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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 763 by tim, Mon Sep 15 16:52:02 2003 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 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
# Line 14 | Line 16 | template<typename T> NVT<T>::NVT ( SimInfo *theInfo, F
16   template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17    T( theInfo, the_ff )
18   {
19 +  GenericData* data;
20 +  DoubleData * chiValue;
21 +  DoubleData * integralOfChidtValue;
22 +
23 +  chiValue = NULL;
24 +  integralOfChidtValue = NULL;
25 +
26    chi = 0.0;
27    have_tau_thermostat = 0;
28    have_target_temp = 0;
29    have_chi_tolerance = 0;
30    integralOfChidt = 0.0;
31  
32 <  oldVel = new double[3*nAtoms];
33 <  oldJi = new double[3*nAtoms];
32 >
33 >  if( theInfo->useInitXSstate ){
34 >
35 >    // retrieve chi and integralOfChidt from simInfo
36 >    data = info->getProperty(CHIVALUE_ID);
37 >    if(data){
38 >      chiValue = dynamic_cast<DoubleData*>(data);
39 >    }
40 >    
41 >    data = info->getProperty(INTEGRALOFCHIDT_ID);
42 >    if(data){
43 >      integralOfChidtValue = dynamic_cast<DoubleData*>(data);
44 >    }
45 >    
46 >    // chi and integralOfChidt should appear by pair
47 >    if(chiValue && integralOfChidtValue){
48 >      chi = chiValue->getData();
49 >      integralOfChidt = integralOfChidtValue->getData();
50 >    }
51 >  }
52 >
53 >  oldVel = new double[3*integrableObjects.size()];
54 >  oldJi = new double[3*integrableObjects.size()];
55   }
56  
57   template<typename T> NVT<T>::~NVT() {
# Line 30 | Line 60 | template<typename T> void NVT<T>::moveA() {
60   }
61  
62   template<typename T> void NVT<T>::moveA() {
63 <  
63 >
64    int i, j;
65    DirectionalAtom* dAtom;
66    double Tb[3], ji[3];
67 <  double A[3][3], I[3][3];
38 <  double angle, mass;
67 >  double mass;
68    double vel[3], pos[3], frc[3];
69  
70    double instTemp;
# Line 43 | Line 72 | template<typename T> void NVT<T>::moveA() {
72    // We need the temperature at time = t for the chi update below:
73  
74    instTemp = tStats->getTemperature();
46 –  
47 –  for( i=0; i<nAtoms; i++ ){
75  
76 <    atoms[i]->getVel( vel );
50 <    atoms[i]->getPos( pos );
51 <    atoms[i]->getFrc( frc );
76 >  for( i=0; i < integrableObjects.size(); i++ ){
77  
78 <    mass = atoms[i]->getMass();
78 >    integrableObjects[i]->getVel( vel );
79 >    integrableObjects[i]->getPos( pos );
80 >    integrableObjects[i]->getFrc( frc );
81  
82 +    mass = integrableObjects[i]->getMass();
83 +
84      for (j=0; j < 3; j++) {
85        // velocity half step  (use chi from previous step here):
86        vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
# Line 59 | Line 88 | template<typename T> void NVT<T>::moveA() {
88        pos[j] += dt * vel[j];
89      }
90  
91 <    atoms[i]->setVel( vel );
92 <    atoms[i]->setPos( pos );
64 <  
65 <    if( atoms[i]->isDirectional() ){
91 >    integrableObjects[i]->setVel( vel );
92 >    integrableObjects[i]->setPos( pos );
93  
94 <      dAtom = (DirectionalAtom *)atoms[i];
95 <          
94 >    if( integrableObjects[i]->isDirectional() ){
95 >
96        // get and convert the torque to body frame
97 <      
98 <      dAtom->getTrq( Tb );
99 <      dAtom->lab2Body( Tb );
100 <      
97 >
98 >      integrableObjects[i]->getTrq( Tb );
99 >      integrableObjects[i]->lab2Body( Tb );
100 >
101        // get the angular momentum, and propagate a half step
102  
103 <      dAtom->getJ( ji );
103 >      integrableObjects[i]->getJ( ji );
104  
105 <      for (j=0; j < 3; j++)
105 >      for (j=0; j < 3; j++)
106          ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
80 –      
81 –      // use the angular velocities to propagate the rotation matrix a
82 –      // full time step
107  
108 <      dAtom->getA(A);
85 <      dAtom->getI(I);
86 <    
87 <      // rotate about the x-axis      
88 <      angle = dt2 * ji[0] / I[0][0];
89 <      this->rotate( 1, 2, angle, ji, A );
108 >      this->rotationPropagation( integrableObjects[i], ji );
109  
110 <      // rotate about the y-axis
111 <      angle = dt2 * ji[1] / I[1][1];
93 <      this->rotate( 2, 0, angle, ji, A );
94 <      
95 <      // rotate about the z-axis
96 <      angle = dt * ji[2] / I[2][2];
