OOPSE/libmdtools/NPTxyz.cpp

#include <math.h>
#include "MatVec3.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 non-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> NPTxyz<T>::NPTxyz ( SimInfo *theInfo, ForceFields* the_ff):
  T( theInfo, the_ff )
{
  GenericData* data;
  DoubleArrayData * etaValue;
  vector<double> etaArray;
  int i,j;

  for(i = 0; i < 3; i++){
    for (j = 0; j < 3; j++){

      eta[i][j] = 0.0;
      oldEta[i][j] = 0.0;
    }
  }


  if( theInfo->useInitXSstate ){

    // retrieve eta array from simInfo if it exists
    data = info->getProperty(ETAVALUE_ID);
    if(data){
      etaValue = dynamic_cast<DoubleArrayData*>(data);
      
      if(etaValue){
        etaArray = etaValue->getData();
        
        for(i = 0; i < 3; i++){
          for (j = 0; j < 3; j++){
            eta[i][j] = etaArray[3*i+j];
            oldEta[i][j] = eta[i][j];
          }
        }
      }
    }
  }
}

template<typename T> NPTxyz<T>::~NPTxyz() {

  // empty for now
}

template<typename T> void NPTxyz<T>::resetIntegrator() {

  int i, j;

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      eta[i][j] = 0.0;

  T::resetIntegrator();
}

template<typename T> void NPTxyz<T>::evolveEtaA() {

  int i, j;

  for(i = 0; i < 3; i ++){
    for(j = 0; j < 3; j++){
      if( i == j)
        eta[i][j] += dt2 *  instaVol *
          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
      else
        eta[i][j] = 0.0;
    }
  }

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      oldEta[i][j] = eta[i][j];
}

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

  int i,j;

  for(i = 0; i < 3; i++)
    for (j = 0; j < 3; j++)
      prevEta[i][j] = eta[i][j];

  for(i = 0; i < 3; i ++){
    for(j = 0; j < 3; j++){
      if( i == j) {
        eta[i][j] = oldEta[i][j] + dt2 *  instaVol *
          (press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
      } else {
        eta[i][j] = 0.0;
      }
    }
  }
}

template<typename T> void NPTxyz<T>::calcVelScale(void) {
  int i,j;

  for (i = 0; i < 3; i++ ) {
    for (j = 0; j < 3; j++ ) {
      vScale[i][j] = eta[i][j];

      if (i == j) {
        vScale[i][j] += chi;
      }
    }
  }
}

template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) {
  matVecMul3( vScale, vel, sc );
}

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

  for (j = 0; j < 3; j++)
    myVel[j] = oldVel[3*index + j];

  matVecMul3( vScale, myVel, sc );
}

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

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

  matVecMul3( eta, rj, sc );
}

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

  int i,j,k;
  double scaleMat[3][3];
  double eta2ij, scaleFactor;
  double bigScale, smallScale, offDiagMax;
  double hm[3][3], hmnew[3][3];


  // Scale the box after all the positions have been moved:

  // Use a taylor expansion for eta products:  Hmat = Hmat . exp(dt * etaMat)
  //  Hmat = Hmat . ( Ident + dt * etaMat  + dt^2 * etaMat*etaMat / 2)

  bigScale = 1.0;
  smallScale = 1.0;
  offDiagMax = 0.0;

  for(i=0; i<3; i++){
    for(j=0; j<3; j++){
      scaleMat[i][j] = 0.0;
      if(i==j) scaleMat[i][j] = 1.0;
    }
  }

  for(i=0;i<3;i++){

    // calculate the scaleFactors

    scaleFactor = exp(dt*eta[i][i]);

    scaleMat[i][i] = scaleFactor;

    if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
    if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
  }

//   for(i=0; i<3; i++){
//     for(j=0; j<3; j++){

//       // Calculate the matrix Product of the eta array (we only need
//       // the ij element right now):

//       eta2ij = 0.0;
//       for(k=0; k<3; k++){
//         eta2ij += eta[i][k] * eta[k][j];
//       }

