OOPSE/libmdtools/NVT.cpp

#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 )
{
  chi = 0.0;
  have_tau_thermostat = 0;
  have_target_temp = 0;
  have_chi_tolerance = 0;
  integralOfChidt = 0.0;

  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;
  
  cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic << 
      "\t" << thermostat_potential << "\t" << conservedQuantity << endl;

  return conservedQuantity; 
}
Revision:	778
Committed:	Fri Sep 19 20:00:27 2003 UTC (20 years, 9 months ago) by mmeineke
File size:	5557 byte(s)
Log Message:	added NPT base class. NPTi is up to date. NPTf is not.
#	User	Rev	Content
1	gezelter	560	#include "Atom.hpp"
2			#include "SRI.hpp"
3			#include "AbstractClasses.hpp"
4			#include "SimInfo.hpp"
5			#include "ForceFields.hpp"
6			#include "Thermo.hpp"
7			#include "ReadWrite.hpp"
8			#include "Integrator.hpp"
9	mmeineke	561	#include "simError.h"
10
11
12	gezelter	560	// Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
13
14	tim	645	template<typename T> NVT<T>::NVT ( SimInfo theInfo, ForceFields the_ff):
15			T( theInfo, the_ff )
16	mmeineke	561	{
17	gezelter	565	chi = 0.0;
18	gezelter	560	have_tau_thermostat = 0;
19			have_target_temp = 0;
20	tim	763	have_chi_tolerance = 0;
21			integralOfChidt = 0.0;
22
23			oldVel = new double[3*nAtoms];
24			oldJi = new double[3*nAtoms];
25	gezelter	560	}
26
27	tim	763	template<typename T> NVT<T>::~NVT() {
28			delete[] oldVel;
29			delete[] oldJi;
30			}
31
32	tim	645	template<typename T> void NVT<T>::moveA() {
33	gezelter	560
34	gezelter	600	int i, j;
35	gezelter	560	DirectionalAtom* dAtom;
36	gezelter	600	double Tb[3], ji[3];
37	mmeineke	778	double mass;
38	gezelter	600	double vel[3], pos[3], frc[3];
39
40	gezelter	565	double instTemp;
41	gezelter	560
42	tim	763	// We need the temperature at time = t for the chi update below:
43
44	gezelter	565	instTemp = tStats->getTemperature();
45
46	gezelter	560	for( i=0; i<nAtoms; i++ ){
47
48	gezelter	600	atoms[i]->getVel( vel );
49			atoms[i]->getPos( pos );
50			atoms[i]->getFrc( frc );
51
52			mass = atoms[i]->getMass();
53
54			for (j=0; j < 3; j++) {
55	tim	763	// velocity half step (use chi from previous step here):
56	gezelter	600	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
57			// position whole step
58	gezelter	560	pos[j] += dt * vel[j];
59	gezelter	600	}
60	gezelter	560
61	gezelter	600	atoms[i]->setVel( vel );
62			atoms[i]->setPos( pos );
63	gezelter	560
64			if( atoms[i]->isDirectional() ){
65
66			dAtom = (DirectionalAtom *)atoms[i];
67
68			// get and convert the torque to body frame
69
70	gezelter	600	dAtom->getTrq( Tb );
71	gezelter	560	dAtom->lab2Body( Tb );
72
73			// get the angular momentum, and propagate a half step
74
75	gezelter	600	dAtom->getJ( ji );
76
77			for (j=0; j < 3; j++)
78			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
79	gezelter	560
80	mmeineke	778	this->rotationPropagation( dAtom, ji );
81	gezelter	560
82	gezelter	600	dAtom->setJ( ji );
83			}
84	gezelter	560	}
85	mmeineke	768
86			if (nConstrained){
87			constrainA();
88			}
89	tim	763
90			// Finally, evolve chi a half step (just like a velocity) using
91			// temperature at time t, not time t+dt/2
92
93			chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
94			integralOfChidt += chi*dt2;
95
96	gezelter	560	}
97
98	tim	645	template<typename T> void NVT<T>::moveB( void ){
99	tim	763	int i, j, k;
100	gezelter	560	DirectionalAtom* dAtom;
101	gezelter	600	double Tb[3], ji[3];
102			double vel[3], frc[3];
103			double mass;
104	tim	763	double instTemp;
105			double oldChi, prevChi;
106	gezelter	600
107	tim	763	// Set things up for the iteration:
108
109			oldChi = chi;
110
111	gezelter	560	for( i=0; i<nAtoms; i++ ){
112	gezelter	600
