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();
    }
  }

  oldVel = new double[3*nAtoms];
  oldJi = new double[3*nAtoms];
}

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<nAtoms; i++ ){

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

    mass = atoms[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];
    }

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

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

      dAtom = (DirectionalAtom *)atoms[i];

      // get and convert the torque to body frame

      dAtom->getTrq( Tb );
      dAtom->lab2Body( Tb );

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

      dAtom->getJ( ji );

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

      this->rotationPropagation( dAtom, ji );

      dAtom->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;
  DirectionalAtom* dAtom;
  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<nAtoms; i++ ){

    atoms[i]->getVel( vel );

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

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

      dAtom = (DirectionalAtom *)atoms[i];

      dAtom->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<nAtoms; i++ ){

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

      mass = atoms[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);

      atoms[i]->setVel( vel );

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

        dAtom = (DirectionalAtom *)atoms[i];

        // get and convert the torque to body frame

        dAtom->getTrq( Tb );
        dAtom->lab2Body( Tb );

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

        dAtom->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:	855
Committed:	Thu Nov 6 22:01:37 2003 UTC (21 years, 11 months ago) by mmeineke
File size:	6229 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	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	tim	763	oldVel = new double[3*nAtoms];
54			oldJi = new double[3*nAtoms];
55	gezelter	560	}
56
57	tim	763	template<typename T> NVT<T>::~NVT() {
58			delete[] oldVel;
59			delete[] oldJi;
60			}
61
62	tim	645	template<typename T> void NVT<T>::moveA() {
63	tim	837
64	gezelter	600	int i, j;
65	gezelter	560	DirectionalAtom* dAtom;
66	gezelter	600	double Tb[3], ji[3];
67	mmeineke	778	double mass;
68	gezelter	600	double vel[3], pos[3], frc[3];
69
70	gezelter	565	double instTemp;
71	gezelter	560
72	tim	763	// We need the temperature at time = t for the chi update below:
73
74	gezelter	565	instTemp = tStats->getTemperature();
75	tim	837
76	gezelter	560	for( i=0; i<nAtoms; i++ ){
77
78	gezelter	600	atoms[i]->getVel( vel );
79			atoms[i]->getPos( pos );
80			atoms[i]->getFrc( frc );
81
82			mass = atoms[i]->getMass();
83
84			for (j=0; j < 3; j++) {
85	tim	763	// velocity half step (use chi from previous step here):
86	gezelter	600	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
87			// position whole step
88	gezelter	560	pos[j] += dt * vel[j];
89	gezelter	600	}
90	gezelter	560
91	gezelter	600	atoms[i]->setVel( vel );
92			atoms[i]->setPos( pos );
93	tim	837
94	gezelter	560	if( atoms[i]->isDirectional() ){
95
96			dAtom = (DirectionalAtom *)atoms[i];
97	tim	837
98	gezelter	560	// get and convert the torque to body frame
99	tim	837
100	gezelter	600	dAtom->getTrq( Tb );
101	gezelter	560	dAtom->lab2Body( Tb );
102	tim	837
103	gezelter	560	// get the angular momentum, and propagate a half step
104
105	gezelter	600	dAtom->getJ( ji );
106
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	mmeineke	778	this->rotationPropagation( dAtom, ji );
111	tim	837
112	gezelter	600	dAtom->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	560	DirectionalAtom* dAtom;
131	gezelter	600	double Tb[3], ji[3];
132			double vel[3], frc[3];
133			double mass;
134	tim	763	double instTemp;
135			double oldChi, prevChi;
136	gezelter	600
137	tim	763	// Set things up for the iteration:
138
139			oldChi = chi;
140
141	gezelter	560	for( i=0; i<nAtoms; i++ ){
142	gezelter	600
143			atoms[i]->getVel( vel );
144
145	tim	763	for (j=0; j < 3; j++)
