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.

NPTi::NPTi ( SimInfo *theInfo, ForceFields* the_ff):
  NPT( theInfo, the_ff )
{
  GenericData* data;
  double *etaArray;

  eta = 0.0;
  oldEta = 0.0;

  // retrieve eta array from simInfo if it exists
  data = info->getProperty(ETAVALUE_ID);
  if(data != NULL){
    
    int test = data->getDarray(etaArray);
    
    if( test == 9 ){
      
      eta = etaArray[0];
      }    
      delete[] etaArray;
    }
    else
      std::cerr << "NPTi error: etaArray is not length 9 (actual = " << test
                << ").\n"
                << "            Simulation wil proceed with eta = 0;\n";
  }
}

NPTi::~NPTi() {
  //nothing for now
}

void NPTi::resetIntegrator() {
  eta = 0.0;
  NPT::resetIntegrator();
}

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

void NPTi::evolveEtaB() {

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

void NPTi::getVelScaleA(double sc[3], double vel[3]) {
  int i;

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

void NPTi::getVelScaleB(double sc[3], int index ){
  int i;

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


void NPTi::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;
}

void NPTi::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);
  }

}

bool NPTi::etaConverged() {

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

double NPTi::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;
}

string NPTi::getAdditionalParameters(void){
  string parameters;
  const int BUFFERSIZE = 2000; // size of the read buffer
  char buffer[BUFFERSIZE];

  sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt);
  parameters += buffer;

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

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

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

  return parameters;

