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 (20 years, 8 months ago) by mmeineke
File size:	6229 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	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*nAtoms];
54	oldJi = new double[3*nAtoms];
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<nAtoms; i++ ){
77
78	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	// 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	atoms[i]->setVel( vel );
92	atoms[i]->setPos( pos );
93
94	if( atoms[i]->isDirectional() ){
95
96	dAtom = (DirectionalAtom *)atoms[i];
97
98	// get and convert the torque to body frame
99
100	dAtom->getTrq( Tb );
101	dAtom->lab2Body( Tb );
102
103	// get the angular momentum, and propagate a half step
104
105	dAtom->getJ( ji );
106
107	for (j=0; j < 3; j++)
108	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
109
110	this->rotationPropagation( dAtom, ji );
111
112	dAtom->setJ( ji );
113	}
114	}
115
116	if (nConstrained){
117	constrainA();
118	}
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	chi += dt2 * ( instTemp / targetTemp - 1.0) / (tauThermostat*tauThermostat);
124	integralOfChidt += chi*dt2;
125
126	}
127
128	template<typename T> void NVT<T>::moveB( void ){
129	int i, j, k;
130	DirectionalAtom* dAtom;
131	double Tb[3], ji[3];
132	double vel[3], frc[3];
133	double mass;
134	double instTemp;
135	double oldChi, prevChi;
136
137	// Set things up for the iteration:
138
139	oldChi = chi;
140
141	for( i=0; i<nAtoms; i++ ){
142
143	atoms[i]->getVel( vel );
144
145	for (j=0; j < 3; j++)
146	oldVel[3*i + j] = vel[j];
147
148	if( atoms[i]->isDirectional() ){
149
150	dAtom = (DirectionalAtom *)atoms[i];
151
152	dAtom->getJ( ji );
153
154	for (j=0; j < 3; j++)
155	oldJi[3*i + j] = ji[j];
156
157	}
158	}
159
160	// do the iteration:
161
162	for (k=0; k < 4; k++) {
163
164	instTemp = tStats->getTemperature();
165
166	// evolve chi another half step using the temperature at t + dt/2
167
168	prevChi = chi;
169	chi = oldChi + dt2 * ( instTemp / targetTemp - 1.0) /
170	(tauThermostat*tauThermostat);
171
172	for( i=0; i<nAtoms; i++ ){
173
174	atoms[i]->getFrc( frc );
175	atoms[i]->getVel(vel);
176
177	mass = atoms[i]->getMass();
178
179	// velocity half step
180	for (j=0; j < 3; j++)
181	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - oldVel[3i + j]chi);
182
183	atoms[i]->setVel( vel );
184
185	if( atoms[i]->isDirectional() ){
186
187	dAtom = (DirectionalAtom *)atoms[i];
188
189	// get and convert the torque to body frame
190
191	dAtom->getTrq( Tb );
192	dAtom->lab2Body( Tb );
193
194	for (j=0; j < 3; j++)
195	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
196
197	dAtom->setJ( ji );
198	}
199	}
200
201	if (nConstrained){
202	constrainB();
203	}
204
205	if (fabs(prevChi - chi) <= chiTolerance) break;
206	}
207
208	integralOfChidt += dt2*chi;
209	}
210
211	template<typename T> void NVT<T>::resetIntegrator( void ){
212
213	chi = 0.0;
214	integralOfChidt = 0.0;
215	}
216
217	template<typename T> int NVT<T>::readyCheck() {
218
219	//check parent's readyCheck() first
220	if (T::readyCheck() == -1)
221	return -1;
222
223	// First check to see if we have a target temperature.
224	// Not having one is fatal.
225
226	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
235	// We must set tauThermostat.
236
237	if (!have_tau_thermostat) {
238	sprintf( painCave.errMsg,
239	"NVT error: If you use the constant temperature\n"
240	" integrator, you must set tauThermostat.\n");
241	painCave.isFatal = 1;
242	simError();
243	return -1;
244	}
245
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	}
254
255	return 1;
256
257	}
258
259	template<typename T> double NVT<T>::getConservedQuantity(void){
260
261	double conservedQuantity;
262	double fkBT;
263	double Energy;
264	double thermostat_kinetic;
265	double thermostat_potential;
266
267	fkBT = (double)(info->getNDF() ) * kB * targetTemp;
268
269	Energy = tStats->getTotalE();
270
271	thermostat_kinetic = fkBT* tauThermostat * tauThermostat * chi * chi /
272	(2.0 * eConvert);
273
274	thermostat_potential = fkBT * integralOfChidt / eConvert;
275
276	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential;
277
278	return conservedQuantity;
279	}
280
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	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
287	parameters += buffer;
288
289	return parameters;
290	}