97 <      this->rotate( 0, 1, angle, ji, A);
98 <      
99 <      // rotate about the y-axis
100 <      angle = dt2 * ji[1] / I[1][1];
101 <      this->rotate( 2, 0, angle, ji, A );
102 <      
103 <       // rotate about the x-axis
104 <      angle = dt2 * ji[0] / I[0][0];
105 <      this->rotate( 1, 2, angle, ji, A );
106 <      
107 <      dAtom->setJ( ji );
108 <      dAtom->setA( A  );    
109 <    }    
110 >      integrableObjects[i]->setJ( ji );
111 >    }
112    }
113  
114 <  // Finally, evolve chi a half step (just like a velocity) using
114 >  rattle->doRattleA();
115 >
116 >  // Finally, evolve chi a half step (just like a velocity) using
117    // temperature at time t, not time t+dt/2
118  
119 +  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
120 +  
121    chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
122    integralOfChidt += chi*dt2;
123  
# Line 119 | Line 125 | template<typename T> void NVT<T>::moveB( void ){
125  
126   template<typename T> void NVT<T>::moveB( void ){
127    int i, j, k;
122 –  DirectionalAtom* dAtom;
128    double Tb[3], ji[3];
129    double vel[3], frc[3];
130    double mass;
# Line 130 | Line 135 | template<typename T> void NVT<T>::moveB( void ){
135  
136    oldChi = chi;
137  
138 <  for( i=0; i<nAtoms; i++ ){
138 >  for( i=0; i < integrableObjects.size(); i++ ){
139  
140 <    atoms[i]->getVel( vel );
140 >    integrableObjects[i]->getVel( vel );
141  
142      for (j=0; j < 3; j++)
143        oldVel[3*i + j]  = vel[j];
144  
145 <    if( atoms[i]->isDirectional() ){
145 >    if( integrableObjects[i]->isDirectional() ){
146  
147 <      dAtom = (DirectionalAtom *)atoms[i];
147 >      integrableObjects[i]->getJ( ji );
148  
144 –      dAtom->getJ( ji );
145 –
149        for (j=0; j < 3; j++)
150          oldJi[3*i + j] = ji[j];
151  
# Line 152 | Line 155 | template<typename T> void NVT<T>::moveB( void ){
155    // do the iteration:
156  
157    for (k=0; k < 4; k++) {
158 <    
158 >
159      instTemp = tStats->getTemperature();
160  
161      // evolve chi another half step using the temperature at t + dt/2
162  
163      prevChi = chi;
164 <    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
164 >    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
165        (tauThermostat*tauThermostat);
166 <  
167 <    for( i=0; i<nAtoms; i++ ){
166 >
167 >    for( i=0; i < integrableObjects.size(); i++ ){
168  
169 <      atoms[i]->getFrc( frc );
170 <      atoms[i]->getVel(vel);
171 <      
172 <      mass = atoms[i]->getMass();
173 <      
169 >      integrableObjects[i]->getFrc( frc );
170 >      integrableObjects[i]->getVel(vel);
171 >
172 >      mass = integrableObjects[i]->getMass();
173 >
174        // velocity half step
175 <      for (j=0; j < 3; j++)
175 >      for (j=0; j < 3; j++)
176          vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
177 <      
178 <      atoms[i]->setVel( vel );
179 <      
180 <      if( atoms[i]->isDirectional() ){
181 <        
182 <        dAtom = (DirectionalAtom *)atoms[i];
183 <        
184 <        // get and convert the torque to body frame      
185 <        
186 <        dAtom->getTrq( Tb );
187 <        dAtom->lab2Body( Tb );      
185 <            
186 <        for (j=0; j < 3; j++)
177 >
178 >      integrableObjects[i]->setVel( vel );
179 >
180 >      if( integrableObjects[i]->isDirectional() ){
181 >
182 >        // get and convert the torque to body frame
183 >
184 >        integrableObjects[i]->getTrq( Tb );
185 >        integrableObjects[i]->lab2Body( Tb );
186 >
187 >        for (j=0; j < 3; j++)
188            ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
189 <      
190 <        dAtom->setJ( ji );
189 >
190 >        integrableObjects[i]->setJ( ji );
191        }
192      }
193  
194 +    rattle->doRattleB();
195 +
196      if (fabs(prevChi - chi) <= chiTolerance) break;
197    }
198 <  
198 >
199    integralOfChidt += dt2*chi;
200   }
201  
202   template<typename T> void NVT<T>::resetIntegrator( void ){
203 <  
203 >
204    chi = 0.0;
205    integralOfChidt = 0.0;
206   }
# Line 207 | Line 210 | template<typename T> int NVT<T>::readyCheck() {
210    //check parent's readyCheck() first
211    if (T::readyCheck() == -1)
212      return -1;
213 <  
214 <  // First check to see if we have a target temperature.
