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*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 );
    }
  }

  consFramework->doConstrainA();

  // 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 );
      }
    }

    consFramework->doConstrainB();

    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:	1268
Committed:	Fri Jun 11 17:16:21 2004 UTC (20 years ago) by tim
File size:	6708 byte(s)
Log Message:	roll in progress
#	Content
1	#include <math.h>
2
3	#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	#include "simError.h"
12
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	consFramework->doConstrainA();
115
116	// Finally, evolve chi a half step (just like a velocity) using
117	// temperature at time t, not time t+dt/2
118
119	//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
120
121	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
122	integralOfChidt += chi*dt2;
123
124	}
125
126	template<typename T> void NVT<T>::moveB( void ){
127	int i, j, k;
128	double Tb[3], ji[3];
129	double vel[3], frc[3];
130	double mass;
131	double instTemp;
132	double oldChi, prevChi;
133
134	// Set things up for the iteration:
135
136	oldChi = chi;
137
138	for( i=0; i < integrableObjects.size(); i++ ){
139
140	integrableObjects[i]->getVel( vel );
141
142	for (j=0; j < 3; j++)
143	oldVel[3*i + j] = vel[j];
144
145	if( integrableObjects[i]->isDirectional() ){
146
147	integrableObjects[i]->getJ( ji );
148
149	for (j=0; j < 3; j++)
150	oldJi[3*i + j] = ji[j];
151
152	}
153	}
154
155	// do the iteration:
156
157	for (k=0; k < 4; k++) {
158
159	instTemp = tStats->getTemperature();
160
161	// evolve chi another half step using the temperature at t + dt/2
162
163	prevChi = chi;
164	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
165	(tauThermostat*tauThermostat);
166
167	for( i=0; i < integrableObjects.size(); i++ ){
168
169	integrableObjects[i]->getFrc( frc );
170	integrableObjects[i]->getVel(vel);
171
172	mass = integrableObjects[i]->getMass();
173
174	// velocity half step
175	for (j=0; j < 3; j++)
176	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
177
178	integrableObjects[i]->setVel( vel );
179
180	if( integrableObjects[i]->isDirectional() ){
181
182	// get and convert the torque to body frame
183
184	integrableObjects[i]->getTrq( Tb );
185	integrableObjects[i]->lab2Body( Tb );
186
187	for (j=0; j < 3; j++)
188	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
189
190	integrableObjects[i]->setJ( ji );
191	}
192	}
193
194	consFramework->doConstrainB();
195
196	if (fabs(prevChi - chi) <= chiTolerance) break;
197	}
198
199	integralOfChidt += dt2*chi;
200	}
201
202	template<typename T> void NVT<T>::resetIntegrator( void ){
203
204	chi = 0.0;
205	integralOfChidt = 0.0;
206	}
207
208	template<typename T> int NVT<T>::readyCheck() {
209
210	//check parent's readyCheck() first
211	if (T::readyCheck() == -1)
212	return -1;
213
214	// First check to see if we have a target temperature.
215	// Not having one is fatal.
216
217	if (!have_target_temp) {
218	sprintf( painCave.errMsg,
219	"You can't use the NVT integrator without a targetTemp!\n"
220	);
221	painCave.isFatal = 1;
222	painCave.severity = OOPSE_ERROR;
223	simError();
224	return -1;
225	}
226
227	// We must set tauThermostat.
228
229	if (!have_tau_thermostat) {
230	sprintf( painCave.errMsg,
231	"If you use the constant temperature\n"
232	"\tintegrator, you must set tauThermostat.\n");
233	painCave.severity = OOPSE_ERROR;
234	painCave.isFatal = 1;
235	simError();
236	return -1;
237	}
238
239	if (!have_chi_tolerance) {
240	sprintf( painCave.errMsg,
241	"In NVT integrator: setting chi tolerance to 1e-6\n");
242	chiTolerance = 1e-6;
243	have_chi_tolerance = 1;
244	painCave.severity = OOPSE_INFO;
245	painCave.isFatal = 0;
246	simError();
247	}
248
249	return 1;
250
251	}
252
253	template<typename T> double NVT<T>::getConservedQuantity(void){
254
255	double conservedQuantity;
256	double fkBT;
257	double Energy;
258	double thermostat_kinetic;
259	double thermostat_potential;
260
261	fkBT = (double)(info->ndf) * kB * targetTemp;
262
263	Energy = tStats->getTotalE();
264
265	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
266	(2.0 * eConvert);
267
268	thermostat_potential = fkBT * integralOfChidt / eConvert;
269
270	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
271
272	return conservedQuantity;
273	}
274
275	template<typename T> string NVT<T>::getAdditionalParameters(void){
276	string parameters;
277	const int BUFFERSIZE = 2000; // size of the read buffer
278	char buffer[BUFFERSIZE];
279
280	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
281	parameters += buffer;
282
283	return parameters;
284	}