OOPSE/libmdtools/NPT.cpp

#include <stdlib.h>
#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.

NPT::NPT ( SimInfo *theInfo, ForceFields* the_ff):
  Integrator( theInfo, the_ff )
{
  GenericData* data;
  
  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 != NULL ){
    chi = data->getDval();
  }

  data = info->getProperty(INTEGRALOFCHIDT_ID);
  if(data != NULL ){
    integralOfChidt = data->getDval();
  }

  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

}

NPT::~NPT() {
  delete[] oldPos;
  delete[] oldVel;
  delete[] oldJi;
}

void NPT::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
  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();
}

void NPT::moveB( void ){

  //new version of NPT
  int i, j, k;
  DirectionalAtom* dAtom;
  double Tb[3], ji[3], sc[3];
  double vel[3], frc[3], qVel[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++) {

    atoms[0]->getVel(vel);

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

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

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

    for( i=0; i<nAtoms; i++ ){

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

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

      getVelScaleB( sc, i );

      for(j=0;j<3;j++)
        qVel[j] = vel[j];

      // 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;


}

void NPT::resetIntegrator() {
  chi = 0.0;
  Integrator::resetIntegrator();
}

void NPT::evolveChiA() {

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

void NPT::evolveChiB() {

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

bool NPT::chiConverged() {

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

int NPT::readyCheck() {

  //check parent's readyCheck() first
  if (Integrator::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:	852
Committed:	Thu Nov 6 18:20:47 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	7804 byte(s)
Log Message:	fixed the "Sudden Death" bug. The box was not switching between orthorhombic and non-orthorhombic wrapping correctly. we added a fabs() to the check.which should fix it.
#	User	Rev	Content
1	mmeineke	850	#include <stdlib.h>
2	gezelter	829	#include <math.h>
3	mmeineke	850
4	mmeineke	778	#include "Atom.hpp"
5			#include "SRI.hpp"
6			#include "AbstractClasses.hpp"
7			#include "SimInfo.hpp"
8			#include "ForceFields.hpp"
9			#include "Thermo.hpp"
10			#include "ReadWrite.hpp"
11			#include "Integrator.hpp"
12	tim	837	#include "simError.h"
13	mmeineke	778
14			#ifdef IS_MPI
15			#include "mpiSimulation.hpp"
16			#endif
17
18
19			// Basic isotropic thermostating and barostating via the Melchionna
20			// modification of the Hoover algorithm:
21			//
22			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
23	tim	837	// Molec. Phys., 78, 533.
24	mmeineke	778	//
25			// and
26	tim	837	//
27	mmeineke	778	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
28
29	mmeineke	849	NPT::NPT ( SimInfo theInfo, ForceFields the_ff):
30			Integrator( theInfo, the_ff )
31	mmeineke	778	{
32	tim	837	GenericData* data;
33	mmeineke	849
34	mmeineke	778	chi = 0.0;
35			integralOfChidt = 0.0;
36			have_tau_thermostat = 0;
37			have_tau_barostat = 0;
38			have_target_temp = 0;
39			have_target_pressure = 0;
40			have_chi_tolerance = 0;
41			have_eta_tolerance = 0;
42			have_pos_iter_tolerance = 0;
43
44	tim	837	// retrieve chi and integralOfChidt from simInfo
45			data = info->getProperty(CHIVALUE_ID);
46	mmeineke	850	if(data != NULL ){
47			chi = data->getDval();
48	tim	837	}
49
50			data = info->getProperty(INTEGRALOFCHIDT_ID);
51	mmeineke	850	if(data != NULL ){
52			integralOfChidt = data->getDval();
53	tim	837	}
54
55	mmeineke	778	oldPos = new double[3*nAtoms];
56			oldVel = new double[3*nAtoms];
57			oldJi = new double[3*nAtoms];
58			#ifdef IS_MPI
59			Nparticles = mpiSim->getTotAtoms();
60			#else
61			Nparticles = theInfo->n_atoms;
62			#endif
63
64			}
65
66	mmeineke	849	NPT::~NPT() {
67	mmeineke	778	delete[] oldPos;
68			delete[] oldVel;
69			delete[] oldJi;
