OOPSE/libmdtools/NPTi.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> 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;

  // 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>::getVelScaleA(double sc[3], double vel[3]) {
  int i;

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

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] * ( chi + eta );
}


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:	837
Committed:	Wed Oct 29 00:19:10 2003 UTC (20 years, 8 months ago) by tim
File size:	4119 byte(s)
Log Message:	add chi and eta to the comment line of dump file.
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	gezelter	574	#include "Atom.hpp"
3			#include "SRI.hpp"
4			#include "AbstractClasses.hpp"
5			#include "SimInfo.hpp"
6			#include "ForceFields.hpp"
7			#include "Thermo.hpp"
8			#include "ReadWrite.hpp"
9			#include "Integrator.hpp"
10	tim	837	#include "simError.h"
11	gezelter	574
12	tim	763	#ifdef IS_MPI
13			#include "mpiSimulation.hpp"
14			#endif
15	gezelter	574
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	tim	837	// Molec. Phys., 78, 533.
21	gezelter	574	//
22			// and
23	tim	837	//
24	gezelter	574	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25
26	tim	645	template<typename T> NPTi<T>::NPTi ( SimInfo theInfo, ForceFields the_ff):
27			T( theInfo, the_ff )
28	gezelter	574	{
29	tim	837	GenericData* data;
30			DoubleArrayData * etaValue;
31			vector<double> etaArray;
32
33	gezelter	574	eta = 0.0;
34	mmeineke	778	oldEta = 0.0;
35	tim	837
36			// retrieve eta from simInfo if
37			data = info->getProperty(ETAVALUE_ID);
38			if(data){
39			etaValue = dynamic_cast<DoubleArrayData*>(data);
40
41			if(etaValue){
42			etaArray = etaValue->getData();
43			eta = etaArray[0];
44			oldEta = eta;
45			}
46			}
47
48	gezelter	574	}
49
50	tim	763	template<typename T> NPTi<T>::~NPTi() {
51	mmeineke	778	//nothing for now
52	tim	763	}
53
54	mmeineke	778	template<typename T> void NPTi<T>::resetIntegrator() {
55			eta = 0.0;
56			T::resetIntegrator();
57			}
58	gezelter	600
59	mmeineke	778	template<typename T> void NPTi<T>::evolveEtaA() {
60	tim	837	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
61	mmeineke	778	(p_convertNkBTtb2));
62			oldEta = eta;
63			}
64	gezelter	574
65	mmeineke	778	template<typename T> void NPTi<T>::evolveEtaB() {
66	tim	837
67	mmeineke	778	prevEta = eta;
68	tim	837	eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
69	mmeineke	778	(p_convertNkBTtb2));
70			}
71	gezelter	574
72	mmeineke	778	template<typename T> void NPTi<T>::getVelScaleA(double sc[3], double vel[3]) {
73			int i;
74	gezelter	574
75	mmeineke	778	for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
76			}
77	gezelter	574
78	mmeineke	778	template<typename T> void NPTi<T>::getVelScaleB(double sc[3], int index ){
79			int i;
80	gezelter	600
81	mmeineke	778	for(i=0; i<3; i++) sc[i] = oldVel[index3 + i] ( chi + eta );
82			}
83	gezelter	574
84	tim	763
85	tim	837	template<typename T> void NPTi<T>::getPosScale(double pos[3], double COM[3],
86	mmeineke	778	int index, double sc[3]){
87			int j;
88	gezelter	574
89	mmeineke	778	for(j=0; j<3; j++)
90			sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
91	gezelter	600
92	mmeineke	778	for(j=0; j<3; j++)
93			sc[j] *= eta;
94			}
95	gezelter	600
96	mmeineke	778	template<typename T> void NPTi<T>::scaleSimBox( void ){
97	gezelter	600
98	mmeineke	778	double scaleFactor;
99	gezelter	600
100	gezelter	611	scaleFactor = exp(dt*eta);
101
102	mmeineke	614	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
103	gezelter	611	sprintf( painCave.errMsg,
104			"NPTi error: Attempting a Box scaling of more than 10 percent"
105			" check your tauBarostat, as it is probably too small!\n"
106			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
107			);
108			painCave.isFatal = 1;
109			simError();
110	tim	837	} else {
111			info->scaleBox(scaleFactor);
112			}
113	mmeineke	614
114	gezelter	574	}
115
116	mmeineke	778	template<typename T> bool NPTi<T>::etaConverged() {
117	tim	763
118	mmeineke	778	return ( fabs(prevEta - eta) <= etaTolerance );
119	gezelter	574	}
120
121	tim	763	template<typename T> double NPTi<T>::getConservedQuantity(void){
122
123			double conservedQuantity;
124	tim	769	double Energy;
125			double thermostat_kinetic;
126			double thermostat_potential;
127			double barostat_kinetic;
128			double barostat_potential;
129	tim	837
130	tim	769	Energy = tStats->getTotalE();
131	tim	763
132	tim	837	thermostat_kinetic = fkBT* tt2 * chi * chi /
133	tim	769	(2.0 * eConvert);
134	tim	763
135	tim	769	thermostat_potential = fkBT* integralOfChidt / eConvert;
136	tim	763
137
138	tim	837	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
139	tim	769	(2.0 * eConvert);
140	tim	837
141			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
142	tim	769	eConvert;
143	tim	767
144	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
145			barostat_kinetic + barostat_potential;
146	tim	837
147	mmeineke	778	// cout.width(8);
148			// cout.precision(8);
149	tim	763
150	tim	837	// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
151			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
152	mmeineke	778	// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
153	tim	837	return conservedQuantity;
154	tim	763	}
155	tim	837
156			template<typename T> string NPTi<T>::getAdditionalParameters(void){
157			string parameters;
158			const int BUFFERSIZE = 2000; // size of the read buffer
159			char buffer[BUFFERSIZE];
160
161			sprintf(buffer,"\t%g\t%g;", chi, integralOfChidt);
162			parameters += buffer;
163
164			sprintf(buffer,"\t%g\t0\t0;", eta);
165			parameters += buffer;
166
167			sprintf(buffer,"\t0\t%g\t0;", eta);
168			parameters += buffer;
169
170			sprintf(buffer,"\t0\t0\t%g;", eta);
171			parameters += buffer;
172
173			return parameters;
174
175			}