//       scaleMat[i][j] = 0.0;
//       // identity matrix (see above):
//       if (i == j) scaleMat[i][j] = 1.0;
//       // Taylor expansion for the exponential truncated at second order:
//       scaleMat[i][j] += dt*eta[i][j]  + 0.5*dt*dt*eta2ij;

//       if (i != j)
//         if (fabs(scaleMat[i][j]) > offDiagMax)
//           offDiagMax = fabs(scaleMat[i][j]);
//     }

//     if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
//     if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
//   }

  if ((bigScale > 1.1) || (smallScale < 0.9)) {
    sprintf( painCave.errMsg,
             "NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
             " Check your tauBarostat, as it is probably too small!\n\n"
             " scaleMat = [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n"
             "            [%lf\t%lf\t%lf]\n",
             scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
             scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
             scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
    painCave.isFatal = 1;
    simError();
  } else {
    info->getBoxM(hm);
    matMul3(hm, scaleMat, hmnew);
    info->setBoxM(hmnew);
  }
}

template<typename T> bool NPTxyz<T>::etaConverged() {
  int i;
  double diffEta, sumEta;

  sumEta = 0;
  for(i = 0; i < 3; i++)
    sumEta += pow(prevEta[i][i] - eta[i][i], 2);

  diffEta = sqrt( sumEta / 3.0 );

  return ( diffEta <= etaTolerance );
}

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

  double conservedQuantity;
  double totalEnergy;
  double thermostat_kinetic;
  double thermostat_potential;
  double barostat_kinetic;
  double barostat_potential;
  double trEta;
  double a[3][3], b[3][3];

  totalEnergy = tStats->getTotalE();

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

  thermostat_potential = fkBT* integralOfChidt / eConvert;

  transposeMat3(eta, a);
  matMul3(a, eta, b);
  trEta = matTrace3(b);

  barostat_kinetic = NkBT * tb2 * trEta /
    (2.0 * eConvert);

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

  conservedQuantity = totalEnergy + 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 NPTxyz<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;

  for(int i = 0; i < 3; i++){
    sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
    parameters += buffer;
  }

  return parameters;