}
Revision:	850
Committed:	Mon Nov 3 22:07:17 2003 UTC (21 years, 9 months ago) by mmeineke
File size:	3970 byte(s)
Log Message:	begun work on removing templates and most of standard template library from OOPSE.
#	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	mmeineke	849	NPTi::NPTi ( SimInfo theInfo, ForceFields the_ff):
27	mmeineke	850	NPT( theInfo, the_ff )
28	gezelter	574	{
29	tim	837	GenericData* data;
30	mmeineke	850	double *etaArray;
31	tim	837
32	gezelter	574	eta = 0.0;
33	mmeineke	778	oldEta = 0.0;
34	tim	837
35	mmeineke	850	// retrieve eta array from simInfo if it exists
36	tim	837	data = info->getProperty(ETAVALUE_ID);
37	mmeineke	850	if(data != NULL){
38
39			int test = data->getDarray(etaArray);
40
41			if( test == 9 ){
42
43	tim	837	eta = etaArray[0];
44	mmeineke	850	}
45			delete[] etaArray;
46	tim	837	}
47	mmeineke	850	else
48			std::cerr << "NPTi error: etaArray is not length 9 (actual = " << test
49			<< ").\n"
50			<< " Simulation wil proceed with eta = 0;\n";
51	tim	837	}
52	gezelter	574	}
53
54	mmeineke	849	NPTi::~NPTi() {
55	mmeineke	778	//nothing for now
56	tim	763	}
57
58	mmeineke	849	void NPTi::resetIntegrator() {
59	mmeineke	778	eta = 0.0;
60	mmeineke	850	NPT::resetIntegrator();
61	mmeineke	778	}
62	gezelter	600
63	mmeineke	849	void NPTi::evolveEtaA() {
64	tim	837	eta += dt2 * ( instaVol * (instaPress - targetPressure) /
65	mmeineke	778	(p_convertNkBTtb2));
66			oldEta = eta;
67			}
68	gezelter	574
69	mmeineke	849	void NPTi::evolveEtaB() {
70	tim	837
71	mmeineke	778	prevEta = eta;
72	tim	837	eta = oldEta + dt2 * ( instaVol * (instaPress - targetPressure) /
73	mmeineke	778	(p_convertNkBTtb2));
74			}
75	gezelter	574
76	mmeineke	849	void NPTi::getVelScaleA(double sc[3], double vel[3]) {
77	mmeineke	778	int i;
78	gezelter	574
79	mmeineke	778	for(i=0; i<3; i++) sc[i] = vel[i] * ( chi + eta );
80			}
81	gezelter	574
82	mmeineke	849	void NPTi::getVelScaleB(double sc[3], int index ){
83	mmeineke	778	int i;
84	gezelter	600
85	mmeineke	778	for(i=0; i<3; i++) sc[i] = oldVel[index3 + i] ( chi + eta );
86			}
87	gezelter	574
88	tim	763
89	mmeineke	849	void NPTi::getPosScale(double pos[3], double COM[3],
90	mmeineke	778	int index, double sc[3]){
91			int j;
92	gezelter	574
93	mmeineke	778	for(j=0; j<3; j++)
94			sc[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
95	gezelter	600
96	mmeineke	778	for(j=0; j<3; j++)
97			sc[j] *= eta;
98			}
99	gezelter	600
100	mmeineke	849	void NPTi::scaleSimBox( void ){
101	gezelter	600
102	mmeineke	778	double scaleFactor;
103	gezelter	600
104	gezelter	611	scaleFactor = exp(dt*eta);
105
106	mmeineke	614	if ((scaleFactor > 1.1) \|\| (scaleFactor < 0.9)) {
107	gezelter	611	sprintf( painCave.errMsg,
108			"NPTi error: Attempting a Box scaling of more than 10 percent"
109			" check your tauBarostat, as it is probably too small!\n"
110			" eta = %lf, scaleFactor = %lf\n", eta, scaleFactor
111			);
112			painCave.isFatal = 1;
113			simError();
114	tim	837	} else {
115			info->scaleBox(scaleFactor);
116			}
117	mmeineke	614
118	gezelter	574	}
119
120	mmeineke	849	bool NPTi::etaConverged() {
121	tim	763
122	mmeineke	778	return ( fabs(prevEta - eta) <= etaTolerance );
123	gezelter	574	}
124
125	mmeineke	849	double NPTi::getConservedQuantity(void){
126	tim	763
127			double conservedQuantity;
128	tim	769	double Energy;
129			double thermostat_kinetic;
130			double thermostat_potential;
131			double barostat_kinetic;
132			double barostat_potential;
133	tim	837
134	tim	769	Energy = tStats->getTotalE();
135	tim	763
136	tim	837	thermostat_kinetic = fkBT* tt2 * chi * chi /
137	tim	769	(2.0 * eConvert);
138	tim	763
139	tim	769	thermostat_potential = fkBT* integralOfChidt / eConvert;
140	tim	763
141
142	tim	837	barostat_kinetic = 3.0 * NkBT * tb2 * eta * eta /
143	tim	769	(2.0 * eConvert);
144	tim	837
145			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
146	tim	769	eConvert;
147	tim	767
148	tim	769	conservedQuantity = Energy + thermostat_kinetic + thermostat_potential +
149			barostat_kinetic + barostat_potential;
150	tim	837
151	mmeineke	778	// cout.width(8);
152			// cout.precision(8);
153	tim	763
154	tim	837	// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
155			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
156	mmeineke	778	// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
157	tim	837	return conservedQuantity;
158	tim	763	}
159	tim	837
160	mmeineke	849	string NPTi::getAdditionalParameters(void){
161	tim	837	string parameters;
162			const int BUFFERSIZE = 2000; // size of the read buffer
163			char buffer[BUFFERSIZE];
164
165	mmeineke	847	sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt);
166	tim	837	parameters += buffer;
167
168	mmeineke	847	sprintf(buffer,"\t%lf\t0\t0;", eta);
169	tim	837	parameters += buffer;
170
171	mmeineke	847	sprintf(buffer,"\t0\t%lf\t0;", eta);
172	tim	837	parameters += buffer;
173
174	mmeineke	847	sprintf(buffer,"\t0\t0\t%lf;", eta);
175	tim	837	parameters += buffer;
176
177			return parameters;
178
179			}