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Comparing trunk/OOPSE/libmdtools/NVT.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 853 by mmeineke, Thu Nov 6 19:11:38 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 < NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 <  Integrator( theInfo, the_ff )
16 > template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
17 >  T( theInfo, the_ff )
18   {
19 <  zeta = 0.0;
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_qmass = 0;
29 >  have_chi_tolerance = 0;
30 >  integralOfChidt = 0.0;
31 >
32 >  // retrieve chi and integralOfChidt from simInfo
33 >  data = info->getProperty(CHIVALUE_ID);
34 >  if(data){
35 >    chiValue = dynamic_cast<DoubleData*>(data);
36 >  }
37 >
38 >  data = info->getProperty(INTEGRALOFCHIDT_ID);
39 >  if(data){
40 >    integralOfChidtValue = dynamic_cast<DoubleData*>(data);
41 >  }
42 >
43 >  // chi and integralOfChidt should appear by pair
44 >  if(chiValue && integralOfChidtValue){
45 >    chi = chiValue->getData();
46 >    integralOfChidt = integralOfChidtValue->getData();
47 >  }
48 >
49 >  oldVel = new double[3*nAtoms];
50 >  oldJi = new double[3*nAtoms];
51   }
52  
53 < void NVT::moveA() {
54 <  
55 <  int i,j,k;
56 <  int atomIndex, aMatIndex;
53 > template<typename T> NVT<T>::~NVT() {
54 >  delete[] oldVel;
55 >  delete[] oldJi;
56 > }
57 >
58 > template<typename T> void NVT<T>::moveA() {
59 >
60 >  int i, j;
61    DirectionalAtom* dAtom;
62 <  double Tb[3];
63 <  double ji[3];
64 <  double ke;
31 <  double angle;
62 >  double Tb[3], ji[3];
63 >  double mass;
64 >  double vel[3], pos[3], frc[3];
65  
66 +  double instTemp;
67  
68 <  ke = tStats->getKinetic() * eConvert;
35 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
68 >  // We need the temperature at time = t for the chi update below:
69  
70 +  instTemp = tStats->getTemperature();
71 +
72    for( i=0; i<nAtoms; i++ ){
38 –    atomIndex = i * 3;
39 –    aMatIndex = i * 9;
40 –    
41 –    // velocity half step
42 –    for( j=atomIndex; j<(atomIndex+3); j++ )
43 –      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
73  
74 <    // position whole step    
75 <    for( j=atomIndex; j<(atomIndex+3); j++ )
74 >    atoms[i]->getVel( vel );
75 >    atoms[i]->getPos( pos );
76 >    atoms[i]->getFrc( frc );
77 >
78 >    mass = atoms[i]->getMass();
79 >
80 >    for (j=0; j < 3; j++) {
81 >      // velocity half step  (use chi from previous step here):
82 >      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
83 >      // position whole step
84        pos[j] += dt * vel[j];
85 +    }
86  
87 <  
87 >    atoms[i]->setVel( vel );
88 >    atoms[i]->setPos( pos );
89 >
90      if( atoms[i]->isDirectional() ){
91  
92        dAtom = (DirectionalAtom *)atoms[i];
93 <          
93 >
94        // get and convert the torque to body frame
95 <      
96 <      Tb[0] = dAtom->getTx();
57 <      Tb[1] = dAtom->getTy();
58 <      Tb[2] = dAtom->getTz();
59 <      
95 >
96 >      dAtom->getTrq( Tb );
97        dAtom->lab2Body( Tb );
98 <      
98 >
99        // get the angular momentum, and propagate a half step
100  
101 <      ji[0] = dAtom->getJx();
102 <      ji[1] = dAtom->getJy();
103 <      ji[2] = dAtom->getJz();
104 <      
105 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
106 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
107 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
108 <      
72 <      // use the angular velocities to propagate the rotation matrix a
73 <      // full time step
74 <      
75 <      // rotate about the x-axis      
76 <      angle = dt2 * ji[0] / dAtom->getIxx();
77 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
78 <      
79 <      // rotate about the y-axis
80 <      angle = dt2 * ji[1] / dAtom->getIyy();
81 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
82 <      
83 <      // rotate about the z-axis
84 <      angle = dt * ji[2] / dAtom->getIzz();
85 <      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
86 <      
87 <      // rotate about the y-axis
88 <      angle = dt2 * ji[1] / dAtom->getIyy();
89 <      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
