src/integrators/NVT.cpp

#include <math.h>

#include "primitives/Atom.hpp"
#include "primitives/SRI.hpp"
#include "primitives/AbstractClasses.hpp"
#include "brains/SimInfo.hpp"
#include "UseTheForce/ForceFields.hpp"
#include "brains/Thermo.hpp"
#include "io/ReadWrite.hpp"
#include "integrators/Integrator.hpp"
#include "utils/simError.h"


// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697

template<typename T> NVT<T>::NVT ( SimInfo *theInfo, ForceFields* the_ff):
  T( theInfo, the_ff )
{
  GenericData* data;
  DoubleData * chiValue;
  DoubleData * integralOfChidtValue;

  chiValue = NULL;
  integralOfChidtValue = NULL;

  chi = 0.0;
  have_tau_thermostat = 0;
  have_target_temp = 0;
  have_chi_tolerance = 0;
  integralOfChidt = 0.0;


  if( theInfo->useInitXSstate ){

    // retrieve chi and integralOfChidt from simInfo
    data = info->getProperty(CHIVALUE_ID);
    if(data){
      chiValue = dynamic_cast<DoubleData*>(data);
    }
    
    data = info->getProperty(INTEGRALOFCHIDT_ID);
    if(data){
      integralOfChidtValue = dynamic_cast<DoubleData*>(data);
    }
    
    // chi and integralOfChidt should appear by pair
    if(chiValue && integralOfChidtValue){
      chi = chiValue->getData();
      integralOfChidt = integralOfChidtValue->getData();
    }
  }

  oldVel = new double[3*integrableObjects.size()];
  oldJi = new double[3*integrableObjects.size()];
}

template<typename T> NVT<T>::~NVT() {
  delete[] oldVel;
  delete[] oldJi;
}

template<typename T> void NVT<T>::moveA() {

  int i, j;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3];
  double mass;
  double vel[3], pos[3], frc[3];

  double instTemp;

  // We need the temperature at time = t for the chi update below:

  instTemp = tStats->getTemperature();

  for( i=0; i < integrableObjects.size(); i++ ){

    integrableObjects[i]->getVel( vel );
    integrableObjects[i]->getPos( pos );
    integrableObjects[i]->getFrc( frc );

    mass = integrableObjects[i]->getMass();

    for (j=0; j < 3; j++) {
      // velocity half step  (use chi from previous step here):
      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
      // position whole step
      pos[j] += dt * vel[j];
    }

    integrableObjects[i]->setVel( vel );
    integrableObjects[i]->setPos( pos );

    if( integrableObjects[i]->isDirectional() ){

      // get and convert the torque to body frame

      integrableObjects[i]->getTrq( Tb );
      integrableObjects[i]->lab2Body( Tb );

      // get the angular momentum, and propagate a half step

      integrableObjects[i]->getJ( ji );

      for (j=0; j < 3; j++)
        ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);

      this->rotationPropagation( integrableObjects[i], ji );

      integrableObjects[i]->setJ( ji );
    }
  }
  
  if(nConstrained)
    constrainA();

  // Finally, evolve chi a half step (just like a velocity) using
  // temperature at time t, not time t+dt/2

  //std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
  
  chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
  integralOfChidt += chi*dt2;

}

template<typename T> void NVT<T>::moveB( void ){
  int i, j, k;
  double Tb[3], ji[3];
  double vel[3], frc[3];
  double mass;
  double instTemp;
  double oldChi, prevChi;

  // Set things up for the iteration:

  oldChi = chi;

  for( i=0; i < integrableObjects.size(); i++ ){

    integrableObjects[i]->getVel( vel );

    for (j=0; j < 3; j++)
      oldVel[3*i + j]  = vel[j];

    if( integrableObjects[i]->isDirectional() ){

      integrableObjects[i]->getJ( ji );

      for (j=0; j < 3; j++)
        oldJi[3*i + j] = ji[j];

    }
  }

  // do the iteration:

  for (k=0; k < 4; k++) {

    instTemp = tStats->getTemperature();