}
Revision:	1097
Committed:	Mon Apr 12 20:32:20 2004 UTC (20 years, 2 months ago) by gezelter
File size:	7230 byte(s)
Log Message:	Changes for RigidBody dynamics (Somewhat extensive)
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	gezelter	1097	#include "MatVec3.h"
3	mmeineke	812	#include "Atom.hpp"
4			#include "SRI.hpp"
5			#include "AbstractClasses.hpp"
6			#include "SimInfo.hpp"
7			#include "ForceFields.hpp"
8			#include "Thermo.hpp"
9			#include "ReadWrite.hpp"
10			#include "Integrator.hpp"
11	tim	837	#include "simError.h"
12	mmeineke	812
13			#ifdef IS_MPI
14			#include "mpiSimulation.hpp"
15			#endif
16
17			// Basic non-isotropic thermostating and barostating via the Melchionna
18			// modification of the Hoover algorithm:
19			//
20			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
21	tim	837	// Molec. Phys., 78, 533.
22	mmeineke	812	//
23			// and
24	tim	837	//
25	mmeineke	812	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
26
27			template<typename T> NPTxyz<T>::NPTxyz ( SimInfo theInfo, ForceFields the_ff):
28			T( theInfo, the_ff )
29			{
30	tim	837	GenericData* data;
31			DoubleArrayData * etaValue;
32			vector<double> etaArray;
33	mmeineke	812	int i,j;
34	tim	837
35	mmeineke	812	for(i = 0; i < 3; i++){
36			for (j = 0; j < 3; j++){
37	tim	837
38	mmeineke	812	eta[i][j] = 0.0;
39			oldEta[i][j] = 0.0;
40			}
41			}
42	tim	837
43
44	mmeineke	855	if( theInfo->useInitXSstate ){
45	tim	837
46	mmeineke	855	// retrieve eta array from simInfo if it exists
47			data = info->getProperty(ETAVALUE_ID);
48			if(data){
49			etaValue = dynamic_cast<DoubleArrayData*>(data);
50
51			if(etaValue){
52			etaArray = etaValue->getData();
53
54			for(i = 0; i < 3; i++){
55			for (j = 0; j < 3; j++){
56			eta[i][j] = etaArray[3*i+j];
57			oldEta[i][j] = eta[i][j];
58			}
59			}
60	tim	837	}
61			}
62			}
63	mmeineke	812	}
64
65			template<typename T> NPTxyz<T>::~NPTxyz() {
66
67			// empty for now
68			}
69
70			template<typename T> void NPTxyz<T>::resetIntegrator() {
71	tim	837
72	mmeineke	812	int i, j;
73	tim	837
74	mmeineke	812	for(i = 0; i < 3; i++)
75			for (j = 0; j < 3; j++)
76			eta[i][j] = 0.0;
77	tim	837
78	mmeineke	812	T::resetIntegrator();
79			}
80
81			template<typename T> void NPTxyz<T>::evolveEtaA() {
82	tim	837
83	mmeineke	812	int i, j;
84	tim	837
85	mmeineke	812	for(i = 0; i < 3; i ++){
86			for(j = 0; j < 3; j++){
87			if( i == j)
88	tim	837	eta[i][j] += dt2 * instaVol *
89	mmeineke	812	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
90			else
91			eta[i][j] = 0.0;
92			}
93			}
94	tim	837
95	mmeineke	812	for(i = 0; i < 3; i++)
96			for (j = 0; j < 3; j++)
97			oldEta[i][j] = eta[i][j];
98			}
99
100			template<typename T> void NPTxyz<T>::evolveEtaB() {
101	tim	837
102	mmeineke	812	int i,j;
103
104			for(i = 0; i < 3; i++)
105			for (j = 0; j < 3; j++)
106			prevEta[i][j] = eta[i][j];
107
108			for(i = 0; i < 3; i ++){
109			for(j = 0; j < 3; j++){
110			if( i == j) {
111	tim	837	eta[i][j] = oldEta[i][j] + dt2 * instaVol *
112	mmeineke	812	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
113			} else {
114			eta[i][j] = 0.0;
115			}
116			}
117			}
118			}
119
120	mmeineke	857	template<typename T> void NPTxyz<T>::calcVelScale(void) {
121	mmeineke	812	int i,j;
122
123			for (i = 0; i < 3; i++ ) {
124			for (j = 0; j < 3; j++ ) {
125			vScale[i][j] = eta[i][j];
126	tim	837
127	mmeineke	812	if (i == j) {
128	tim	837	vScale[i][j] += chi;
129			}
130	mmeineke	812	}
131			}
132	mmeineke	857	}
133	tim	837
134	mmeineke	857	template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) {
135	gezelter	1097	matVecMul3( vScale, vel, sc );
136	mmeineke	812	}
137
138			template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){
139	mmeineke	857	int j;
140	mmeineke	812	double myVel[3];
141
142			for (j = 0; j < 3; j++)
143			myVel[j] = oldVel[3*index + j];
144
145	gezelter	1097	matVecMul3( vScale, myVel, sc );
146	mmeineke	812	}
147
148	tim	837	template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3],
149	mmeineke	812	int index, double sc[3]){
150			int j;
151			double rj[3];
152
153			for(j=0; j<3; j++)
154			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
155
156	gezelter	1097	matVecMul3( eta, rj, sc );
157	mmeineke	812	}
158
159			template<typename T> void NPTxyz<T>::scaleSimBox( void ){
160
161			int i,j,k;
162			double scaleMat[3][3];
163			double eta2ij, scaleFactor;
164			double bigScale, smallScale, offDiagMax;
165			double hm[3][3], hmnew[3][3];
166
167
168	tim	837
