src/integrators/NVT.cpp

#include <math.h>

#include "primitives/Atom.hpp"
#include "primitives/SRI.hpp"
#include "primitives/AbstractClasses.hpp"
#include "brains/SimInfo.hpp"
#include "UseTheForce/ForceFields.hpp"
#include "brains/Thermo.hpp"
#include "io/ReadWrite.hpp"
#include "integrators/Integrator.hpp"
#include "utils/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;
  DoubleGenericData * chiValue;
  DoubleGenericData * 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->getPropertyByName(CHIVALUE_ID);
    if(data){
      chiValue = dynamic_cast<DoubleGenericData*>(data);
    }
    
    data = info->getPropertyByName(INTEGRALOFCHIDT_ID);
    if(data){
      integralOfChidtValue = dynamic_cast<DoubleGenericData*>(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;
  Vector3d Tb;
  Vector3d ji;
  double mass;
  Vector3d vel;
  Vector3d pos;
  Vector3d frc;

  double instTemp;

  // We need the temperature at time = t for the chi update below:

  instTemp = tStats->getTemperature();

  for( i=0; i < integrableObjects.size(); i++ ){

    vel = integrableObjects[i]->getVel();
    pos = integrableObjects[i]->getPos();
    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

      Tb = integrableObjects[i]->getTrq();
      integrableObjects[i]->lab2Body( Tb );

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

      ji = integrableObjects[i]->getJ();

      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

  //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++ ){

    vel = integrableObjects[i]->getVel();

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

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

      ji = integrableObjects[i]->getJ();

      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 );
      vel = integrableObjects[i]->getVel();

