OOPSE/libmdtools/NVT.cpp

#include <math.h>

#include "Atom.hpp"
#include "SRI.hpp"
#include "AbstractClasses.hpp"
#include "SimInfo.hpp"
#include "ForceFields.hpp"
#include "Thermo.hpp"
#include "ReadWrite.hpp"
#include "Integrator.hpp"
#include "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();
    }
  }


  std::cerr << "building oldVel with \t" << integrableObjects.size() << "\n";
  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

  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,
             "NVT error: You can't use the NVT integrator without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  // We must set tauThermostat.

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

  if (!have_chi_tolerance) {
    sprintf( painCave.errMsg,
             "NVT warning: setting chi tolerance to 1e-6\n");
    chiTolerance = 1e-6;
    have_chi_tolerance = 1;
    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->getNDF()    ) * 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:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	6554 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	User	Rev	Content
1	mmeineke	853	#include <math.h>
2
3	gezelter	560	#include "Atom.hpp"
4			#include "SRI.hpp"
5			#include "AbstractClasses.hpp"
6			#include "SimInfo.hpp"
7			#include "ForceFields.hpp"
8			#include "Thermo.hpp"
9			#include "ReadWrite.hpp"
10			#include "Integrator.hpp"
11	tim	837	#include "simError.h"
12	mmeineke	561
13
14	gezelter	560	// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
15
16	tim	645	template<typename T> NVT<T>::NVT ( SimInfo theInfo, ForceFields the_ff):
17			T( theInfo, the_ff )
18	mmeineke	561	{
19	tim	837	GenericData* data;
20			DoubleData * chiValue;
21			DoubleData * integralOfChidtValue;
22
23			chiValue = NULL;
24			integralOfChidtValue = NULL;
25
26	gezelter	565	chi = 0.0;
27	gezelter	560	have_tau_thermostat = 0;
28			have_target_temp = 0;
29	tim	763	have_chi_tolerance = 0;
30			integralOfChidt = 0.0;
31
32	tim	837
33	mmeineke	855	if( theInfo->useInitXSstate ){
34	tim	837
35	mmeineke	855	// 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	tim	837	}
52
53	gezelter	1097
54			std::cerr << "building oldVel with \t" << integrableObjects.size() << "\n";
55			oldVel = new double[3*integrableObjects.size()];
56			oldJi = new double[3*integrableObjects.size()];
57	gezelter	560	}
58
59	tim	763	template<typename T> NVT<T>::~NVT() {
60			delete[] oldVel;
61			delete[] oldJi;
62			}
63
64	tim	645	template<typename T> void NVT<T>::moveA() {
65	tim	837
66	gezelter	600	int i, j;
67	gezelter	560	DirectionalAtom* dAtom;
68	gezelter	600	double Tb[3], ji[3];
69	mmeineke	778	double mass;
70	gezelter	600	double vel[3], pos[3], frc[3];
71
72	gezelter	565	double instTemp;
73	gezelter	560
74	tim	763	// We need the temperature at time = t for the chi update below:
75
76	gezelter	565	instTemp = tStats->getTemperature();
77	tim	837
78	gezelter	1097	for( i=0; i < integrableObjects.size(); i++ ){
79	gezelter	560
80	gezelter	1097	integrableObjects[i]->getVel( vel );
81			integrableObjects[i]->getPos( pos );
82			integrableObjects[i]->getFrc( frc );
83	gezelter	600
84	gezelter	1097	mass = integrableObjects[i]->getMass();
85	gezelter	600
86			for (j=0; j < 3; j++) {
87	tim	763	// velocity half step (use chi from previous step here):
88	gezelter	600	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
89			// position whole step
90	gezelter	560	pos[j] += dt * vel[j];
91	gezelter	600	}
92	gezelter	560
93	gezelter	1097	integrableObjects[i]->setVel( vel );
94			integrableObjects[i]->setPos( pos );
95	tim	837
96	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
97	gezelter	560
98			// get and convert the torque to body frame
99	tim	837
100	gezelter	1097	integrableObjects[i]->getTrq( Tb );
101			integrableObjects[i]->lab2Body( Tb );
102	tim	837
103	gezelter	560	// get the angular momentum, and propagate a half step
104
105	gezelter	1097	integrableObjects[i]->getJ( ji );
106	gezelter	600
107	tim	837	for (j=0; j < 3; j++)
108	gezelter	600	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
109	tim	837
110	gezelter	1097	this->rotationPropagation( integrableObjects[i], ji );
111	tim	837
112	gezelter	1097	integrableObjects[i]->setJ( ji );
113	tim	837	}
114	gezelter	560	}
115	tim	837
116	mmeineke	768	if (nConstrained){
117			constrainA();
118			}
119	tim	763
120	tim	837	// Finally, evolve chi a half step (just like a velocity) using
121	tim	763	// temperature at time t, not time t+dt/2
122
123			chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
124			integralOfChidt += chi*dt2;
125
126	gezelter	560	}
127
128	tim	645	template<typename T> void NVT<T>::moveB( void ){
