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Comparing:
trunk/OOPSE/libmdtools/NVT.cpp (file contents), Revision 645 by tim, Tue Jul 22 19:54:52 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/NVT.cpp (file contents), Revision 851 by mmeineke, Wed Nov 5 19:18:17 2003 UTC

# Line 1 | Line 1
1 + #include <math.h>
2 +
3   #include "Atom.hpp"
4   #include "SRI.hpp"
5   #include "AbstractClasses.hpp"
# Line 6 | Line 8
8   #include "Thermo.hpp"
9   #include "ReadWrite.hpp"
10   #include "Integrator.hpp"
11 < #include "simError.h"
11 > #include "simError.h"
12  
13  
14   // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
15  
16 < template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 <  T( theInfo, the_ff )
16 > NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 >  Integrator( theInfo, the_ff )
18   {
19 +  GenericData* data;
20 +
21    chi = 0.0;
22    have_tau_thermostat = 0;
23    have_target_temp = 0;
24 +  have_chi_tolerance = 0;
25 +  integralOfChidt = 0.0;
26 +
27 +  // retrieve chi and integralOfChidt from simInfo
28 +  data = info->getProperty(CHIVALUE_ID);
29 +  if(data != NULL ){
30 +    chi = data->getDval();
31 +  }
32 +
33 +  data = info->getProperty(INTEGRALOFCHIDT_ID);
34 +  if(data != NULL ){
35 +    integralOfChidt = data->getDval();
36 +  }
37 +
38 +  oldVel = new double[3*nAtoms];
39 +  oldJi = new double[3*nAtoms];
40   }
41  
42 < template<typename T> void NVT<T>::moveA() {
43 <  
42 > NVT::~NVT() {
43 >  delete[] oldVel;
44 >  delete[] oldJi;
45 > }
46 >
47 > void NVT::moveA() {
48 >
49    int i, j;
50    DirectionalAtom* dAtom;
51    double Tb[3], ji[3];
52 <  double A[3][3], I[3][3];
28 <  double angle, mass;
52 >  double mass;
53    double vel[3], pos[3], frc[3];
54  
55    double instTemp;
56  
57 +  // We need the temperature at time = t for the chi update below:
58 +
59    instTemp = tStats->getTemperature();
60  
35 –  // first evolve chi a half step
36 –  
37 –  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
38 –
61    for( i=0; i<nAtoms; i++ ){
62  
63      atoms[i]->getVel( vel );
# Line 45 | Line 67 | template<typename T> void NVT<T>::moveA() {
67      mass = atoms[i]->getMass();
68  
69      for (j=0; j < 3; j++) {
70 <      // velocity half step
70 >      // velocity half step  (use chi from previous step here):
71        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
72        // position whole step
73        pos[j] += dt * vel[j];
# Line 53 | Line 75 | template<typename T> void NVT<T>::moveA() {
75  
76      atoms[i]->setVel( vel );
77      atoms[i]->setPos( pos );
78 <  
78 >
79      if( atoms[i]->isDirectional() ){
80  
81        dAtom = (DirectionalAtom *)atoms[i];
82 <          
82 >
83        // get and convert the torque to body frame
84 <      
84 >
85        dAtom->getTrq( Tb );
86        dAtom->lab2Body( Tb );
87 <      
87 >
88        // get the angular momentum, and propagate a half step
89  
90        dAtom->getJ( ji );
91  
92 <      for (j=0; j < 3; j++)
92 >      for (j=0; j < 3; j++)
93          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
72 –      
73 –      // use the angular velocities to propagate the rotation matrix a
74 –      // full time step
94  
95 <      dAtom->getA(A);
77 <      dAtom->getI(I);
78 <    
79 <      // rotate about the x-axis      
80 <      angle = dt2 * ji[0] / I[0][0];
81 <      this->rotate( 1, 2, angle, ji, A );
95 >      this->rotationPropagation( dAtom, ji );
96  
83 –      // rotate about the y-axis
84 –      angle = dt2 * ji[1] / I[1][1];
85 –      this->rotate( 2, 0, angle, ji, A );
86 –      
87 –      // rotate about the z-axis
88 –      angle = dt * ji[2] / I[2][2];
89 –      this->rotate( 0, 1, angle, ji, A);
90 –      
91 –      // rotate about the y-axis
92 –      angle = dt2 * ji[1] / I[1][1];
93 –      this->rotate( 2, 0, angle, ji, A );
94 –      
95 –       // rotate about the x-axis
96 –      angle = dt2 * ji[0] / I[0][0];
97 –      this->rotate( 1, 2, angle, ji, A );
98 –      
97        dAtom->setJ( ji );
98 <      dAtom->setA( A  );    
101 <    }    
98 >    }
99    }
100 +
101 +  if (nConstrained){
102 +    constrainA();
103 +  }
104 +
105 +  // Finally, evolve chi a half step (just like a velocity) using
106 +  // temperature at time t, not time t+dt/2
107 +
108 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
109 +  integralOfChidt += chi*dt2;
110 +
111   }
112  
113 < template<typename T> void NVT<T>::moveB( void ){
114 <  int i, j;
113 > void NVT::moveB( void ){
114 >  int i, j, k;
115    DirectionalAtom* dAtom;
116    double Tb[3], ji[3];
117    double vel[3], frc[3];
118    double mass;
111 –
119    double instTemp;
120 <  
121 <  instTemp = tStats->getTemperature();
122 <  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
123 <  
120 >  double oldChi, prevChi;
