src/integrators/NPT.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"

#ifdef IS_MPI
#include "brains/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()];

}

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,
             "If you use the NPT integrator, you must set tauBarostat.\n");
    painCave.severity = OOPSE_ERROR;
    painCave.isFatal = 1;
    simError();
    return -1;
  }

  if (!have_chi_tolerance) {
    sprintf( painCave.errMsg,
             "Setting chi tolerance to 1e-6 in NPT integrator\n");
    chiTolerance = 1e-6;
    have_chi_tolerance = 1;
    painCave.severity = OOPSE_INFO;
    painCave.isFatal = 0;
    simError();
  }

  if (!have_eta_tolerance) {
    sprintf( painCave.errMsg,
             "Setting eta tolerance to 1e-6 in NPT integrator");
    etaTolerance = 1e-6;
    have_eta_tolerance = 1;
    painCave.severity = OOPSE_INFO;
    painCave.isFatal = 0;
    simError();
  }

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

  NkBT = (double)(info->getTotIntegrableObjects()) * 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).  

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

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

  return 1;
}
Revision:	3
Committed:	Fri Sep 24 16:27:58 2004 UTC (20 years, 7 months ago) by tim
Original Path:	*trunk/src/integrators/NPT.cpp*
File size:	8576 byte(s)
Log Message:	change the #include in source files
#	User	Rev	Content
1	gezelter	2	#include <math.h>
2
3	tim	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	gezelter	2
13			#ifdef IS_MPI
14	tim	3	#include "brains/mpiSimulation.hpp"
15	gezelter	2	#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			// Molec. Phys., 78, 533.
23			//
24			// and
25			//
26			// 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			GenericData* data;
32			DoubleData * chiValue;
33			DoubleData * integralOfChidtValue;
34
35			chiValue = NULL;
36			integralOfChidtValue = NULL;
37
38			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			// 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			oldPos = new double[3*integrableObjects.size()];
66			oldVel = new double[3*integrableObjects.size()];
67			oldJi = new double[3*integrableObjects.size()];
68
69			}
70
71			template<typename T> NPT<T>::~NPT() {
72			delete[] oldPos;
73			delete[] oldVel;
74			delete[] oldJi;
75			}
76
77			template<typename T> void NPT<T>::moveA() {
78
79			//new version of NPT
80			int i, j, k;
81			double Tb[3], ji[3];
82			double mass;
83			double vel[3], pos[3], frc[3];
84			double sc[3];
85			double COM[3];
86
87			instaTemp = tStats->getTemperature();
88			tStats->getPressureTensor( press );
89			instaPress = p_convert * (press[0][0] + press[1][1] + press[2][2]) / 3.0;
90			instaVol = tStats->getVolume();
91
92			tStats->getCOM(COM);
93
94			//evolve velocity half step
95
96			calcVelScale();
97
98			for( i=0; i<integrableObjects.size(); i++ ){
99
100			integrableObjects[i]->getVel( vel );
101			integrableObjects[i]->getFrc( frc );
102
103			mass = integrableObjects[i]->getMass();
104
105			getVelScaleA( sc, vel );
106
107			for (j=0; j < 3; j++) {
108
109			// velocity half step (use chi from previous step here):
110			vel[j] += dt2 * ((frc[j] / mass ) * eConvert - sc[j]);
111
112			}
113
114			integrableObjects[i]->setVel( vel );
115
116			if( integrableObjects[i]->isDirectional() ){
117
118			// get and convert the torque to body frame
119
120			integrableObjects[i]->getTrq( Tb );
121			integrableObjects[i]->lab2Body( Tb );
122
123			// get the angular momentum, and propagate a half step
124
125			integrableObjects[i]->getJ( ji );
126
127			for (j=0; j < 3; j++)
128			ji[j] += dt2 * (Tb[j] * eConvert - ji[j]*chi);
129
130			this->rotationPropagation( integrableObjects[i], ji );
131
132			integrableObjects[i]->setJ( ji );
133			}
134			}
135
136			// evolve chi and eta half step
137
138			evolveChiA();
139			evolveEtaA();
140
141			//calculate the integral of chidt
142			integralOfChidt += dt2*chi;
143
144			//save the old positions
145			for(i = 0; i < integrableObjects.size(); i++){
146			integrableObjects[i]->getPos(pos);
147			for(j = 0; j < 3; j++)
148			oldPos[i*3 + j] = pos[j];
149			}
150
151			//the first estimation of r(t+dt) is equal to r(t)
152
153			for(k = 0; k < 5; k ++){
154
155			for(i =0 ; i < integrableObjects.size(); i++){
156
157			integrableObjects[i]->getVel(vel);
158			integrableObjects[i]->getPos(pos);
159
160			this->getPosScale( pos, COM, i, sc );
161
162			for(j = 0; j < 3; j++)
163			pos[j] = oldPos[i3 + j] + dt(vel[j] + sc[j]);
164
165			integrableObjects[i]->setPos( pos );
166			}
167
168			if(nConstrained)
169			constrainA();
170			}
171
172
173			// Scale the box after all the positions have been moved:
174
175			this->scaleSimBox();
176			}
177
178			template<typename T> void NPT<T>::moveB( void ){
179
180			//new version of NPT
