ke from kcal/mol to amu*Ang^2*fs^-2/K
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 >  atoms = entry_plug->atoms;
94  
95 <  pressure_ext = pressure * pressure_units;
96 <  volume = boxx*boxy*boxz;
97 <  ke_temp = ke * keconverter;
98 <  NkBT = degrees_freedom*kB*temp;
95 >  p_ext = targetPressure * p_units;
96 >  p_mol = p_int * p_units;
97  
98 +  entry_plug->getBox(oldBox);
99 +  volume = oldBox[0]*oldBox[1]*oldBox[2];
100 +
101 +  ke_temp = ke * e_convert;
102 +  NkBT = (double)entry_plug->ndf * kB * targetTemp;
103 +
104    // propogate the strain rate
105  
106 <  epsilon_dot +=  dt * ( (p_mol - pressure_ext)*volume
107 <                         / (tau_relax*tau_relax * kB * targetTemp) );
106 >  epsilonDot +=  dt * ((p_mol - p_ext) * volume /
107 >                       (tauRelax*tauRelax * kB * targetTemp) );
108  
109    // determine the change in cell volume
110 <  scale = pow( (1.0 + dt * 3.0 * epsilon_dot), (1.0 / 3.0));
110 >  scale = pow( (1.0 + dt * 3.0 * epsilonDot), (1.0 / 3.0));
111  
112 <  volume = volume * pow(scale, 3.0);
112 >  newBox[0] = oldBox[0] * scale;
113 >  newBox[1] = oldBox[1] * scale;
114 >  newBox[2] = oldBox[2] * scale;
115 >  volume = newBox[0]*newBox[1]*newBox[2];
116  
117 +  entry_plug->setBox(newBox);
118 +
119    // perform affine transform to update positions with volume fluctuations
120 <  affine_transform( scale );
120 >  this->AffineTransform( oldBox, newBox );
121  
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 –
122    epsilonScale = epsilonDot * dt;
123  
124    // advance the zeta term to zeta(t + dt) - zeta is 0.0d0 on config. readin
125    // qmass is set in the parameter file
126 <  zeta += dt * ( (ke_temp*2 - NkBT) / qmass );
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 < n_atoms; i++){
133 >  for(i = 0; i < entry_plug->n_atoms; i++){
134      
135      vx = atoms[i]->get_vx();
136      vy = atoms[i]->get_vy();
137      vz = atoms[i]->get_vz();
138      
139 <    atoms[i]->set_vx(vx * (1.0 - zetaScale * epsilonScale));
140 <    atoms[i]->set_vy(vy * (1.0 - zetaScale * epsilonScale));
141 <    atoms[i]->set_vz(vz * (1.0 - zetaScale * epsilonScale));
139 >    atoms[i]->set_vx(vx * (1.0 - zetaScale - epsilonScale));
140 >    atoms[i]->set_vy(vy * (1.0 - zetaScale - epsilonScale));
141 >    atoms[i]->set_vz(vz * (1.0 - zetaScale - epsilonScale));
142    }
143 <  if( n_oriented ){
143 >  if( entry_plug->n_oriented ){
144      
145 <    for( i=0; i < n_atoms; i++ ){
145 >    for( i=0; i < entry_plug->n_atoms; i++ ){
146        
147        if( atoms[i]->isDirectional() ){
148          
# Line 157 | Line 160 | void ExtendedSystem::AffineTransform( double scale ){
160    }
161   }
162  
163 < void ExtendedSystem::AffineTransform( double scale ){
163 > void ExtendedSystem::AffineTransform( double oldBox[3], double newBox[3] ){
164  
165    int i;
166 <  double boxx_old, boxy_old, boxz_old, percentScale;
167 <  double boxx_num, boxy_num, boxz_num, rxi, ryi, rzi;
168 <  double[3] r;
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 = (boxx - boxx_old)/boxx_old;
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 < entry_plug->n_mol; i++) {
180 +    
181 +    molecules[i].getCOM(r);
182  
183 <  for (i=0; i < nMols; i++) {
183 >    // find the minimum image coordinates of the molecular centers of mass:    
184      
185 <    molecules[i]->getCOM(r);
186 <    
175 <    // find the minimum image coordinates of the molecular centers of mass:
176 <    
177 <    
178 <    boxx_num = boxx_old*copysign(1.0,r[0])*(double)(int)(fabs(r[0]/boxx_old)+0.5);
185 >    boxNum[0] = oldBox[0] * copysign(1.0,r[0]) *
186 >      (double)(int)(fabs(r[0]/oldBox[0]) + 0.5);
187  
188 <    boxx_num = boxx_old*dsign(1.0d0,rx(i))*int(abs(rx(i)/boxx_old)+0.5d0);
189 <    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);
188 >    boxNum[1] = oldBox[1] * copysign(1.0,r[1]) *
189 >      (double)(int)(fabs(r[1]/oldBox[1]) + 0.5);
190  
191 <    rxi = rx(i) - boxx_num;
192 <    ryi = ry(i) - boxy_num;
186 <    rzi = rz(i) - boxz_num;
191 >    boxNum[2] = oldBox[2] * copysign(1.0,r[2]) *
192 >      (double)(int)(fabs(r[2]/oldBox[2]) + 0.5);
193  
194 +    rxi = r[0] - boxNum[0];
195 +    ryi = r[1] - boxNum[1];
196 +    rzi = r[2] - boxNum[2];
197 +
198      // update the minimum image coordinates using the scaling factor
199 <    rxi = rxi + rxi*percentScale;
200 <    ryi = ryi + ryi*percentScale;
201 <    rzi = rzi + rzi*percentScale;
199 >    rxi += rxi*percentScale[0];
200 >    ryi += ryi*percentScale[1];
201 >    rzi += rzi*percentScale[2];
202  
203 <    rx(i) = rxi + boxx_num;
204 <    ry(i) = ryi + boxy_num;
205 <    rz(i) = rzi + boxz_num;
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(delta);
208    }
209   }

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