70			}
71
72	mmeineke	849	void NPT::moveA() {
73	tim	837
74	mmeineke	778	//new version of NPT
75			int i, j, k;
76			DirectionalAtom* dAtom;
77			double Tb[3], ji[3];
78			double mass;
79			double vel[3], pos[3], frc[3];
80			double sc[3];
81			double COM[3];
82
83			instaTemp = tStats->getTemperature();
84	mmeineke	852
85	mmeineke	780	tStats->getPressureTensor( press );
86			instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
87	mmeineke	852
88	mmeineke	778	instaVol = tStats->getVolume();
89	tim	837
90	mmeineke	778	tStats->getCOM(COM);
91	tim	837
92	mmeineke	778	//evolve velocity half step
93			for( i=0; i<nAtoms; i++ ){
94
95			atoms[i]->getVel( vel );
96			atoms[i]->getFrc( frc );
97
98			mass = atoms[i]->getMass();
99
100			getVelScaleA( sc, vel );
101
102			for (j=0; j < 3; j++) {
103	tim	837
104	mmeineke	778	// velocity half step (use chi from previous step here):
105			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
106	tim	837
107	mmeineke	778	}
108
109			atoms[i]->setVel( vel );
110	tim	837
111	mmeineke	778	if( atoms[i]->isDirectional() ){
112
113			dAtom = (DirectionalAtom *)atoms[i];
114
115			// get and convert the torque to body frame
116	tim	837
117	mmeineke	778	dAtom->getTrq( Tb );
118			dAtom->lab2Body( Tb );
119	tim	837
120	mmeineke	778	// get the angular momentum, and propagate a half step
121
122			dAtom->getJ( ji );
123
124	tim	837	for (j=0; j < 3; j++)
125	mmeineke	778	ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
126	tim	837
127	mmeineke	778	this->rotationPropagation( dAtom, ji );
128	tim	837
129	mmeineke	778	dAtom->setJ( ji );
130	tim	837	}
131	mmeineke	778	}
132
133			// evolve chi and eta half step
134	tim	837
135	mmeineke	778	evolveChiA();
136			evolveEtaA();
137
138			//calculate the integral of chidt
139			integralOfChidt += dt2*chi;
140
141			//save the old positions
142			for(i = 0; i < nAtoms; i++){
143			atoms[i]->getPos(pos);
144			for(j = 0; j < 3; j++)
145			oldPos[i*3 + j] = pos[j];
146			}
147	tim	837
148			//the first estimation of r(t+dt) is equal to r(t)
149
150	mmeineke	778	for(k = 0; k < 5; k ++){
151
152			for(i =0 ; i < nAtoms; i++){
153
154			atoms[i]->getVel(vel);
155			atoms[i]->getPos(pos);
156
157			this->getPosScale( pos, COM, i, sc );
158	tim	837
159	mmeineke	778	for(j = 0; j < 3; j++)
160			pos[j] = oldPos[i3 + j] + dt(vel[j] + sc[j]);
161
162			atoms[i]->setPos( pos );
163			}
164	tim	837
165	mmeineke	778	if (nConstrained){
166			constrainA();
167			}
168			}
169
170	tim	837
171	mmeineke	778	// Scale the box after all the positions have been moved:
172	tim	837
173	mmeineke	778	this->scaleSimBox();
174			}
175
176	mmeineke	849	void NPT::moveB( void ){
177	tim	837
178	mmeineke	778	//new version of NPT
179			int i, j, k;
180			DirectionalAtom* dAtom;
181			double Tb[3], ji[3], sc[3];
182	mmeineke	851	double vel[3], frc[3], qVel[3];
183	mmeineke	778	double mass;
184	tim	837
185	mmeineke	778	// Set things up for the iteration:
186
187			for( i=0; i<nAtoms; i++ ){
188
189			atoms[i]->getVel( vel );
190
191			for (j=0; j < 3; j++)
192			oldVel[3*i + j] = vel[j];
193
194			if( atoms[i]->isDirectional() ){
195
196			dAtom = (DirectionalAtom *)atoms[i];
197
198			dAtom->getJ( ji );
199
200			for (j=0; j < 3; j++)
201			oldJi[3*i + j] = ji[j];
202
203			}
204			}
205
206			// do the iteration:
207
208			instaVol = tStats->getVolume();
209	tim	837
210	mmeineke	778	for (k=0; k < 4; k++) {
211	tim	837
212	mmeineke	851	atoms[0]->getVel(vel);
213
214	mmeineke	778	instaTemp = tStats->getTemperature();
215	mmeineke	851
216	mmeineke	778	instaPress = tStats->getPressure();
217
218			// evolve chi another half step using the temperature at t + dt/2
219
220			this->evolveChiB();
221			this->evolveEtaB();
222	tim	837
223	mmeineke	778	for( i=0; i<nAtoms; i++ ){
224
225			atoms[i]->getFrc( frc );
226			atoms[i]->getVel(vel);
227	tim	837
228	mmeineke	778	mass = atoms[i]->getMass();
229	tim	837
230	mmeineke	778	getVelScaleB( sc, i );
231
232	mmeineke	851	for(j=0;j<3;j++)
233			qVel[j] = vel[j];
234