    // evolve chi another half step using the temperature at t + dt/2

    prevChi = chi;
    chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
      (tauThermostat*tauThermostat);

    for( i=0; i < integrableObjects.size(); i++ ){

      integrableObjects[i]->getFrc( frc );
      integrableObjects[i]->getVel(vel);

      mass = integrableObjects[i]->getMass();

      // velocity half step
      for (j=0; j < 3; j++)
        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - oldVel[3*i + j]*chi);

      integrableObjects[i]->setVel( vel );

      if( integrableObjects[i]->isDirectional() ){

        // get and convert the torque to body frame

        integrableObjects[i]->getTrq( Tb );
        integrableObjects[i]->lab2Body( Tb );

        for (j=0; j < 3; j++)
          ji[j] = oldJi[3*i + j] + dt2 * (Tb[j] * eConvert - oldJi[3*i+j]*chi);

        integrableObjects[i]->setJ( ji );
      }
    }
    
    if(nConstrained)
      constrainB();

    if (fabs(prevChi - chi) <= chiTolerance) break;
  }

  integralOfChidt += dt2*chi;
}

template<typename T> void NVT<T>::resetIntegrator( void ){

  chi = 0.0;
  integralOfChidt = 0.0;
}

template<typename T> int NVT<T>::readyCheck() {

  //check parent's readyCheck() first
  if (T::readyCheck() == -1)
    return -1;

  // First check to see if we have a target temperature.
  // Not having one is fatal.

  if (!have_target_temp) {
    sprintf( painCave.errMsg,
             "You can't use the NVT integrator without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    painCave.severity = OOPSE_ERROR;
    simError();
    return -1;
  }

  // We must set tauThermostat.

  if (!have_tau_thermostat) {
    sprintf( painCave.errMsg,
             "If you use the constant temperature\n"
             "\tintegrator, you must set tauThermostat.\n");
    painCave.severity = OOPSE_ERROR;
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_chi_tolerance) {
    sprintf( painCave.errMsg,
             "In NVT integrator: setting chi tolerance to 1e-6\n");
    chiTolerance = 1e-6;
    have_chi_tolerance = 1;
    painCave.severity = OOPSE_INFO;
    painCave.isFatal = 0;
    simError();
  }

  return 1;

}

template<typename T> double NVT<T>::getConservedQuantity(void){

  double conservedQuantity;
  double fkBT;
  double Energy;
  double thermostat_kinetic;
  double thermostat_potential;

  fkBT = (double)(info->ndf) * kB * targetTemp;

  Energy = tStats->getTotalE();

  thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
    (2.0 * eConvert);

  thermostat_potential = fkBT * integralOfChidt / eConvert;

  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;

  return conservedQuantity;
}

template<typename T> string NVT<T>::getAdditionalParameters(void){
  string parameters;
  const int BUFFERSIZE = 2000; // size of the read buffer
  char buffer[BUFFERSIZE];

  sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
  parameters += buffer;

