OOPSE/libmdtools/NPT.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"

#ifdef IS_MPI
#include "mpiSimulation.hpp"
#endif


// Basic isotropic thermostating and barostating via the Melchionna
// modification of the Hoover algorithm:
//
//    Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
//       Molec. Phys., 78, 533.
//
//           and
//
//    Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.

template<typename T> NPT<T>::NPT ( SimInfo *theInfo, ForceFields* the_ff):
  T( theInfo, the_ff )
{
  GenericData* data;
  DoubleData * chiValue;
  DoubleData * integralOfChidtValue;

  chiValue = NULL;
  integralOfChidtValue = NULL;

  chi = 0.0;
  integralOfChidt = 0.0;
  have_tau_thermostat = 0;
  have_tau_barostat = 0;
  have_target_temp = 0;
  have_target_pressure = 0;
  have_chi_tolerance = 0;
  have_eta_tolerance = 0;
  have_pos_iter_tolerance = 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();
  }

  oldPos = new double[3*integrableObjects.size()];
  oldVel = new double[3*integrableObjects.size()];
  oldJi = new double[3*integrableObjects.size()];
#ifdef IS_MPI
  Nparticles = mpiSim->getTotAtoms();
#else
  Nparticles = theInfo->n_atoms;
#endif

}

template<typename T> NPT<T>::~NPT() {
  delete[] oldPos;
  delete[] oldVel;
  delete[] oldJi;
}

template<typename T> void NPT<T>::moveA() {

  //new version of NPT
  int i, j, k;
  double Tb[3], ji[3];
  double mass;
  double vel[3], pos[3], frc[3];
  double sc[3];
  double COM[3];

  instaTemp = tStats->getTemperature();
  tStats->getPressureTensor( press );
  instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
  instaVol = tStats->getVolume();

  tStats->getCOM(COM);

  //evolve velocity half step

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

    integrableObjects[i]->getVel( vel );
    integrableObjects[i]->getFrc( frc );

    mass = integrableObjects[i]->getMass();

    getVelScaleA( sc, vel );

    for (j=0; j < 3; j++) {

      // velocity half step  (use chi from previous step here):
      vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);

    }

    integrableObjects[i]->setVel( vel );

    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 );
    }
  }

  // evolve chi and eta  half step

  evolveChiA();
  evolveEtaA();

  //calculate the integral of chidt
  integralOfChidt += dt2*chi;

  //save the old positions
  for(i = 0; i < integrableObjects.size(); i++){
    integrableObjects[i]->getPos(pos);
    for(j = 0; j < 3; j++)
      oldPos[i*3 + j] = pos[j];
  }

  //the first estimation of r(t+dt) is equal to  r(t)

  for(k = 0; k < 5; k ++){

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

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

      this->getPosScale( pos, COM, i, sc );

      for(j = 0; j < 3; j++)
        pos[j] = oldPos[i*3 + j] + dt*(vel[j] + sc[j]);

      integrableObjects[i]->setPos( pos );
    }

    if (nConstrained){
      constrainA();
    }
  }


  // Scale the box after all the positions have been moved:

  this->scaleSimBox();
}

template<typename T> void NPT<T>::moveB( void ){

  //new version of NPT
  int i, j, k;
  double Tb[3], ji[3], sc[3];
  double vel[3], frc[3];
  double mass;

  // Set things up for the iteration:

  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:

  instaVol = tStats->getVolume();

  for (k=0; k < 4; k++) {

    instaTemp = tStats->getTemperature();
    instaPress = tStats->getPressure();

    // evolve chi another half step using the temperature at t + dt/2

    this->evolveChiB();
    this->evolveEtaB();
    this->calcVelScale();

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

      integrableObjects[i]->getFrc( frc );
      integrableObjects[i]->getVel(vel);

      mass = integrableObjects[i]->getMass();

      getVelScaleB( sc, i );

      // velocity half step
      for (j=0; j < 3; j++)
        vel[j] = oldVel[3*i+j] + dt2 * ((frc[j] / mass ) * eConvert - sc[j]);

      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 );
      }
    }

    if (nConstrained){
      constrainB();
    }

    if ( this->chiConverged() && this->etaConverged() ) break;
  }

  //calculate integral of chida
  integralOfChidt += dt2*chi;


}

template<typename T> void NPT<T>::resetIntegrator() {
  chi = 0.0;
  T::resetIntegrator();
}

template<typename T> void NPT<T>::evolveChiA() {
  chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
  oldChi = chi;
}

template<typename T> void NPT<T>::evolveChiB() {

  prevChi = chi;
  chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
}

template<typename T> bool NPT<T>::chiConverged() {

  return ( fabs( prevChi - chi ) <= chiTolerance );
}

template<typename T> int NPT<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,
             "NPT error: You can't use the NPT integrator\n"
             "   without a targetTemp!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_target_pressure) {
    sprintf( painCave.errMsg,
             "NPT error: You can't use the NPT integrator\n"
             "   without a targetPressure!\n"
             );
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  // We must set tauThermostat.

