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;

  // 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:	853
Committed:	Thu Nov 6 19:11:38 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	6154 byte(s)
Log Message:	did a merge by hand from the new-templateless branch to the main trunk. bug Fixes include: * fixed the switching function from ortho to non-ortho box. !!!!! THis was responsible for all of the sudden deaths we saw. * some formating in the string when we write out the extended system state. * added NPT.cpp to the makefile.in
#	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	// 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	tim	763	oldVel = new double[3*nAtoms];
50			oldJi = new double[3*nAtoms];
51	gezelter	560	}
52
53	tim	763	template<typename T> NVT<T>::~NVT() {
54			delete[] oldVel;
55			delete[] oldJi;
56			}
57
58	tim	645	template<typename T> void NVT<T>::moveA() {
59	tim	837
60	gezelter	600	int i, j;
61	gezelter	560	DirectionalAtom* dAtom;
62	gezelter	600	double Tb[3], ji[3];
63	mmeineke	778	double mass;
64	gezelter	600	double vel[3], pos[3], frc[3];
65
66	gezelter	565	double instTemp;
67	gezelter	560
68	tim	763	// We need the temperature at time = t for the chi update below:
69
70	gezelter	565	instTemp = tStats->getTemperature();
71	tim	837
72	gezelter	560	for( i=0; i<nAtoms; i++ ){
73
74	gezelter	600	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	tim	763	// velocity half step (use chi from previous step here):
82	gezelter	600	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
83			// position whole step
84	gezelter	560	pos[j] += dt * vel[j];
85	gezelter	600	}
86	gezelter	560
87	gezelter	600	atoms[i]->setVel( vel );
88			atoms[i]->setPos( pos );
89	tim	837
90	gezelter	560	if( atoms[i]->isDirectional() ){
91
92			dAtom = (DirectionalAtom *)atoms[i];
93	tim	837
94	gezelter	560	// get and convert the torque to body frame
95	tim	837
96	gezelter	600	dAtom->getTrq( Tb );
97	gezelter	560	dAtom->lab2Body( Tb );
98	tim	837
99	gezelter	560	// get the angular momentum, and propagate a half step
100
101	gezelter	600	dAtom->getJ( ji );
102
103	tim	837	for (j=0; j < 3; j++)
104	gezelter	600	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
105	tim	837
106	mmeineke	778	this->rotationPropagation( dAtom, ji );
107	tim	837
108	gezelter	600	dAtom->setJ( ji );
109	tim	837	}
110	gezelter	560	}
111	tim	837
112	mmeineke	768	if (nConstrained){
113			constrainA();
114			}
115	tim	763
116	tim	837	// Finally, evolve chi a half step (just like a velocity) using
117	tim	763	// 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	gezelter	560	}
123
124	tim	645	template<typename T> void NVT<T>::moveB( void ){
125	tim	763	int i, j, k;
126	gezelter	560	DirectionalAtom* dAtom;
127	gezelter	600	double Tb[3], ji[3];
128			double vel[3], frc[3];
129			double mass;
130	tim	763	double instTemp;
131			double oldChi, prevChi;
132	gezelter	600
133	tim	763	// Set things up for the iteration:
134
135			oldChi = chi;
136
137	gezelter	560	for( i=0; i<nAtoms; i++ ){
138	gezelter	600
139			atoms[i]->getVel( vel );
140
141	tim	763	for (j=0; j < 3; j++)
142			oldVel[3*i + j] = vel[j];
143	gezelter	600
144	gezelter	560	if( atoms[i]->isDirectional() ){
145	gezelter	600
146	gezelter	560	dAtom = (DirectionalAtom *)atoms[i];
147	gezelter	600
148	tim	763	dAtom->getJ( ji );
149	gezelter	600
150	tim	763	for (j=0; j < 3; j++)
151			oldJi[3*i + j] = ji[j];
152	gezelter	600
153	tim	763	}