181			int i, j, k;
182			double Tb[3], ji[3], sc[3];
183			double vel[3], frc[3];
184			double mass;
185
186			// Set things up for the iteration:
187
188			for( i=0; i<integrableObjects.size(); i++ ){
189
190			integrableObjects[i]->getVel( vel );
191
192			for (j=0; j < 3; j++)
193			oldVel[3*i + j] = vel[j];
194
195			if( integrableObjects[i]->isDirectional() ){
196
197			integrableObjects[i]->getJ( ji );
198
199			for (j=0; j < 3; j++)
200			oldJi[3*i + j] = ji[j];
201
202			}
203			}
204
205			// do the iteration:
206
207			instaVol = tStats->getVolume();
208
209			for (k=0; k < 4; k++) {
210
211			instaTemp = tStats->getTemperature();
212			instaPress = tStats->getPressure();
213
214			// evolve chi another half step using the temperature at t + dt/2
215
216			this->evolveChiB();
217			this->evolveEtaB();
218			this->calcVelScale();
219
220			for( i=0; i<integrableObjects.size(); i++ ){
221
222			integrableObjects[i]->getFrc( frc );
223			integrableObjects[i]->getVel(vel);
224
225			mass = integrableObjects[i]->getMass();
226
227			getVelScaleB( sc, i );
228
229			// velocity half step
230			for (j=0; j < 3; j++)
231			vel[j] = oldVel[3i+j] + dt2 ((frc[j] / mass ) * eConvert - sc[j]);
232
233			integrableObjects[i]->setVel( vel );
234
235			if( integrableObjects[i]->isDirectional() ){
236
237			// get and convert the torque to body frame
238
239			integrableObjects[i]->getTrq( Tb );
240			integrableObjects[i]->lab2Body( Tb );
241
242			for (j=0; j < 3; j++)
243			ji[j] = oldJi[3i + j] + dt2 (Tb[j] * eConvert - oldJi[3i+j]chi);
244
245			integrableObjects[i]->setJ( ji );
246			}
247			}
248
249			if(nConstrained)
250			constrainB();
251
252			if ( this->chiConverged() && this->etaConverged() ) break;
253			}
254
255			//calculate integral of chida
256			integralOfChidt += dt2*chi;
257
258
259			}
260
261			template<typename T> void NPT<T>::resetIntegrator() {
262			chi = 0.0;
263			T::resetIntegrator();
264			}
265
266			template<typename T> void NPT<T>::evolveChiA() {
267			chi += dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
268			oldChi = chi;
269			}
270
271			template<typename T> void NPT<T>::evolveChiB() {
272
273			prevChi = chi;
274			chi = oldChi + dt2 * ( instaTemp / targetTemp - 1.0) / tt2;
275			}
276
277			template<typename T> bool NPT<T>::chiConverged() {
278
279			return ( fabs( prevChi - chi ) <= chiTolerance );
280			}
281
282			template<typename T> int NPT<T>::readyCheck() {
283
284			//check parent's readyCheck() first
285			if (T::readyCheck() == -1)
286			return -1;
287
288			// First check to see if we have a target temperature.
289			// Not having one is fatal.
290
291			if (!have_target_temp) {
292			sprintf( painCave.errMsg,
293			"NPT error: You can't use the NPT integrator\n"
294			" without a targetTemp!\n"
295			);
296			painCave.isFatal = 1;
297			simError();
298			return -1;
299			}
300
301			if (!have_target_pressure) {
302			sprintf( painCave.errMsg,
303			"NPT error: You can't use the NPT integrator\n"
304			" without a targetPressure!\n"
305			);
306			painCave.isFatal = 1;
307			simError();
308			return -1;
309			}
310
311			// We must set tauThermostat.
312
313			if (!have_tau_thermostat) {
314			sprintf( painCave.errMsg,
315			"NPT error: If you use the NPT\n"
316			" integrator, you must set tauThermostat.\n");
317			painCave.isFatal = 1;
318			simError();
319			return -1;
320			}
321
322			// We must set tauBarostat.
323
324			if (!have_tau_barostat) {
325			sprintf( painCave.errMsg,
326			"If you use the NPT integrator, you must set tauBarostat.\n");
327			painCave.severity = OOPSE_ERROR;
328			painCave.isFatal = 1;
329			simError();
330			return -1;
331			}
332
333			if (!have_chi_tolerance) {
334			sprintf( painCave.errMsg,
335			"Setting chi tolerance to 1e-6 in NPT integrator\n");
336			chiTolerance = 1e-6;
337			have_chi_tolerance = 1;
338			painCave.severity = OOPSE_INFO;
339			painCave.isFatal = 0;
340			simError();
341			}
342
343			if (!have_eta_tolerance) {
344			sprintf( painCave.errMsg,
345			"Setting eta tolerance to 1e-6 in NPT integrator");
346			etaTolerance = 1e-6;
347			have_eta_tolerance = 1;
348			painCave.severity = OOPSE_INFO;
349			painCave.isFatal = 0;
350			simError();
351			}
352
353			// We need NkBT a lot, so just set it here: This is the RAW number
354			// of integrableObjects, so no subtraction or addition of constraints or
355			// orientational degrees of freedom:
356
357			NkBT = (double)(info->getTotIntegrableObjects()) * kB * targetTemp;
358
359			// fkBT is used because the thermostat operates on more degrees of freedom
360			// than the barostat (when there are particles with orientational degrees
361			// of freedom).
362
363			fkBT = (double)(info->getNDF()) * kB * targetTemp;
364
365			tt2 = tauThermostat * tauThermostat;
366			tb2 = tauBarostat * tauBarostat;
367
368			return 1;
369			}