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*nAtoms];
  oldVel = new double[3*nAtoms];
  oldJi = new double[3*nAtoms];
#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;
  DirectionalAtom* dAtom;
  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<nAtoms; i++ ){

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

    mass = atoms[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]);

    }

    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 );

      // 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 );
    }
  }

  // evolve chi and eta  half step

  evolveChiA();
  evolveEtaA();

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

  //save the old positions
  for(i = 0; i < nAtoms; i++){
    atoms[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 < nAtoms; i++){

      atoms[i]->getVel(vel);
      atoms[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]);

      atoms[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;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3], sc[3];
  double vel[3], frc[3];
  double mass;

  // Set things up for the iteration:

  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:

  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<nAtoms; i++ ){

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

      mass = atoms[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]);

      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 ( 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:	857
Committed:	Fri Nov 7 17:09:48 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	8249 byte(s)
Log Message:	moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
#	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	mmeineke	778	oldPos = new double[3*nAtoms];
66			oldVel = new double[3*nAtoms];
67			oldJi = new double[3*nAtoms];
68			#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			DirectionalAtom* dAtom;
87			double Tb[3], ji[3];
88			double mass;
89			double vel[3], pos[3], frc[3];
90			double sc[3];
91			double COM[3];
92
93			instaTemp = tStats->getTemperature();
94	mmeineke	780	tStats->getPressureTensor( press );
95			instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
96	mmeineke	778	instaVol = tStats->getVolume();
97	tim	837
98	mmeineke	778	tStats->getCOM(COM);
99	tim	837
100	mmeineke	778	//evolve velocity half step
101	mmeineke	857
102			calcVelScale();
103
104	mmeineke	778	for( i=0; i<nAtoms; i++ ){
105
106			atoms[i]->getVel( vel );
107			atoms[i]->getFrc( frc );
108
109			mass = atoms[i]->getMass();
110
111			getVelScaleA( sc, vel );
112
113			for (j=0; j < 3; j++) {
114	tim	837
115	mmeineke	778	// velocity half step (use chi from previous step here):
116			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
117	tim	837
118	mmeineke	778	}
119
120			atoms[i]->setVel( vel );
121	tim	837
122	mmeineke	778	if( atoms[i]->isDirectional() ){
123
124			dAtom = (DirectionalAtom *)atoms[i];
125
126			// get and convert the torque to body frame
127	tim	837
128	mmeineke	778	dAtom->getTrq( Tb );
129			dAtom->lab2Body( Tb );
130	tim	837
131	mmeineke	778	// get the angular momentum, and propagate a half step
132
133			dAtom->getJ( ji );
134
135	tim	837	for (j=0; j < 3; j++)
136	mmeineke	778	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
137	tim	837
138	mmeineke	778	this->rotationPropagation( dAtom, ji );
139	tim	837
140	mmeineke	778	dAtom->setJ( ji );
141	tim	837	}
142	mmeineke	778	}
143
144			// evolve chi and eta half step
145	tim	837
146	mmeineke	778	evolveChiA();
147			evolveEtaA();
148
149			//calculate the integral of chidt
150			integralOfChidt += dt2*chi;
151
152			//save the old positions
153			for(i = 0; i < nAtoms; i++){
154			atoms[i]->getPos(pos);
155			for(j = 0; j < 3; j++)
156			oldPos[i*3 + j] = pos[j];
157			}
158	tim	837
159			//the first estimation of r(t+dt) is equal to r(t)
160
161	mmeineke	778	for(k = 0; k < 5; k ++){
162
163			for(i =0 ; i < nAtoms; i++){
164
165			atoms[i]->getVel(vel);
166			atoms[i]->getPos(pos);
167
168			this->getPosScale( pos, COM, i, sc );
169	tim	837
170	mmeineke	778	for(j = 0; j < 3; j++)
171			pos[j] = oldPos[i3 + j] + dt(vel[j] + sc[j]);
172
173			atoms[i]->setPos( pos );
174			}
175	tim	837
176	mmeineke	778	if (nConstrained){
177			constrainA();
178			}
179			}
180
181	tim	837
182	mmeineke	778	// Scale the box after all the positions have been moved:
183	tim	837
184	mmeineke	778	this->scaleSimBox();
185			}
186
187			template<typename T> void NPT<T>::moveB( void ){
188	tim	837
189	mmeineke	778	//new version of NPT
190			int i, j, k;
191			DirectionalAtom* dAtom;
192			double Tb[3], ji[3], sc[3];
193			double vel[3], frc[3];
194			double mass;
195	tim	837
196	mmeineke	778	// Set things up for the iteration:
197
198			for( i=0; i<nAtoms; i++ ){
199
200			atoms[i]->getVel( vel );
201
202			for (j=0; j < 3; j++)
203			oldVel[3*i + j] = vel[j];