  if (!have_tau_thermostat) {
    sprintf( painCave.errMsg,
             "NPT error: If you use the NPT\n"
             "   integrator, you must set tauThermostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  // We must set tauBarostat.

  if (!have_tau_barostat) {
    sprintf( painCave.errMsg,
             "NPT error: If you use the NPT\n"
             "   integrator, you must set tauBarostat.\n");
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_chi_tolerance) {
    sprintf( painCave.errMsg,
             "NPT warning: setting chi tolerance to 1e-6\n");
    chiTolerance = 1e-6;
    have_chi_tolerance = 1;
    painCave.isFatal = 0;
    simError();
  }

  if (!have_eta_tolerance) {
    sprintf( painCave.errMsg,
             "NPT warning: setting eta tolerance to 1e-6\n");
    etaTolerance = 1e-6;
    have_eta_tolerance = 1;
    painCave.isFatal = 0;
    simError();
  }

  // We need NkBT a lot, so just set it here: This is the RAW number
  // of particles, so no subtraction or addition of constraints or
  // orientational degrees of freedom:

  NkBT = (double)Nparticles * kB * targetTemp;

  // fkBT is used because the thermostat operates on more degrees of freedom
  // than the barostat (when there are particles with orientational degrees
  // of freedom).  ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons

  fkBT = (double)info->ndf * kB * targetTemp;

  tt2 = tauThermostat * tauThermostat;
  tb2 = tauBarostat * tauBarostat;