154			}
155	gezelter	600
156	tim	763	// do the iteration:
157	gezelter	600
158	tim	763	for (k=0; k < 4; k++) {
159	tim	837
160	tim	763	instTemp = tStats->getTemperature();
161
162			// evolve chi another half step using the temperature at t + dt/2
163
164			prevChi = chi;
165	tim	837	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
166	tim	763	(tauThermostat*tauThermostat);
167	tim	837
168	tim	763	for( i=0; i<nAtoms; i++ ){
169
170			atoms[i]->getFrc( frc );
171			atoms[i]->getVel(vel);
172	tim	837
173	tim	763	mass = atoms[i]->getMass();
174	tim	837
175	tim	763	// velocity half step
176	tim	837	for (j=0; j < 3; j++)
177	tim	763	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
178	tim	837
179	tim	763	atoms[i]->setVel( vel );
180	tim	837
181	tim	763	if( atoms[i]->isDirectional() ){
182	tim	837
183	tim	763	dAtom = (DirectionalAtom *)atoms[i];
184	tim	837
185			// get and convert the torque to body frame
186
187	tim	763	dAtom->getTrq( Tb );
188	tim	837	dAtom->lab2Body( Tb );
189
190			for (j=0; j < 3; j++)
191	tim	763	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
192	tim	837
193	tim	763	dAtom->setJ( ji );
194			}
195			}
196	gezelter	600
197	mmeineke	768	if (nConstrained){
198			constrainB();
199			}
200
201	tim	763	if (fabs(prevChi - chi) <= chiTolerance) break;
202	gezelter	560	}
203	tim	837
204	tim	763	integralOfChidt += dt2*chi;
205	gezelter	560	}
206
207	mmeineke	746	template<typename T> void NVT<T>::resetIntegrator( void ){
208	tim	837
209	mmeineke	746	chi = 0.0;
210	tim	763	integralOfChidt = 0.0;
211	mmeineke	746	}
212
213	tim	645	template<typename T> int NVT<T>::readyCheck() {
214	tim	658
215			//check parent's readyCheck() first
216			if (T::readyCheck() == -1)
217			return -1;
218	tim	837
219			// First check to see if we have a target temperature.
220			// Not having one is fatal.
221
222	gezelter	560	if (!have_target_temp) {
223			sprintf( painCave.errMsg,
224			"NVT error: You can't use the NVT integrator without a targetTemp!\n"
225			);
226			painCave.isFatal = 1;
227			simError();
228			return -1;
229			}
230	tim	837
231	gezelter	565	// We must set tauThermostat.
232	tim	837
233	gezelter	565	if (!have_tau_thermostat) {
234	gezelter	560	sprintf( painCave.errMsg,
235	gezelter	565	"NVT error: If you use the constant temperature\n"
236			" integrator, you must set tauThermostat.\n");
237	gezelter	560	painCave.isFatal = 1;
238			simError();
239			return -1;
240	tim	837	}
241	tim	763
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	tim	837	}
250	tim	763
251	tim	837	return 1;
252	tim	763
253	gezelter	560	}
254	tim	763
255			template<typename T> double NVT<T>::getConservedQuantity(void){
256
257			double conservedQuantity;
258	tim	769	double fkBT;
259			double Energy;
260			double thermostat_kinetic;
261			double thermostat_potential;
262	tim	763
263	tim	837	fkBT = (double)(info->getNDF() ) * kB * targetTemp;
264
265	tim	769	Energy = tStats->getTotalE();
266	tim	763
267	tim	837	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
268	tim	769	(2.0 * eConvert);
269	tim	763
270	tim	769	thermostat_potential = fkBT * integralOfChidt / eConvert;
271	tim	763
272	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
273	tim	837
274			return conservedQuantity;
275	tim	763	}
276	tim	837
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	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
283	tim	837	parameters += buffer;
284
285			return parameters;
286			}