204
205			if( atoms[i]->isDirectional() ){
206
207			dAtom = (DirectionalAtom *)atoms[i];
208
209			dAtom->getJ( ji );
210
211			for (j=0; j < 3; j++)
212			oldJi[3*i + j] = ji[j];
213
214			}
215			}
216
217			// do the iteration:
218
219			instaVol = tStats->getVolume();
220	tim	837
221	mmeineke	778	for (k=0; k < 4; k++) {
222	tim	837
223	mmeineke	778	instaTemp = tStats->getTemperature();
224			instaPress = tStats->getPressure();
225
226			// evolve chi another half step using the temperature at t + dt/2
227
228			this->evolveChiB();
229			this->evolveEtaB();
230	mmeineke	857	this->calcVelScale();
231	tim	837
232	mmeineke	778	for( i=0; i<nAtoms; i++ ){
233
234			atoms[i]->getFrc( frc );
235			atoms[i]->getVel(vel);
236	tim	837
237	mmeineke	778	mass = atoms[i]->getMass();
238	tim	837
239	mmeineke	778	getVelScaleB( sc, i );
240
241			// velocity half step
242	tim	837	for (j=0; j < 3; j++)
243	mmeineke	778	vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - sc[j]);
244	tim	837
245	mmeineke	778	atoms[i]->setVel( vel );
246	tim	837
247	mmeineke	778	if( atoms[i]->isDirectional() ){
248
249			dAtom = (DirectionalAtom *)atoms[i];
250	tim	837
251			// get and convert the torque to body frame
252
253	mmeineke	778	dAtom->getTrq( Tb );
254	tim	837	dAtom->lab2Body( Tb );
255
256			for (j=0; j < 3; j++)
257	mmeineke	778	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
258	tim	837
259	mmeineke	778	dAtom->setJ( ji );
260			}
261			}
262	tim	837
263	mmeineke	778	if (nConstrained){
264			constrainB();
265	tim	837	}
266
267	mmeineke	778	if ( this->chiConverged() && this->etaConverged() ) break;
268			}
269
270			//calculate integral of chida
271			integralOfChidt += dt2*chi;
272
273
274			}
275
276			template<typename T> void NPT<T>::resetIntegrator() {
277			chi = 0.0;
278			T::resetIntegrator();
279			}
280
281			template<typename T> void NPT<T>::evolveChiA() {
282			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
283			oldChi = chi;
284			}
285
286			template<typename T> void NPT<T>::evolveChiB() {
287	tim	837
288	mmeineke	778	prevChi = chi;
289			chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
290			}
291
292			template<typename T> bool NPT<T>::chiConverged() {
293	tim	837
294			return ( fabs( prevChi - chi ) <= chiTolerance );
295	mmeineke	778	}
296
297			template<typename T> int NPT<T>::readyCheck() {
298
299			//check parent's readyCheck() first
300			if (T::readyCheck() == -1)
301			return -1;
302	tim	837
303			// First check to see if we have a target temperature.
304			// Not having one is fatal.
305
306	mmeineke	778	if (!have_target_temp) {
307			sprintf( painCave.errMsg,
308			"NPT error: You can't use the NPT integrator\n"
309			" without a targetTemp!\n"
310			);
311			painCave.isFatal = 1;
312			simError();
313			return -1;
314			}
315
316			if (!have_target_pressure) {
317			sprintf( painCave.errMsg,
318			"NPT error: You can't use the NPT integrator\n"
319			" without a targetPressure!\n"
320			);
321			painCave.isFatal = 1;
322			simError();
323			return -1;
324			}
325	tim	837
326	mmeineke	778	// We must set tauThermostat.
327	tim	837
328	mmeineke	778	if (!have_tau_thermostat) {
329			sprintf( painCave.errMsg,
330			"NPT error: If you use the NPT\n"
331			" integrator, you must set tauThermostat.\n");
332			painCave.isFatal = 1;
333			simError();
334			return -1;
335	tim	837	}
336	mmeineke	778
337			// We must set tauBarostat.
338	tim	837
339	mmeineke	778	if (!have_tau_barostat) {
340			sprintf( painCave.errMsg,
341			"NPT error: If you use the NPT\n"
342			" integrator, you must set tauBarostat.\n");
343			painCave.isFatal = 1;
344			simError();
345			return -1;
346	tim	837	}
347	mmeineke	778
348			if (!have_chi_tolerance) {
349			sprintf( painCave.errMsg,
350			"NPT warning: setting chi tolerance to 1e-6\n");
351			chiTolerance = 1e-6;
352			have_chi_tolerance = 1;
353			painCave.isFatal = 0;
354			simError();
355	tim	837	}
356	mmeineke	778
357			if (!have_eta_tolerance) {
358			sprintf( painCave.errMsg,
359			"NPT warning: setting eta tolerance to 1e-6\n");
360			etaTolerance = 1e-6;
361			have_eta_tolerance = 1;
362			painCave.isFatal = 0;
363			simError();
364	tim	837	}
365
366	mmeineke	778	// We need NkBT a lot, so just set it here: This is the RAW number
367			// of particles, so no subtraction or addition of constraints or
368			// orientational degrees of freedom:
369	tim	837
370	mmeineke	778	NkBT = (double)Nparticles * kB * targetTemp;
371	tim	837
372	mmeineke	778	// fkBT is used because the thermostat operates on more degrees of freedom
373			// than the barostat (when there are particles with orientational degrees
374			// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
375	tim	837
376	mmeineke	778	fkBT = (double)info->ndf * kB * targetTemp;
377
378			tt2 = tauThermostat * tauThermostat;
379			tb2 = tauBarostat * tauBarostat;
380
381			return 1;
382			}