113			atoms[i]->getVel( vel );
114
115	tim	763	for (j=0; j < 3; j++)
116			oldVel[3*i + j] = vel[j];
117	gezelter	600
118	gezelter	560	if( atoms[i]->isDirectional() ){
119	gezelter	600
120	gezelter	560	dAtom = (DirectionalAtom *)atoms[i];
121	gezelter	600
122	tim	763	dAtom->getJ( ji );
123	gezelter	600
124	tim	763	for (j=0; j < 3; j++)
125			oldJi[3*i + j] = ji[j];
126	gezelter	600
127	tim	763	}
128			}
129	gezelter	600
130	tim	763	// do the iteration:
131	gezelter	600
132	tim	763	for (k=0; k < 4; k++) {
133
134			instTemp = tStats->getTemperature();
135
136			// evolve chi another half step using the temperature at t + dt/2
137
138			prevChi = chi;
139			chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
140			(tauThermostat*tauThermostat);
141
142			for( i=0; i<nAtoms; i++ ){
143
144			atoms[i]->getFrc( frc );
145			atoms[i]->getVel(vel);
146
147			mass = atoms[i]->getMass();
148
149			// velocity half step
150	gezelter	600	for (j=0; j < 3; j++)
151	tim	763	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
152	gezelter	560
153	tim	763	atoms[i]->setVel( vel );
154
155			if( atoms[i]->isDirectional() ){
156
157			dAtom = (DirectionalAtom *)atoms[i];
158
159			// get and convert the torque to body frame
160
161			dAtom->getTrq( Tb );
162			dAtom->lab2Body( Tb );
163
164			for (j=0; j < 3; j++)
165			ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
166
167			dAtom->setJ( ji );
168			}
169			}
170	gezelter	600
171	mmeineke	768	if (nConstrained){
172			constrainB();
173			}
174
175	tim	763	if (fabs(prevChi - chi) <= chiTolerance) break;
176	gezelter	560	}
177	tim	763
178			integralOfChidt += dt2*chi;
179	gezelter	560	}
180
181	mmeineke	746	template<typename T> void NVT<T>::resetIntegrator( void ){
182
183			chi = 0.0;
184	tim	763	integralOfChidt = 0.0;
185	mmeineke	746	}
186
187	tim	645	template<typename T> int NVT<T>::readyCheck() {
188	tim	658
189			//check parent's readyCheck() first
190			if (T::readyCheck() == -1)
191			return -1;
192
193	gezelter	560	// First check to see if we have a target temperature.
194			// Not having one is fatal.
195
196			if (!have_target_temp) {
197			sprintf( painCave.errMsg,
198			"NVT error: You can't use the NVT integrator without a targetTemp!\n"
199			);
200			painCave.isFatal = 1;
201			simError();
202			return -1;
203			}
204	gezelter	565
205			// We must set tauThermostat.
206
207			if (!have_tau_thermostat) {
208	gezelter	560	sprintf( painCave.errMsg,
209	gezelter	565	"NVT error: If you use the constant temperature\n"
210			" integrator, you must set tauThermostat.\n");
211	gezelter	560	painCave.isFatal = 1;
212			simError();
213			return -1;
214	gezelter	565	}
215	tim	763
216			if (!have_chi_tolerance) {
217			sprintf( painCave.errMsg,
218			"NVT warning: setting chi tolerance to 1e-6\n");
219			chiTolerance = 1e-6;
220			have_chi_tolerance = 1;
221			painCave.isFatal = 0;
222			simError();
223			}
224
225			return 1;
226
227	gezelter	560	}
228	tim	763
229			template<typename T> double NVT<T>::getConservedQuantity(void){
230
231			double conservedQuantity;
232	tim	769	double fkBT;
233			double Energy;
234			double thermostat_kinetic;
235			double thermostat_potential;
236	tim	763
237	tim	769	fkBT = (double)(info->getNDF() ) * kB * targetTemp;
238
239			Energy = tStats->getTotalE();
240	tim	763
241	tim	769	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
242			(2.0 * eConvert);
243	tim	763
244	tim	769	thermostat_potential = fkBT * integralOfChidt / eConvert;
245	tim	763
246	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
247
248			cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
249			"\t" << thermostat_potential << "\t" << conservedQuantity << endl;
250
251	tim	763	return conservedQuantity;
252			}