src/integrators/NPTi.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> NPTi<T>::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
  T( theInfo, the_ff )
{
  GenericData* data;
  DoubleArrayData * etaValue;
  vector<double> etaArray;

  eta = 0.0;
  oldEta = 0.0;

  if( theInfo->useInitXSstate ){
    // retrieve eta from simInfo if
    data = info->getProperty(ETAVALUE_ID);
    if(data){
      etaValue = dynamic_cast<DoubleArrayData*>(data);
      
      if(etaValue){
        etaArray = etaValue->getData();
        eta = etaArray[0];
        oldEta = eta;
      }
    }
  }
}

template<typename T> NPTi<T>::~NPTi() {
  //nothing for now
}

template<typename T> void NPTi<T>::resetIntegrator() {
  eta = 0.0;
  T::resetIntegrator();
}

template<typename T> void NPTi<T>::evolveEtaA() {
  eta += dt2 * ( instaVol * (instaPress - targetPressure) /
                 (p_convert*NkBT*tb2));
  oldEta = eta;
}

template<typename T> void NPTi<T>::evolveEtaB() {

  prevEta = eta;
  eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
                 (p_convert*NkBT*tb2));
}

template<typename T> void NPTi<T>::calcVelScale(void) {
  vScale = chi + eta;
}

template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
  int i;

  for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
}

template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
  int i;

  for(i=0; i<3; i++) sc[i] = oldVel[index*3 + i] * vScale;
}


template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
                                               int index, double sc[3]){
  int j;

  for(j=0; j<3; j++)
    sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];

  for(j=0; j<3; j++)
    sc[j] *= eta;
}

template<typename T> void NPTi<T>::scaleSimBox( void ){

  double scaleFactor;

  scaleFactor = exp(dt*eta);

  if ((scaleFactor > 1.1) || (scaleFactor < 0.9)) {
    sprintf( painCave.errMsg,
             "NPTi error: Attempting a Box scaling of more than 10 percent"
             " check your tauBarostat, as it is probably too small!\n"
             " eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
             );
    painCave.isFatal = 1;
    simError();
  } else {
    info->scaleBox(scaleFactor);
  }

}

template<typename T> bool NPTi<T>::etaConverged() {

  return ( fabs(prevEta - eta) <= etaTolerance );
}

template<typename T> double NPTi<T>::getConservedQuantity(void){

  double conservedQuantity;
  double Energy;
  double thermostat_kinetic;
  double thermostat_potential;
  double barostat_kinetic;
  double barostat_potential;

  Energy = tStats->getTotalE();

  thermostat_kinetic = fkBT* tt2 * chi * chi /
    (2.0 * eConvert);

  thermostat_potential = fkBT* integralOfChidt / eConvert;


  barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
    (2.0 * eConvert);

  barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
    eConvert;

  conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
    barostat_kinetic + barostat_potential;

//   cout.width(8);
//   cout.precision(8);

//   cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
//       "\t" << thermostat_potential << "\t" << barostat_kinetic <<
//       "\t" << barostat_potential << "\t" << conservedQuantity << endl;
  return conservedQuantity;
}

template<typename T> string NPTi<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;

  sprintf(buffer,"\t%G\t0\t0;", eta);
  parameters += buffer;

  sprintf(buffer,"\t0\t%G\t0;", eta);
  parameters += buffer;

  sprintf(buffer,"\t0\t0\t%G;", eta);
  parameters += buffer;

  return parameters;