  return 1;
}
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	8534 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	mmeineke	857
3	mmeineke	778	#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	778
13			#ifdef IS_MPI
14			#include "mpiSimulation.hpp"
15			#endif
16
17
18			// Basic isotropic thermostating and barostating via the Melchionna
19			// modification of the Hoover algorithm:
20			//
21			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22	tim	837	// Molec. Phys., 78, 533.
23	mmeineke	778	//
24			// and
25	tim	837	//
26	mmeineke	778	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27
28			template<typename T> NPT<T>::NPT ( SimInfo theInfo, ForceFields the_ff):
29			T( theInfo, the_ff )
30			{
31	tim	837	GenericData* data;
32			DoubleData * chiValue;
33			DoubleData * integralOfChidtValue;
34
35			chiValue = NULL;
36			integralOfChidtValue = NULL;
37
38	mmeineke	778	chi = 0.0;
39			integralOfChidt = 0.0;
40			have_tau_thermostat = 0;
41			have_tau_barostat = 0;
42			have_target_temp = 0;
43			have_target_pressure = 0;
44			have_chi_tolerance = 0;
45			have_eta_tolerance = 0;
46			have_pos_iter_tolerance = 0;
47
48	tim	837	// retrieve chi and integralOfChidt from simInfo
49			data = info->getProperty(CHIVALUE_ID);
50			if(data){
51			chiValue = dynamic_cast<DoubleData*>(data);
52			}
53
54			data = info->getProperty(INTEGRALOFCHIDT_ID);
55			if(data){
56			integralOfChidtValue = dynamic_cast<DoubleData*>(data);
57			}
58
59			// chi and integralOfChidt should appear by pair
60			if(chiValue && integralOfChidtValue){
61			chi = chiValue->getData();
62			integralOfChidt = integralOfChidtValue->getData();
63			}
64
65	gezelter	1097	oldPos = new double[3*integrableObjects.size()];
66			oldVel = new double[3*integrableObjects.size()];
67			oldJi = new double[3*integrableObjects.size()];
68	mmeineke	778	#ifdef IS_MPI
69			Nparticles = mpiSim->getTotAtoms();
70			#else
71			Nparticles = theInfo->n_atoms;
72			#endif
73
74			}
75
76			template<typename T> NPT<T>::~NPT() {
77			delete[] oldPos;
78			delete[] oldVel;
79			delete[] oldJi;
80			}
81
82			template<typename T> void NPT<T>::moveA() {
83	tim	837
84	mmeineke	778	//new version of NPT
85			int i, j, k;
86			double Tb[3], ji[3];
87			double mass;
88			double vel[3], pos[3], frc[3];
89			double sc[3];
90			double COM[3];
91
92			instaTemp = tStats->getTemperature();
93	mmeineke	780	tStats->getPressureTensor( press );
94			instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
95	mmeineke	778	instaVol = tStats->getVolume();
96	tim	837
97	mmeineke	778	tStats->getCOM(COM);
98	tim	837
99	mmeineke	778	//evolve velocity half step
100	mmeineke	857
101			calcVelScale();
102
103	gezelter	1097	for( i=0; i<integrableObjects.size(); i++ ){
104	mmeineke	778
105	gezelter	1097	integrableObjects[i]->getVel( vel );
106			integrableObjects[i]->getFrc( frc );
107	mmeineke	778
108	gezelter	1097	mass = integrableObjects[i]->getMass();
109	mmeineke	778
110			getVelScaleA( sc, vel );
111
112			for (j=0; j < 3; j++) {
113	tim	837
114	mmeineke	778	// velocity half step (use chi from previous step here):
115			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
116	tim	837
117	mmeineke	778	}
118
119	gezelter	1097	integrableObjects[i]->setVel( vel );
120	tim	837
121	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
122	mmeineke	778
123			// get and convert the torque to body frame
124	tim	837
125	gezelter	1097	integrableObjects[i]->getTrq( Tb );
126			integrableObjects[i]->lab2Body( Tb );
127	tim	837
128	mmeineke	778	// get the angular momentum, and propagate a half step
129
130	gezelter	1097	integrableObjects[i]->getJ( ji );
131	mmeineke	778
132	tim	837	for (j=0; j < 3; j++)
133	mmeineke	778	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
134	tim	837
135	gezelter	1097	this->rotationPropagation( integrableObjects[i], ji );
136	tim	837
137	gezelter	1097	integrableObjects[i]->setJ( ji );
138	tim	837	}
139	mmeineke	778	}
140
141			// evolve chi and eta half step
142	tim	837
143	mmeineke	778	evolveChiA();
144			evolveEtaA();
145
146			//calculate the integral of chidt
147			integralOfChidt += dt2*chi;
148
149			//save the old positions
150	gezelter	1097	for(i = 0; i < integrableObjects.size(); i++){
151			integrableObjects[i]->getPos(pos);
152	mmeineke	778	for(j = 0; j < 3; j++)
153			oldPos[i*3 + j] = pos[j];
154			}
155	tim	837
156			//the first estimation of r(t+dt) is equal to r(t)
157
158	mmeineke	778	for(k = 0; k < 5; k ++){
159
160	gezelter	1097	for(i =0 ; i < integrableObjects.size(); i++){
161	mmeineke	778
162	gezelter	1097	integrableObjects[i]->getVel(vel);
163			integrableObjects[i]->getPos(pos);
164	mmeineke	778
165			this->getPosScale( pos, COM, i, sc );
166	tim	837
167	mmeineke	778	for(j = 0; j < 3; j++)
168			pos[j] = oldPos[i3 + j] + dt(vel[j] + sc[j]);
169
170	gezelter	1097	integrableObjects[i]->setPos( pos );
171	mmeineke	778	}
172	tim	837
173	mmeineke	778	if (nConstrained){
174			constrainA();
175			}
176			}
177
178	tim	837
179	mmeineke	778	// Scale the box after all the positions have been moved:
180	tim	837
181	mmeineke	778	this->scaleSimBox();
182			}
183
184			template<typename T> void NPT<T>::moveB( void ){
185	tim	837
186	mmeineke	778	//new version of NPT
187			int i, j, k;
188			double Tb[3], ji[3], sc[3];
189			double vel[3], frc[3];