146			oldVel[3*i + j] = vel[j];
147	gezelter	600
148	gezelter	560	if( atoms[i]->isDirectional() ){
149	gezelter	600
150	gezelter	560	dAtom = (DirectionalAtom *)atoms[i];
151	gezelter	600
152	tim	763	dAtom->getJ( ji );
153	gezelter	600
154	tim	763	for (j=0; j < 3; j++)
155			oldJi[3*i + j] = ji[j];
156	gezelter	600
157	tim	763	}
158			}
159	gezelter	600
160	tim	763	// do the iteration:
161	gezelter	600
162	tim	763	for (k=0; k < 4; k++) {
163	tim	837
164	tim	763	instTemp = tStats->getTemperature();
165
166			// evolve chi another half step using the temperature at t + dt/2
167
168			prevChi = chi;
169	tim	837	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
170	tim	763	(tauThermostat*tauThermostat);
171	tim	837
172	tim	763	for( i=0; i<nAtoms; i++ ){
173
174			atoms[i]->getFrc( frc );
175			atoms[i]->getVel(vel);
176	tim	837
177	tim	763	mass = atoms[i]->getMass();
178	tim	837
179	tim	763	// velocity half step
180	tim	837	for (j=0; j < 3; j++)
181	tim	763	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
182	tim	837
183	tim	763	atoms[i]->setVel( vel );
184	tim	837
185	tim	763	if( atoms[i]->isDirectional() ){
186	tim	837
187	tim	763	dAtom = (DirectionalAtom *)atoms[i];
188	tim	837
189			// get and convert the torque to body frame
190
191	tim	763	dAtom->getTrq( Tb );
192	tim	837	dAtom->lab2Body( Tb );
193
194			for (j=0; j < 3; j++)
195	tim	763	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
196	tim	837
197	tim	763	dAtom->setJ( ji );
198			}
199			}
200	gezelter	600
201	mmeineke	768	if (nConstrained){
202			constrainB();
203			}
204
205	tim	763	if (fabs(prevChi - chi) <= chiTolerance) break;
206	gezelter	560	}
207	tim	837
208	tim	763	integralOfChidt += dt2*chi;
209	gezelter	560	}
210
211	mmeineke	746	template<typename T> void NVT<T>::resetIntegrator( void ){
212	tim	837
213	mmeineke	746	chi = 0.0;
214	tim	763	integralOfChidt = 0.0;
215	mmeineke	746	}
216
217	tim	645	template<typename T> int NVT<T>::readyCheck() {
218	tim	658
219			//check parent's readyCheck() first
220			if (T::readyCheck() == -1)
221			return -1;
222	tim	837
223			// First check to see if we have a target temperature.
224			// Not having one is fatal.
225
226	gezelter	560	if (!have_target_temp) {
227			sprintf( painCave.errMsg,
228			"NVT error: You can't use the NVT integrator without a targetTemp!\n"
229			);
230			painCave.isFatal = 1;
231			simError();
232			return -1;
233			}
234	tim	837
235	gezelter	565	// We must set tauThermostat.
236	tim	837
237	gezelter	565	if (!have_tau_thermostat) {
238	gezelter	560	sprintf( painCave.errMsg,
239	gezelter	565	"NVT error: If you use the constant temperature\n"
240			" integrator, you must set tauThermostat.\n");
241	gezelter	560	painCave.isFatal = 1;
242			simError();
243			return -1;
244	tim	837	}
245	tim	763
246			if (!have_chi_tolerance) {
247			sprintf( painCave.errMsg,
248			"NVT warning: setting chi tolerance to 1e-6\n");
249			chiTolerance = 1e-6;
250			have_chi_tolerance = 1;
251			painCave.isFatal = 0;
252			simError();
253	tim	837	}
254	tim	763
255	tim	837	return 1;
256	tim	763
257	gezelter	560	}
258	tim	763
259			template<typename T> double NVT<T>::getConservedQuantity(void){
260
261			double conservedQuantity;
262	tim	769	double fkBT;
263			double Energy;
264			double thermostat_kinetic;
265			double thermostat_potential;
266	tim	763
267	tim	837	fkBT = (double)(info->getNDF() ) * kB * targetTemp;
268
269	tim	769	Energy = tStats->getTotalE();
270	tim	763
271	tim	837	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
272	tim	769	(2.0 * eConvert);
273	tim	763
274	tim	769	thermostat_potential = fkBT * integralOfChidt / eConvert;
275	tim	763
276	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
277	tim	837
278			return conservedQuantity;
279	tim	763	}
280	tim	837
281			template<typename T> string NVT<T>::getAdditionalParameters(void){
282			string parameters;
283			const int BUFFERSIZE = 2000; // size of the read buffer
284			char buffer[BUFFERSIZE];
285
286	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
287	tim	837	parameters += buffer;
288
289			return parameters;
290			}