215 <  // Not having one is fatal.
216 <  
213 >
214 >  // First check to see if we have a target temperature.
215 >  // Not having one is fatal.
216 >
217    if (!have_target_temp) {
218      sprintf( painCave.errMsg,
219 <             "NVT error: You can't use the NVT integrator without a targetTemp!\n"
219 >             "You can't use the NVT integrator without a targetTemp!\n"
220               );
221      painCave.isFatal = 1;
222 +    painCave.severity = OOPSE_ERROR;
223      simError();
224      return -1;
225    }
226 <  
226 >
227    // We must set tauThermostat.
228 <  
228 >
229    if (!have_tau_thermostat) {
230      sprintf( painCave.errMsg,
231 <             "NVT error: If you use the constant temperature\n"
232 <             "   integrator, you must set tauThermostat.\n");
231 >             "If you use the constant temperature\n"
232 >             "\tintegrator, you must set tauThermostat.\n");
233 >    painCave.severity = OOPSE_ERROR;
234      painCave.isFatal = 1;
235      simError();
236      return -1;
237 <  }    
237 >  }
238  
239    if (!have_chi_tolerance) {
240      sprintf( painCave.errMsg,
241 <             "NVT warning: setting chi tolerance to 1e-6\n");
241 >             "In NVT integrator: setting chi tolerance to 1e-6\n");
242      chiTolerance = 1e-6;
243      have_chi_tolerance = 1;
244 +    painCave.severity = OOPSE_INFO;
245      painCave.isFatal = 0;
246      simError();
247 <  }    
247 >  }
248  
249 <  return 1;    
249 >  return 1;
250  
251   }
252  
253   template<typename T> double NVT<T>::getConservedQuantity(void){
254  
255    double conservedQuantity;
256 <  double E_NVT;
256 >  double fkBT;
257 >  double Energy;
258 >  double thermostat_kinetic;
259 >  double thermostat_potential;
260  
261 <  //HNVE
253 <  conservedQuantity = tStats->getTotalE();
254 <  //HNVE
255 <  
256 <  E_NVT =  (info->getNDF() * kB * targetTemp *
257 <                (integralOfChidt + tauThermostat * tauThermostat * chi * chi / 2.0 )) / eConvert;
261 >  fkBT = (double)(info->ndf) * kB * targetTemp;
262  
263 <  conservedQuantity += E_NVT;
263 >  Energy = tStats->getTotalE();
264  
265 <  //cerr << info->getTime() << "\t" << chi << "\t" << integralOfChidt << "\t" << E_NVT << endl;
265 >  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
266 >    (2.0 * eConvert);
267  
268 <  return conservedQuantity;
268 >  thermostat_potential = fkBT * integralOfChidt / eConvert;
269 >
270 >  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
271 >
272 >  return conservedQuantity;
273   }
274 +
275 + template<typename T> string NVT<T>::getAdditionalParameters(void){
276 +  string parameters;
277 +  const int BUFFERSIZE = 2000; // size of the read buffer
278 +  char buffer[BUFFERSIZE];
279 +
280 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
281 +  parameters += buffer;
282 +
283 +  return parameters;
284 + }

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