90 <      
91 <       // rotate about the x-axis
92 <      angle = dt2 * ji[0] / dAtom->getIxx();
93 <      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
94 <      
95 <      dAtom->setJx( ji[0] );
96 <      dAtom->setJy( ji[1] );
97 <      dAtom->setJz( ji[2] );
101 >      dAtom->getJ( ji );
102 >
103 >      for (j=0; j < 3; j++)
104 >        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
105 >
106 >      this->rotationPropagation( dAtom, ji );
107 >
108 >      dAtom->setJ( ji );
109      }
99 –    
110    }
111 +
112 +  if (nConstrained){
113 +    constrainA();
114 +  }
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 +  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
120 +  integralOfChidt += chi*dt2;
121 +
122   }
123  
124 < void NVT::moveB( void ){
125 <  int i,j,k;
105 <  int atomIndex;
124 > template<typename T> void NVT<T>::moveB( void ){
125 >  int i, j, k;
126    DirectionalAtom* dAtom;
127 <  double Tb[3];
128 <  double ji[3];
129 <  double ke;
130 <  
127 >  double Tb[3], ji[3];
128 >  double vel[3], frc[3];
129 >  double mass;
130 >  double instTemp;
131 >  double oldChi, prevChi;
132  
133 <  ke = tStats->getKinetic() * eConvert;
134 <  zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
135 <  
133 >  // Set things up for the iteration:
134 >
135 >  oldChi = chi;
136 >
137    for( i=0; i<nAtoms; i++ ){
138 <    atomIndex = i * 3;
139 <    
140 <    // velocity half step
141 <    for( j=atomIndex; j<(atomIndex+3); j++ )
142 <      vel[j] += dt2 * ((frc[j]/atoms[i]->getMass())*eConvert - vel[j]*zeta);
143 <    
138 >
139 >    atoms[i]->getVel( vel );
140 >
141 >    for (j=0; j < 3; j++)
142 >      oldVel[3*i + j]  = vel[j];
143 >
144      if( atoms[i]->isDirectional() ){
145 <      
145 >
146        dAtom = (DirectionalAtom *)atoms[i];
147 <      
148 <      // get and convert the torque to body frame
149 <      
150 <      Tb[0] = dAtom->getTx();
151 <      Tb[1] = dAtom->getTy();
152 <      Tb[2] = dAtom->getTz();
131 <      
132 <      dAtom->lab2Body( Tb );
133 <      
134 <      // get the angular momentum, and complete the angular momentum
135 <      // half step
136 <      
137 <      ji[0] = dAtom->getJx();
138 <      ji[1] = dAtom->getJy();
139 <      ji[2] = dAtom->getJz();
140 <      
141 <      ji[0] += dt2 * (Tb[0] * eConvert - ji[0]*zeta);
142 <      ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
143 <      ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
144 <      
145 <      dAtom->setJx( ji[0] );
146 <      dAtom->setJy( ji[1] );
147 <      dAtom->setJz( ji[2] );
147 >
148 >      dAtom->getJ( ji );
149 >
150 >      for (j=0; j < 3; j++)
151 >        oldJi[3*i + j] = ji[j];
152 >
153      }
154    }
155 +
156 +  // do the iteration:
157 +
158 +  for (k=0; k < 4; k++) {
159 +
160 +    instTemp = tStats->getTemperature();
161 +
162 +    // evolve chi another half step using the temperature at t + dt/2
163 +
164 +    prevChi = chi;
165 +    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
166 +      (tauThermostat*tauThermostat);
167 +
168 +    for( i=0; i<nAtoms; i++ ){
169 +
170 +      atoms[i]->getFrc( frc );
171 +      atoms[i]->getVel(vel);
172 +
173 +      mass = atoms[i]->getMass();
174 +
175 +      // velocity half step
176 +      for (j=0; j < 3; j++)
177 +        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);
178 +
179 +      atoms[i]->setVel( vel );
180 +
181 +      if( atoms[i]->isDirectional() ){
182 +
183 +        dAtom = (DirectionalAtom *)atoms[i];
184 +
185 +        // get and convert the torque to body frame
186 +
187 +        dAtom->getTrq( Tb );
188 +        dAtom->lab2Body( Tb );
189 +
190 +        for (j=0; j < 3; j++)
191 +          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);
192 +
193 +        dAtom->setJ( ji );
194 +      }
195 +    }
196 +
197 +    if (nConstrained){
198 +      constrainB();
199 +    }
200 +
201 +    if (fabs(prevChi - chi) <= chiTolerance) break;
202 +  }
203 +
204 +  integralOfChidt += dt2*chi;
205   }
206  
207 < int NVT::readyCheck() {
208 <
209 <  // First check to see if we have a target temperature.