169	mmeineke	812	// Scale the box after all the positions have been moved:
170	tim	837
171	mmeineke	812	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
172			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
173	tim	837
174	mmeineke	812	bigScale = 1.0;
175			smallScale = 1.0;
176			offDiagMax = 0.0;
177	tim	837
178	mmeineke	812	for(i=0; i<3; i++){
179			for(j=0; j<3; j++){
180			scaleMat[i][j] = 0.0;
181			if(i==j) scaleMat[i][j] = 1.0;
182			}
183			}
184	tim	837
185	mmeineke	812	for(i=0;i<3;i++){
186	tim	837
187	mmeineke	812	// calculate the scaleFactors
188	tim	837
189	mmeineke	812	scaleFactor = exp(dt*eta[i][i]);
190	tim	837
191	mmeineke	812	scaleMat[i][i] = scaleFactor;
192
193			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
194			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
195			}
196
197			// for(i=0; i<3; i++){
198			// for(j=0; j<3; j++){
199	tim	837
200	mmeineke	812	// // Calculate the matrix Product of the eta array (we only need
201			// // the ij element right now):
202	tim	837
203	mmeineke	812	// eta2ij = 0.0;
204			// for(k=0; k<3; k++){
205			// eta2ij += eta[i][k] * eta[k][j];
206			// }
207	tim	837
208	mmeineke	812	// scaleMat[i][j] = 0.0;
209			// // identity matrix (see above):
210			// if (i == j) scaleMat[i][j] = 1.0;
211			// // Taylor expansion for the exponential truncated at second order:
212			// scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
213
214			// if (i != j)
215	tim	837	// if (fabs(scaleMat[i][j]) > offDiagMax)
216	mmeineke	812	// offDiagMax = fabs(scaleMat[i][j]);
217			// }
218
219			// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
220			// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
221			// }
222	tim	837
223	mmeineke	812	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
224			sprintf( painCave.errMsg,
225			"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
226			" Check your tauBarostat, as it is probably too small!\n\n"
227			" scaleMat = [%lf\t%lf\t%lf]\n"
228			" [%lf\t%lf\t%lf]\n"
229			" [%lf\t%lf\t%lf]\n",
230			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
231			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
232			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
233			painCave.isFatal = 1;
234			simError();
235			} else {
236			info->getBoxM(hm);
237	gezelter	1097	matMul3(hm, scaleMat, hmnew);
238	mmeineke	812	info->setBoxM(hmnew);
239			}
240			}
241
242			template<typename T> bool NPTxyz<T>::etaConverged() {
243			int i;
244			double diffEta, sumEta;
245
246			sumEta = 0;
247			for(i = 0; i < 3; i++)
248	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
249
250	mmeineke	812	diffEta = sqrt( sumEta / 3.0 );
251	tim	837
252	mmeineke	812	return ( diffEta <= etaTolerance );
253			}
254
255			template<typename T> double NPTxyz<T>::getConservedQuantity(void){
256	tim	837
257	mmeineke	812	double conservedQuantity;
258			double totalEnergy;
259			double thermostat_kinetic;
260			double thermostat_potential;
261			double barostat_kinetic;
262			double barostat_potential;
263			double trEta;
264			double a[3][3], b[3][3];
265
266			totalEnergy = tStats->getTotalE();
267
268	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
269	mmeineke	812	(2.0 * eConvert);
270
271			thermostat_potential = fkBT* integralOfChidt / eConvert;
272
273	gezelter	1097	transposeMat3(eta, a);
274			matMul3(a, eta, b);
275			trEta = matTrace3(b);
276	mmeineke	812
277	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
278	mmeineke	812	(2.0 * eConvert);
279	tim	837
280			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
281	mmeineke	812	eConvert;
282
283			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
284			barostat_kinetic + barostat_potential;
285	tim	837
286	mmeineke	812	// cout.width(8);
287			// cout.precision(8);
288
289	tim	837	// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
290			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
291	mmeineke	812	// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
292
293	tim	837	return conservedQuantity;
294
295	mmeineke	812	}
296	tim	837
297			template<typename T> string NPTxyz<T>::getAdditionalParameters(void){
298			string parameters;
299			const int BUFFERSIZE = 2000; // size of the read buffer
300			char buffer[BUFFERSIZE];
301
302	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
303	tim	837	parameters += buffer;
304
305			for(int i = 0; i < 3; i++){
306	mmeineke	853	sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
307	tim	837	parameters += buffer;
308			}
309
310			return parameters;
311
312			}