  return parameters;
}
Revision:	3
Committed:	Fri Sep 24 16:27:58 2004 UTC (21 years, 1 month ago) by tim
File size:	6804 byte(s)
Log Message:	change the #include in source files
#	User	Rev	Content
1	gezelter	2	#include <math.h>
2
3	tim	3	#include "primitives/Atom.hpp"
4			#include "primitives/SRI.hpp"
5			#include "primitives/AbstractClasses.hpp"
6			#include "brains/SimInfo.hpp"
7			#include "UseTheForce/ForceFields.hpp"
8			#include "brains/Thermo.hpp"
9			#include "io/ReadWrite.hpp"
10			#include "integrators/Integrator.hpp"
11			#include "utils/simError.h"
12	gezelter	2
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 )
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
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() {
58			delete[] oldVel;
59			delete[] oldJi;
60			}
61
62			template<typename T> void NVT<T>::moveA() {
63
64			int i, j;
65			DirectionalAtom* dAtom;
66			double Tb[3], ji[3];
67			double mass;
68			double vel[3], pos[3], frc[3];
69
70			double instTemp;
71
72			// We need the temperature at time = t for the chi update below:
73
74			instTemp = tStats->getTemperature();
75
76			for( i=0; i < integrableObjects.size(); i++ ){
77
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);
87			// position whole step
88			pos[j] += dt * vel[j];
89			}
90
91			integrableObjects[i]->setVel( vel );
92			integrableObjects[i]->setPos( pos );
93
94			if( integrableObjects[i]->isDirectional() ){
95
96			// get and convert the torque to body frame
97
98			integrableObjects[i]->getTrq( Tb );
99			integrableObjects[i]->lab2Body( Tb );
100
101			// get the angular momentum, and propagate a half step
102
103			integrableObjects[i]->getJ( ji );
104
105			for (j=0; j < 3; j++)
106			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
107
108			this->rotationPropagation( integrableObjects[i], ji );
109
110			integrableObjects[i]->setJ( ji );
111			}
112			}
113
114			if(nConstrained)
115			constrainA();
116
117			// Finally, evolve chi a half step (just like a velocity) using
118			// temperature at time t, not time t+dt/2
119
120			//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
121
122			chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
123			integralOfChidt += chi*dt2;
124
125			}
126
127			template<typename T> void NVT<T>::moveB( void ){
128			int i, j, k;
129			double Tb[3], ji[3];
130			double vel[3], frc[3];
131			double mass;
132			double instTemp;
133			double oldChi, prevChi;
134
135			// Set things up for the iteration:
136
137			oldChi = chi;
138
139			for( i=0; i < integrableObjects.size(); i++ ){
140
141			integrableObjects[i]->getVel( vel );
142
143			for (j=0; j < 3; j++)
144			oldVel[3*i + j] = vel[j];
145
146			if( integrableObjects[i]->isDirectional() ){
147
148			integrableObjects[i]->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 < integrableObjects.size(); i++ ){
169
170			integrableObjects[i]->getFrc( frc );
171			integrableObjects[i]->getVel(vel);
172
173			mass = integrableObjects[i]->getMass();
174
175			// velocity half step
176			for (j=0; j < 3; j++)
177			vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
178
179			integrableObjects[i]->setVel( vel );
180
181			if( integrableObjects[i]->isDirectional() ){
182
183			// get and convert the torque to body frame
184
185			integrableObjects[i]->getTrq( Tb );
186			integrableObjects[i]->lab2Body( Tb );
187
188			for (j=0; j < 3; j++)
189			ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
190
191			integrableObjects[i]->setJ( ji );
192			}
193			}
194
195			if(nConstrained)
196			constrainB();
197
198			if (fabs(prevChi - chi) <= chiTolerance) break;
199			}
200
201			integralOfChidt += dt2*chi;
202			}
203
204			template<typename T> void NVT<T>::resetIntegrator( void ){
205
206			chi = 0.0;
207			integralOfChidt = 0.0;
208			}
209
210			template<typename T> int NVT<T>::readyCheck() {
211
212			//check parent's readyCheck() first
213			if (T::readyCheck() == -1)
214			return -1;
215
216			// First check to see if we have a target temperature.
217			// Not having one is fatal.
218
219			if (!have_target_temp) {
220			sprintf( painCave.errMsg,
221			"You can't use the NVT integrator without a targetTemp!\n"
222			);
223			painCave.isFatal = 1;
224			painCave.severity = OOPSE_ERROR;
225			simError();
226			return -1;
227			}
228
229			// We must set tauThermostat.
230
231			if (!have_tau_thermostat) {
232			sprintf( painCave.errMsg,
233			"If you use the constant temperature\n"
234			"\tintegrator, you must set tauThermostat.\n");
235			painCave.severity = OOPSE_ERROR;
236			painCave.isFatal = 1;
237			simError();
238			return -1;
239			}
240
241			if (!have_chi_tolerance) {
242			sprintf( painCave.errMsg,
243			"In NVT integrator: setting chi tolerance to 1e-6\n");
244			chiTolerance = 1e-6;
245			have_chi_tolerance = 1;
246			painCave.severity = OOPSE_INFO;
247			painCave.isFatal = 0;
248			simError();
249			}
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->ndf) * 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			}