121 >
122 >  // Set things up for the iteration:
123 >
124 >  oldChi = chi;
125 >
126    for( i=0; i<nAtoms; i++ ){
127  
128      atoms[i]->getVel( vel );
120 –    atoms[i]->getFrc( frc );
129  
130 <    mass = atoms[i]->getMass();
130 >    for (j=0; j < 3; j++)
131 >      oldVel[3*i + j]  = vel[j];
132  
124 –    // velocity half step
125 –    for (j=0; j < 3; j++)
126 –      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
127 –    
128 –    atoms[i]->setVel( vel );
129 –
133      if( atoms[i]->isDirectional() ){
134  
135        dAtom = (DirectionalAtom *)atoms[i];
136  
137 <      // get and convert the torque to body frame      
137 >      dAtom->getJ( ji );
138  
139 <      dAtom->getTrq( Tb );
140 <      dAtom->lab2Body( Tb );
139 >      for (j=0; j < 3; j++)
140 >        oldJi[3*i + j] = ji[j];
141  
142 <      // get the angular momentum, and propagate a half step
142 >    }
143 >  }
144  
145 <      dAtom->getJ( ji );
145 >  // do the iteration:
146  
147 <      for (j=0; j < 3; j++)
144 <        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
145 <      
147 >  for (k=0; k < 4; k++) {
148  
149 <      dAtom->setJ( ji );
149 >    instTemp = tStats->getTemperature();
150 >
151 >    // evolve chi another half step using the temperature at t + dt/2
152 >
153 >    prevChi = chi;
154 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
155 >      (tauThermostat*tauThermostat);
156 >
157 >    for( i=0; i<nAtoms; i++ ){
158 >
159 >      atoms[i]->getFrc( frc );
160 >      atoms[i]->getVel(vel);
161 >
162 >      mass = atoms[i]->getMass();
163 >
164 >      // velocity half step
165 >      for (j=0; j < 3; j++)
166 >        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
167 >
168 >      atoms[i]->setVel( vel );
169 >
170 >      if( atoms[i]->isDirectional() ){
171 >
172 >        dAtom = (DirectionalAtom *)atoms[i];
173 >
174 >        // get and convert the torque to body frame
175 >
176 >        dAtom->getTrq( Tb );
177 >        dAtom->lab2Body( Tb );
178 >
179 >        for (j=0; j < 3; j++)
180 >          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
181 >
182 >        dAtom->setJ( ji );
183 >      }
184      }
185 +
186 +    if (nConstrained){
187 +      constrainB();
188 +    }
189 +
190 +    if (fabs(prevChi - chi) <= chiTolerance) break;
191    }
192 +
193 +  integralOfChidt += dt2*chi;
194   }
195  
196 < template<typename T> int NVT<T>::readyCheck() {
197 <
198 <  // First check to see if we have a target temperature.
199 <  // Not having one is fatal.
200 <  
196 > void NVT::resetIntegrator( void ){
197 >
198 >  chi = 0.0;
199 >  integralOfChidt = 0.0;
200 > }
201 >
202 > int NVT::readyCheck() {
203 >
204 >  //check parent's readyCheck() first
205 >  if (Integrator::readyCheck() == -1)
206 >    return -1;
207 >
208 >  // First check to see if we have a target temperature.
209 >  // Not having one is fatal.
210 >
211    if (!have_target_temp) {
212      sprintf( painCave.errMsg,
213               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 162 | Line 216 | template<typename T> int NVT<T>::readyCheck() {
216      simError();
217      return -1;
218    }
219 <  
219 >
220    // We must set tauThermostat.
221 <  
221 >
222    if (!have_tau_thermostat) {
223      sprintf( painCave.errMsg,
224               "NVT error: If you use the constant temperature\n"
# Line 172 | Line 226 | template<typename T> int NVT<T>::readyCheck() {
226      painCave.isFatal = 1;
227      simError();
228      return -1;
229 <  }    
229 >  }
230 >
231 >  if (!have_chi_tolerance) {
232 >    sprintf( painCave.errMsg,
233 >             "NVT warning: setting chi tolerance to 1e-6\n");
234 >    chiTolerance = 1e-6;
235 >    have_chi_tolerance = 1;
236 >    painCave.isFatal = 0;
237 >    simError();
238 >  }
239 >
240    return 1;
241 +
242   }
243 +
244 + double NVT::getConservedQuantity(void){
245 +
246 +  double conservedQuantity;
247 +  double fkBT;
248 +  double Energy;
249 +  double thermostat_kinetic;
250 +  double thermostat_potential;
251 +
252 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
253 +
254 +  Energy = tStats->getTotalE();
255 +
256 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
257 +    (2.0 * eConvert);
258 +
259 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
260 +
261 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
262 +
263 +  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
264 +      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;
265 +
266 +  return conservedQuantity;
267 + }
268 +
269 + char* NVT::getAdditionalParameters(void){
270 +
271 +  sprintf(addParamBuffer,
272 +          "\t%G\t%G;",
273 +          chi, integralOfChidt
274 +          );
275 +
276 +  return addParamBuffer;
277 + }

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