235	mmeineke	778	// 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	mmeineke	778	atoms[i]->setVel( vel );
240	tim	837
241	mmeineke	778	if( atoms[i]->isDirectional() ){
242
243			dAtom = (DirectionalAtom *)atoms[i];
244	tim	837
245			// get and convert the torque to body frame
246
247	mmeineke	778	dAtom->getTrq( Tb );
248	tim	837	dAtom->lab2Body( Tb );
249
250			for (j=0; j < 3; j++)
251	mmeineke	778	ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
252	tim	837
253	mmeineke	778	dAtom->setJ( ji );
254			}
255			}
256	tim	837
257	mmeineke	778	if (nConstrained){
258			constrainB();
259	tim	837	}
260
261	mmeineke	778	if ( this->chiConverged() && this->etaConverged() ) break;
262			}
263
264			//calculate integral of chida
265			integralOfChidt += dt2*chi;
266
267
268			}
269
270	mmeineke	849	void NPT::resetIntegrator() {
271	mmeineke	778	chi = 0.0;
272	mmeineke	849	Integrator::resetIntegrator();
273	mmeineke	778	}
274
275	mmeineke	849	void NPT::evolveChiA() {
276	mmeineke	851
277	mmeineke	778	chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
278			oldChi = chi;
279			}
280
281	mmeineke	849	void NPT::evolveChiB() {
282	tim	837
283	mmeineke	778	prevChi = chi;
284			chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
285			}
286
287	mmeineke	849	bool NPT::chiConverged() {
288	tim	837
289			return ( fabs( prevChi - chi ) <= chiTolerance );
290	mmeineke	778	}
291
292	mmeineke	849	int NPT::readyCheck() {
293	mmeineke	778
294			//check parent's readyCheck() first
295	mmeineke	849	if (Integrator::readyCheck() == -1)
296	mmeineke	778	return -1;
297	tim	837
298			// First check to see if we have a target temperature.
299			// Not having one is fatal.
300
301	mmeineke	778	if (!have_target_temp) {
302			sprintf( painCave.errMsg,
303			"NPT error: You can't use the NPT integrator\n"
304			" without a targetTemp!\n"
305			);
306			painCave.isFatal = 1;
307			simError();
308			return -1;
309			}
310
311			if (!have_target_pressure) {
312			sprintf( painCave.errMsg,
313			"NPT error: You can't use the NPT integrator\n"
314			" without a targetPressure!\n"
315			);
316			painCave.isFatal = 1;
317			simError();
318			return -1;
319			}
320	tim	837
321	mmeineke	778	// We must set tauThermostat.
322	tim	837
323	mmeineke	778	if (!have_tau_thermostat) {
324			sprintf( painCave.errMsg,
325			"NPT error: If you use the NPT\n"
326			" integrator, you must set tauThermostat.\n");
327			painCave.isFatal = 1;
328			simError();
329			return -1;
330	tim	837	}
331	mmeineke	778
332			// We must set tauBarostat.
333	tim	837
334	mmeineke	778	if (!have_tau_barostat) {
335			sprintf( painCave.errMsg,
336			"NPT error: If you use the NPT\n"
337			" integrator, you must set tauBarostat.\n");
338			painCave.isFatal = 1;
339			simError();
340			return -1;
341	tim	837	}
342	mmeineke	778
343			if (!have_chi_tolerance) {
344			sprintf( painCave.errMsg,
345			"NPT warning: setting chi tolerance to 1e-6\n");
346			chiTolerance = 1e-6;
347			have_chi_tolerance = 1;
348			painCave.isFatal = 0;
349			simError();
350	tim	837	}
351	mmeineke	778
352			if (!have_eta_tolerance) {
353			sprintf( painCave.errMsg,
354			"NPT warning: setting eta tolerance to 1e-6\n");
355			etaTolerance = 1e-6;
356			have_eta_tolerance = 1;
357			painCave.isFatal = 0;
358			simError();
359	tim	837	}
360
361	mmeineke	778	// We need NkBT a lot, so just set it here: This is the RAW number
362			// of particles, so no subtraction or addition of constraints or
363			// orientational degrees of freedom:
364	tim	837
365	mmeineke	778	NkBT = (double)Nparticles * kB * targetTemp;
366	tim	837
367	mmeineke	778	// fkBT is used because the thermostat operates on more degrees of freedom
368			// than the barostat (when there are particles with orientational degrees
369			// of freedom). ndf = 3 * (n_atoms + n_oriented -1) - n_constraint - nZcons
370	tim	837
371	mmeineke	778	fkBT = (double)info->ndf * kB * targetTemp;
372
373			tt2 = tauThermostat * tauThermostat;
374			tb2 = tauBarostat * tauBarostat;
375
376			return 1;
377			}