210 <  // Not having one is fatal.
211 <  
207 > template<typename T> void NVT<T>::resetIntegrator( void ){
208 >
209 >  chi = 0.0;
210 >  integralOfChidt = 0.0;
211 > }
212 >
213 > template<typename T> int NVT<T>::readyCheck() {
214 >
215 >  //check parent's readyCheck() first
216 >  if (T::readyCheck() == -1)
217 >    return -1;
218 >
219 >  // First check to see if we have a target temperature.
220 >  // Not having one is fatal.
221 >
222    if (!have_target_temp) {
223      sprintf( painCave.errMsg,
224               "NVT error: You can't use the NVT integrator without a targetTemp!\n"
# Line 162 | Line 227 | int NVT::readyCheck() {
227      simError();
228      return -1;
229    }
165 –    
166 –  // Next check to see that we have a reasonable number of degrees of freedom
167 –  // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
168 –  // are also fatal.
230  
231 <  if (info->ndf > 0) {
232 <    NkBT = (double)info->ndf * kB * targetTemp;
233 <  } else {
231 >  // We must set tauThermostat.
232 >
233 >  if (!have_tau_thermostat) {
234      sprintf( painCave.errMsg,
235 <             "NVT error: We got a silly number of degrees of freedom!\n"
236 <             );
235 >             "NVT error: If you use the constant temperature\n"
236 >             "   integrator, you must set tauThermostat.\n");
237      painCave.isFatal = 1;
238      simError();
239      return -1;
240    }
180 –    
181 –  // We have our choice on setting qmass or tauThermostat.  One of them
182 –  // must be set.
241  
242 <  if (!have_qmass) {
243 <    if (have_tau_thermostat) {
244 <      sprintf( painCave.errMsg,
245 <               "NVT info: Setting qMass = %lf\n", tauThermostat * NkBT);
246 <      this->setQmass(tauThermostat * NkBT);      
247 <      painCave.isFatal = 0;
248 <      simError();
191 <    } else {
192 <      sprintf( painCave.errMsg,
193 <               "NVT error: If you use the constant temperature\n"
194 <               "   integrator, you must set either tauThermostat or qMass.\n");
195 <      painCave.isFatal = 1;
196 <      simError();
197 <      return -1;
198 <    }
242 >  if (!have_chi_tolerance) {
243 >    sprintf( painCave.errMsg,
244 >             "NVT warning: setting chi tolerance to 1e-6\n");
245 >    chiTolerance = 1e-6;
246 >    have_chi_tolerance = 1;
247 >    painCave.isFatal = 0;
248 >    simError();
249    }
250 <  
250 >
251    return 1;
252 +
253   }
254  
255 + template<typename T> double NVT<T>::getConservedQuantity(void){
256 +
257 +  double conservedQuantity;
258 +  double fkBT;
259 +  double Energy;
260 +  double thermostat_kinetic;
261 +  double thermostat_potential;
262 +
263 +  fkBT = (double)(info->getNDF()    ) * kB * targetTemp;
264 +
265 +  Energy = tStats->getTotalE();
266 +
267 +  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268 +    (2.0 * eConvert);
269 +
270 +  thermostat_potential = fkBT * integralOfChidt / eConvert;
271 +
272 +  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
273 +
274 +  return conservedQuantity;
275 + }
276 +
277 + template<typename T> string NVT<T>::getAdditionalParameters(void){
278 +  string parameters;
279 +  const int BUFFERSIZE = 2000; // size of the read buffer
280 +  char buffer[BUFFERSIZE];
281 +
282 +  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
283 +  parameters += buffer;
284 +
285 +  return parameters;
286 + }

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