      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

        Tb = integrableObjects[i]->getTrq();
        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,
             "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:	1701
Committed:	Wed Nov 3 16:08:43 2004 UTC (19 years, 7 months ago) by tim
File size:	7165 byte(s)
Log Message:	mess up ......
#	Content
1	#include <math.h>
2
3	#include "primitives/Atom.hpp"
4	#include "primitives/SRI.hpp"
5	#include "primitives/AbstractClasses.hpp"
6	#include "brains/SimInfo.hpp"
7	#include "UseTheForce/ForceFields.hpp"
8	#include "brains/Thermo.hpp"
9	#include "io/ReadWrite.hpp"
10	#include "integrators/Integrator.hpp"
11	#include "utils/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	DoubleGenericData * chiValue;
21	DoubleGenericData * 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->getPropertyByName(CHIVALUE_ID);
37	if(data){
38	chiValue = dynamic_cast<DoubleGenericData*>(data);
39	}
40
41	data = info->getPropertyByName(INTEGRALOFCHIDT_ID);
42	if(data){
43	integralOfChidtValue = dynamic_cast<DoubleGenericData*>(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	Vector3d Tb;
67	Vector3d ji;
68	double mass;
69	Vector3d vel;
70	Vector3d pos;
71	Vector3d frc;
72
73	double instTemp;
74
75	// We need the temperature at time = t for the chi update below:
76
77	instTemp = tStats->getTemperature();
78
79	for( i=0; i < integrableObjects.size(); i++ ){
80
81	vel = integrableObjects[i]->getVel();
82	pos = integrableObjects[i]->getPos();
83	integrableObjects[i]->getFrc( frc );
84
85	mass = integrableObjects[i]->getMass();
86
87	for (j=0; j < 3; j++) {
88	// velocity half step (use chi from previous step here):
89	vel[j] += dt2 * ((frc[j] / mass ) * eConvert - vel[j]*chi);
90	// position whole step
91	pos[j] += dt * vel[j];
92	}
93
94	integrableObjects[i]->setVel( vel );
95	integrableObjects[i]->setPos( pos );
96
97	if( integrableObjects[i]->isDirectional() ){
98
99	// get and convert the torque to body frame
100
101	Tb = integrableObjects[i]->getTrq();
102	integrableObjects[i]->lab2Body( Tb );
103
104	// get the angular momentum, and propagate a half step
105
106	ji = integrableObjects[i]->getJ();
107
108	for (j=0; j < 3; j++)
109	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
110
111	this->rotationPropagation( integrableObjects[i], ji );
112
113	integrableObjects[i]->setJ( ji );
114	}
115	}
116
117	if(nConstrained)
118	constrainA();
119
120	// Finally, evolve chi a half step (just like a velocity) using
121	// temperature at time t, not time t+dt/2
122
123	//std::cerr << "targetTemp = " << targetTemp << " instTemp = " << instTemp << " tauThermostat = " << tauThermostat << " integral of Chi = " << integralOfChidt << "\n";
124
125	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
126	integralOfChidt += chi*dt2;
127
128	}
129
130	template<typename T> void NVT<T>::moveB( void ){
131	int i, j, k;
132	double Tb[3], ji[3];
133	double vel[3], frc[3];
134	double mass;
135	double instTemp;
136	double oldChi, prevChi;
137
138	// Set things up for the iteration:
139
140	oldChi = chi;
141
142	for( i=0; i < integrableObjects.size(); i++ ){
143
144	vel = integrableObjects[i]->getVel();
145
146	for (j=0; j < 3; j++)
147	oldVel[3*i + j] = vel[j];
148
149	if( integrableObjects[i]->isDirectional() ){
150
151	ji = integrableObjects[i]->getJ();
152
153	for (j=0; j < 3; j++)
154	oldJi[3*i + j] = ji[j];
155
156	}
157	}
158
159	// do the iteration:
160
161	for (k=0; k < 4; k++) {
162
163	instTemp = tStats->getTemperature();
164
165	// evolve chi another half step using the temperature at t + dt/2
166
167	prevChi = chi;
168	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
169	(tauThermostat*tauThermostat);
170
171	for( i=0; i < integrableObjects.size(); i++ ){
172
173	integrableObjects[i]->getFrc( frc );
174	vel = integrableObjects[i]->getVel();
175
176	mass = integrableObjects[i]->getMass();
177
178	// velocity half step
179	for (j=0; j < 3; j++)
180	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
181
182	integrableObjects[i]->setVel( vel );
183
184	if( integrableObjects[i]->isDirectional() ){
185
186	// get and convert the torque to body frame
187
188	Tb = integrableObjects[i]->getTrq();
189	integrableObjects[i]->lab2Body( Tb );
190
191	for (j=0; j < 3; j++)
192	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
193
194	integrableObjects[i]->setJ( ji );
195	}
196	}
197
198	if(nConstrained)
199	constrainB();
200
201	if (fabs(prevChi - chi) <= chiTolerance) break;
202	}
203
204	integralOfChidt += dt2*chi;
205	}
206
207	template<typename T> void NVT<T>::resetIntegrator( void ){
208
209	chi = 0.0;
210	integralOfChidt = 0.0;
211	}
212
213	template<typename T> int NVT<T>::readyCheck() {
214
215	//check parent's readyCheck() first
216	if (T::readyCheck() == -1)
217	return -1;
218
219	// First check to see if we have a target temperature.
220	// Not having one is fatal.
221
222	if (!have_target_temp) {
223	sprintf( painCave.errMsg,
224	"You can't use the NVT integrator without a targetTemp!\n"
225	);
226	painCave.isFatal = 1;
227	painCave.severity = OOPSE_ERROR;
228	simError();
229	return -1;
230	}
231
232	// We must set tauThermostat.
233
234	if (!have_tau_thermostat) {
235	sprintf( painCave.errMsg,
236	"If you use the constant temperature\n"
237	"\tintegrator, you must set tauThermostat.\n");
238	painCave.severity = OOPSE_ERROR;
239	painCave.isFatal = 1;
240	simError();
241	return -1;
242	}
243
244	if (!have_chi_tolerance) {
245	sprintf( painCave.errMsg,
246	"In NVT integrator: setting chi tolerance to 1e-6\n");
247	chiTolerance = 1e-6;
248	have_chi_tolerance = 1;
249	painCave.severity = OOPSE_INFO;
250	painCave.isFatal = 0;
251	simError();
252	}
253
254	return 1;
255
256	}
257
258	template<typename T> double NVT<T>::getConservedQuantity(void){
259
260	double conservedQuantity;
261	double fkBT;
262	double Energy;
263	double thermostat_kinetic;
264	double thermostat_potential;
265
266	fkBT = (double)(info->ndf) * kB * targetTemp;
267
268	Energy = tStats->getTotalE();
269
270	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
271	(2.0 * eConvert);
272
273	thermostat_potential = fkBT * integralOfChidt / eConvert;
274
275	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
276
277	return conservedQuantity;
278	}
279
280	template<typename T> string NVT<T>::getAdditionalParameters(void){
281	string parameters;
282	const int BUFFERSIZE = 2000; // size of the read buffer
283	char buffer[BUFFERSIZE];
284
285	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
286	parameters += buffer;
287
288	return parameters;
289	}