190			double mass;
191	tim	837
192	mmeineke	778	// Set things up for the iteration:
193
194	gezelter	1097	for( i=0; i<integrableObjects.size(); i++ ){
195	mmeineke	778
196	gezelter	1097	integrableObjects[i]->getVel( vel );
197	mmeineke	778
198			for (j=0; j < 3; j++)
199			oldVel[3*i + j] = vel[j];
200
201	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
202	mmeineke	778
203	gezelter	1097	integrableObjects[i]->getJ( ji );
204	mmeineke	778
205			for (j=0; j < 3; j++)
206			oldJi[3*i + j] = ji[j];
207
208			}
209			}
210
211			// do the iteration:
212
213			instaVol = tStats->getVolume();
214	tim	837
215	mmeineke	778	for (k=0; k < 4; k++) {
216	tim	837
217	mmeineke	778	instaTemp = tStats->getTemperature();
218			instaPress = tStats->getPressure();
219
220			// evolve chi another half step using the temperature at t + dt/2
221
222			this->evolveChiB();
223			this->evolveEtaB();
224	mmeineke	857	this->calcVelScale();
225	tim	837
226	gezelter	1097	for( i=0; i<integrableObjects.size(); i++ ){
227	mmeineke	778
228	gezelter	1097	integrableObjects[i]->getFrc( frc );
229			integrableObjects[i]->getVel(vel);
230	tim	837
231	gezelter	1097	mass = integrableObjects[i]->getMass();
232	tim	837
233	mmeineke	778	getVelScaleB( sc, i );
234
235			// velocity half step
236	tim	837	for (j=0; j < 3; j++)
237	mmeineke	778	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - sc[j]);
238	tim	837
239	gezelter	1097	integrableObjects[i]->setVel( vel );
240	tim	837
241	gezelter	1097	if( integrableObjects[i]->isDirectional() ){
242	mmeineke	778
243	tim	837	// get and convert the torque to body frame
244
245	gezelter	1097	integrableObjects[i]->getTrq( Tb );
246			integrableObjects[i]->lab2Body( Tb );
247	tim	837
248			for (j=0; j < 3; j++)
249	mmeineke	778	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
250	tim	837
251	gezelter	1097	integrableObjects[i]->setJ( ji );
252	mmeineke	778	}
253			}
254	tim	837
255	mmeineke	778	if (nConstrained){
256			constrainB();
257	tim	837	}
258
259	mmeineke	778	if ( this->chiConverged() && this->etaConverged() ) break;
260			}
261
262			//calculate integral of chida
263			integralOfChidt += dt2*chi;
264
265
266			}
267
268			template<typename T> void NPT<T>::resetIntegrator() {
269			chi = 0.0;
270			T::resetIntegrator();
271			}
272
273			template<typename T> void NPT<T>::evolveChiA() {
274			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
275			oldChi = chi;
276			}
277
278			template<typename T> void NPT<T>::evolveChiB() {
279	tim	837
280	mmeineke	778	prevChi = chi;
281			chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
282			}
283
284			template<typename T> bool NPT<T>::chiConverged() {
285	tim	837
286			return ( fabs( prevChi - chi ) <= chiTolerance );
287	mmeineke	778	}
288
289			template<typename T> int NPT<T>::readyCheck() {
290
291			//check parent's readyCheck() first
292			if (T::readyCheck() == -1)
293			return -1;
294	tim	837
295			// First check to see if we have a target temperature.
296			// Not having one is fatal.
297
298	mmeineke	778	if (!have_target_temp) {
299			sprintf( painCave.errMsg,
300			"NPT error: You can't use the NPT integrator\n"
301			" without a targetTemp!\n"
302			);
303			painCave.isFatal = 1;
304			simError();
305			return -1;
306			}
307
308			if (!have_target_pressure) {
309			sprintf( painCave.errMsg,
310			"NPT error: You can't use the NPT integrator\n"
311			" without a targetPressure!\n"
312			);
313			painCave.isFatal = 1;
314			simError();
315			return -1;
316			}
317	tim	837
318	mmeineke	778	// We must set tauThermostat.
319	tim	837
320	mmeineke	778	if (!have_tau_thermostat) {
321			sprintf( painCave.errMsg,
322			"NPT error: If you use the NPT\n"
323			" integrator, you must set tauThermostat.\n");
324			painCave.isFatal = 1;
325			simError();
326			return -1;
327	tim	837	}
328	mmeineke	778
329			// We must set tauBarostat.
330	tim	837
331	mmeineke	778	if (!have_tau_barostat) {
332			sprintf( painCave.errMsg,
333			"NPT error: If you use the NPT\n"
334			" integrator, you must set tauBarostat.\n");
335			painCave.isFatal = 1;
336			simError();
337			return -1;
338	tim	837	}
339	mmeineke	778
340			if (!have_chi_tolerance) {
341			sprintf( painCave.errMsg,
342			"NPT warning: setting chi tolerance to 1e-6\n");
343			chiTolerance = 1e-6;
344			have_chi_tolerance = 1;
345			painCave.isFatal = 0;
346			simError();
347	tim	837	}
348	mmeineke	778
349			if (!have_eta_tolerance) {
350			sprintf( painCave.errMsg,
351			"NPT warning: setting eta tolerance to 1e-6\n");
352			etaTolerance = 1e-6;
353			have_eta_tolerance = 1;
354			painCave.isFatal = 0;
355			simError();
356	tim	837	}
357
358	mmeineke	778	// We need NkBT a lot, so just set it here: This is the RAW number
359			// of particles, so no subtraction or addition of constraints or
360			// orientational degrees of freedom:
361	tim	837
362	mmeineke	778	NkBT = (double)Nparticles * kB * targetTemp;
363	tim	837
364	mmeineke	778	// fkBT is used because the thermostat operates on more degrees of freedom
365			// than the barostat (when there are particles with orientational degrees
366			// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
367	tim	837
368	mmeineke	778	fkBT = (double)info->ndf * kB * targetTemp;
369
370			tt2 = tauThermostat * tauThermostat;
371			tb2 = tauBarostat * tauBarostat;
372
373			return 1;
374			}