129	tim	763	int i, j, k;
130	gezelter	600	double Tb[3], ji[3];
131			double vel[3], frc[3];
132			double mass;
133	tim	763	double instTemp;
134			double oldChi, prevChi;
135	gezelter	600
136	tim	763	// Set things up for the iteration:
137
138			oldChi = chi;
139
140	gezelter	1097	for( i=0; i < integrableObjects.size(); i++ ){
141	gezelter	600
142	gezelter	1097	integrableObjects[i]->getVel( vel );
143	gezelter	600
144	tim	763	for (j=0; j < 3; j++)
145			oldVel[3*i + j] = vel[j];
146	gezelter	600
147	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
148	gezelter	600
149	gezelter	1097	integrableObjects[i]->getJ( ji );
150	gezelter	600
151	tim	763	for (j=0; j < 3; j++)
152			oldJi[3*i + j] = ji[j];
153	gezelter	600
154	tim	763	}
155			}
156	gezelter	600
157	tim	763	// do the iteration:
158	gezelter	600
159	tim	763	for (k=0; k < 4; k++) {
160	tim	837
161	tim	763	instTemp = tStats->getTemperature();
162
163			// evolve chi another half step using the temperature at t + dt/2
164
165			prevChi = chi;
166	tim	837	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
167	tim	763	(tauThermostat*tauThermostat);
168	tim	837
169	gezelter	1097	for( i=0; i < integrableObjects.size(); i++ ){
170	tim	763
171	gezelter	1097	integrableObjects[i]->getFrc( frc );
172			integrableObjects[i]->getVel(vel);
173	tim	837
174	gezelter	1097	mass = integrableObjects[i]->getMass();
175	tim	837
176	tim	763	// velocity half step
177	tim	837	for (j=0; j < 3; j++)
178	tim	763	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
179	tim	837
180	gezelter	1097	integrableObjects[i]->setVel( vel );
181	tim	837
182	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
183	tim	837
184			// get and convert the torque to body frame
185
186	gezelter	1097	integrableObjects[i]->getTrq( Tb );
187			integrableObjects[i]->lab2Body( Tb );
188	tim	837
189			for (j=0; j < 3; j++)
190	tim	763	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
191	tim	837
192	gezelter	1097	integrableObjects[i]->setJ( ji );
193	tim	763	}
194			}
195	gezelter	600
196	mmeineke	768	if (nConstrained){
197			constrainB();
198			}
199
200	tim	763	if (fabs(prevChi - chi) <= chiTolerance) break;
201	gezelter	560	}
202	tim	837
203	tim	763	integralOfChidt += dt2*chi;
204	gezelter	560	}
205
206	mmeineke	746	template<typename T> void NVT<T>::resetIntegrator( void ){
207	tim	837
208	mmeineke	746	chi = 0.0;
209	tim	763	integralOfChidt = 0.0;
210	mmeineke	746	}
211
212	tim	645	template<typename T> int NVT<T>::readyCheck() {
213	tim	658
214			//check parent's readyCheck() first
215			if (T::readyCheck() == -1)
216			return -1;
217	tim	837
218			// First check to see if we have a target temperature.
219			// Not having one is fatal.
220
221	gezelter	560	if (!have_target_temp) {
222			sprintf( painCave.errMsg,
223			"NVT error: You can't use the NVT integrator without a targetTemp!\n"
224			);
225			painCave.isFatal = 1;
226			simError();
227			return -1;
228			}
229	tim	837
230	gezelter	565	// We must set tauThermostat.
231	tim	837
232	gezelter	565	if (!have_tau_thermostat) {
233	gezelter	560	sprintf( painCave.errMsg,
234	gezelter	565	"NVT error: If you use the constant temperature\n"
235			" integrator, you must set tauThermostat.\n");
236	gezelter	560	painCave.isFatal = 1;
237			simError();
238			return -1;
239	tim	837	}
240	tim	763
241			if (!have_chi_tolerance) {
242			sprintf( painCave.errMsg,
243			"NVT warning: setting chi tolerance to 1e-6\n");
244			chiTolerance = 1e-6;
245			have_chi_tolerance = 1;
246			painCave.isFatal = 0;
247			simError();
248	tim	837	}
249	tim	763
250	tim	837	return 1;
251	tim	763
252	gezelter	560	}
253	tim	763
254			template<typename T> double NVT<T>::getConservedQuantity(void){
255
256			double conservedQuantity;
257	tim	769	double fkBT;
258			double Energy;
259			double thermostat_kinetic;
260			double thermostat_potential;
261	tim	763
262	tim	837	fkBT = (double)(info->getNDF() ) * kB * targetTemp;
263
264	tim	769	Energy = tStats->getTotalE();
265	tim	763
266	tim	837	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
267	tim	769	(2.0 * eConvert);
268	tim	763
269	tim	769	thermostat_potential = fkBT * integralOfChidt / eConvert;
270	tim	763
271	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
272	tim	837
273			return conservedQuantity;
274	tim	763	}
275	tim	837
276			template<typename T> string NVT<T>::getAdditionalParameters(void){
277			string parameters;
278			const int BUFFERSIZE = 2000; // size of the read buffer
279			char buffer[BUFFERSIZE];
280
281	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
282	tim	837	parameters += buffer;
283
284			return parameters;
285			}