}
Revision:	3
Committed:	Fri Sep 24 16:27:58 2004 UTC (21 years, 1 month ago) by tim
File size:	4314 byte(s)
Log Message:	change the #include in source files
#	User	Rev	Content
1	gezelter	2	#include <math.h>
2	tim	3	#include "primitives/Atom.hpp"
3			#include "primitives/SRI.hpp"
4			#include "primitives/AbstractClasses.hpp"
5			#include "brains/SimInfo.hpp"
6			#include "UseTheForce/ForceFields.hpp"
7			#include "brains/Thermo.hpp"
8			#include "io/ReadWrite.hpp"
9			#include "integrators/Integrator.hpp"
10			#include "utils/simError.h"
11	gezelter	2
12			#ifdef IS_MPI
13	tim	3	#include "brains/mpiSimulation.hpp"
14	gezelter	2	#endif
15
16			// Basic isotropic thermostating and barostating via the Melchionna
17			// modification of the Hoover algorithm:
18			//
19			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
20			// Molec. Phys., 78, 533.
21			//
22			// and
23			//
24			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25
26			template<typename T> NPTi<T>::NPTi ( SimInfo theInfo, ForceFields the_ff):
27			T( theInfo, the_ff )
28			{
29			GenericData* data;
30			DoubleArrayData * etaValue;
31			vector<double> etaArray;
32
33			eta = 0.0;
34			oldEta = 0.0;
35
36			if( theInfo->useInitXSstate ){
37			// retrieve eta from simInfo if
38			data = info->getProperty(ETAVALUE_ID);
39			if(data){
40			etaValue = dynamic_cast<DoubleArrayData*>(data);
41
42			if(etaValue){
43			etaArray = etaValue->getData();
44			eta = etaArray[0];
45			oldEta = eta;
46			}
47			}
48			}
49			}
50
51			template<typename T> NPTi<T>::~NPTi() {
52			//nothing for now
53			}
54
55			template<typename T> void NPTi<T>::resetIntegrator() {
56			eta = 0.0;
57			T::resetIntegrator();
58			}
59
60			template<typename T> void NPTi<T>::evolveEtaA() {
61			eta += dt2 * ( instaVol * (instaPress - targetPressure) /
62			(p_convertNkBTtb2));
63			oldEta = eta;
64			}
65
66			template<typename T> void NPTi<T>::evolveEtaB() {
67
68			prevEta = eta;
69			eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
70			(p_convertNkBTtb2));
71			}
72
73			template<typename T> void NPTi<T>::calcVelScale(void) {
74			vScale = chi + eta;
75			}
76
77			template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
78			int i;
79
80			for(i=0; i<3; i++) sc[i] = vel[i] * vScale;
81			}
82
83			template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
84			int i;
85
86			for(i=0; i<3; i++) sc[i] = oldVel[index3 + i] vScale;
87			}
88
89
90			template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
91			int index, double sc[3]){
92			int j;
93
94			for(j=0; j<3; j++)
95			sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
96
97			for(j=0; j<3; j++)
98			sc[j] *= eta;
99			}
100
101			template<typename T> void NPTi<T>::scaleSimBox( void ){
102
103			double scaleFactor;
104
105			scaleFactor = exp(dt*eta);
106
107			if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
108			sprintf( painCave.errMsg,
109			"NPTi error: Attempting a Box scaling of more than 10 percent"
110			" check your tauBarostat, as it is probably too small!\n"
111			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
112			);
113			painCave.isFatal = 1;
114			simError();
115			} else {
116			info->scaleBox(scaleFactor);
117			}
118
119			}
120
121			template<typename T> bool NPTi<T>::etaConverged() {
122
123			return ( fabs(prevEta - eta) <= etaTolerance );
124			}
125
126			template<typename T> double NPTi<T>::getConservedQuantity(void){
127
128			double conservedQuantity;
129			double Energy;
130			double thermostat_kinetic;
131			double thermostat_potential;
132			double barostat_kinetic;
133			double barostat_potential;
134
135			Energy = tStats->getTotalE();
136
137			thermostat_kinetic = fkBT* tt2 * chi * chi /
138			(2.0 * eConvert);
139
140			thermostat_potential = fkBT* integralOfChidt / eConvert;
141
142
143			barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
144			(2.0 * eConvert);
145
146			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
147			eConvert;
148
149			conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
150			barostat_kinetic + barostat_potential;
151
152			// cout.width(8);
153			// cout.precision(8);
154
155			// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
156			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
157			// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
158			return conservedQuantity;
159			}
160
161			template<typename T> string NPTi<T>::getAdditionalParameters(void){
162			string parameters;
163			const int BUFFERSIZE = 2000; // size of the read buffer
164			char buffer[BUFFERSIZE];
165
166			sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
167			parameters += buffer;
168
169			sprintf(buffer,"\t%G\t0\t0;", eta);
170			parameters += buffer;
171
172			sprintf(buffer,"\t0\t%G\t0;", eta);
173			parameters += buffer;
174
175			sprintf(buffer,"\t0\t0\t%G;", eta);
176			parameters += buffer;
177
178			return parameters;
179
180			}