OOPSE/libmdtools/NPTxyz.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 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>::getVelScaleA(double sc[3], double vel[3]) {
  int i,j;
  double vScale[3][3];

  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;
      }
    }
  }

  info->matVecMul3( vScale, vel, sc );
}

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

  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;
      }
    }
  }

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

  info->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];

  info->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);
    info->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;

  info->transposeMat3(eta, a);
  info->matMul3(a, eta, b);
  trEta = info->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:	855
Committed:	Thu Nov 6 22:01:37 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	7400 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	mmeineke	812	#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	mmeineke	812
12			#ifdef IS_MPI
13			#include "mpiSimulation.hpp"
14			#endif
15
16			// Basic non-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	mmeineke	812	//
22			// and
23	tim	837	//
24	mmeineke	812	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25
26			template<typename T> NPTxyz<T>::NPTxyz ( SimInfo theInfo, ForceFields the_ff):
27			T( theInfo, the_ff )
28			{
29	tim	837	GenericData* data;
30			DoubleArrayData * etaValue;
31			vector<double> etaArray;
32	mmeineke	812	int i,j;
33	tim	837
34	mmeineke	812	for(i = 0; i < 3; i++){
35			for (j = 0; j < 3; j++){
36	tim	837
37	mmeineke	812	eta[i][j] = 0.0;
38			oldEta[i][j] = 0.0;
39			}
40			}
41	tim	837
42
43	mmeineke	855	if( theInfo->useInitXSstate ){
44	tim	837
45	mmeineke	855	// retrieve eta array from simInfo if it exists
46			data = info->getProperty(ETAVALUE_ID);
47			if(data){
48			etaValue = dynamic_cast<DoubleArrayData*>(data);
49
50			if(etaValue){
51			etaArray = etaValue->getData();
52
53			for(i = 0; i < 3; i++){
54			for (j = 0; j < 3; j++){
55			eta[i][j] = etaArray[3*i+j];
56			oldEta[i][j] = eta[i][j];
57			}
58			}
59	tim	837	}
60			}
61			}
62	mmeineke	812	}
63
64			template<typename T> NPTxyz<T>::~NPTxyz() {
65
66			// empty for now
67			}
68
69			template<typename T> void NPTxyz<T>::resetIntegrator() {
70	tim	837
71	mmeineke	812	int i, j;
72	tim	837
73	mmeineke	812	for(i = 0; i < 3; i++)
74			for (j = 0; j < 3; j++)
75			eta[i][j] = 0.0;
76	tim	837
77	mmeineke	812	T::resetIntegrator();
78			}
79
80			template<typename T> void NPTxyz<T>::evolveEtaA() {
81	tim	837
82	mmeineke	812	int i, j;
83	tim	837
84	mmeineke	812	for(i = 0; i < 3; i ++){
85			for(j = 0; j < 3; j++){
86			if( i == j)
87	tim	837	eta[i][j] += dt2 * instaVol *
88	mmeineke	812	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89			else
90			eta[i][j] = 0.0;
91			}
92			}
93	tim	837
94	mmeineke	812	for(i = 0; i < 3; i++)
95			for (j = 0; j < 3; j++)
96			oldEta[i][j] = eta[i][j];
97			}
98
99			template<typename T> void NPTxyz<T>::evolveEtaB() {
100	tim	837
101	mmeineke	812	int i,j;
102
103			for(i = 0; i < 3; i++)
104			for (j = 0; j < 3; j++)
105			prevEta[i][j] = eta[i][j];
106
107			for(i = 0; i < 3; i ++){
108			for(j = 0; j < 3; j++){
109			if( i == j) {
110	tim	837	eta[i][j] = oldEta[i][j] + dt2 * instaVol *
111	mmeineke	812	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112			} else {
113			eta[i][j] = 0.0;
114			}
115			}
116			}
117			}
118
119			template<typename T> void NPTxyz<T>::getVelScaleA(double sc[3], double vel[3]) {
120			int i,j;
121			double vScale[3][3];
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	tim	837
133	mmeineke	812	info->matVecMul3( vScale, vel, sc );
134			}
135
136			template<typename T> void NPTxyz<T>::getVelScaleB(double sc[3], int index ){
137			int i,j;
138			double myVel[3];
139			double vScale[3][3];
140
141			for (i = 0; i < 3; i++ ) {
142			for (j = 0; j < 3; j++ ) {
143			vScale[i][j] = eta[i][j];
144	tim	837
145	mmeineke	812	if (i == j) {
146	tim	837	vScale[i][j] += chi;
147			}
148	mmeineke	812	}
149			}
150	tim	837
151	mmeineke	812	for (j = 0; j < 3; j++)
152			myVel[j] = oldVel[3*index + j];
153
154			info->matVecMul3( vScale, myVel, sc );
155			}
156
157	tim	837	template<typename T> void NPTxyz<T>::getPosScale(double pos[3], double COM[3],
158	mmeineke	812	int index, double sc[3]){
159			int j;
160			double rj[3];
161
162			for(j=0; j<3; j++)
163			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164
165			info->matVecMul3( eta, rj, sc );
166			}
167
168			template<typename T> void NPTxyz<T>::scaleSimBox( void ){
169
170			int i,j,k;
171			double scaleMat[3][3];
172			double eta2ij, scaleFactor;
173			double bigScale, smallScale, offDiagMax;
174			double hm[3][3], hmnew[3][3];
175
176
177	tim	837
178	mmeineke	812	// Scale the box after all the positions have been moved:
179	tim	837
180	mmeineke	812	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
181			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
182	tim	837
183	mmeineke	812	bigScale = 1.0;
184			smallScale = 1.0;
185			offDiagMax = 0.0;
186	tim	837
187	mmeineke	812	for(i=0; i<3; i++){
188			for(j=0; j<3; j++){
189			scaleMat[i][j] = 0.0;
190			if(i==j) scaleMat[i][j] = 1.0;
191			}
192			}
193	tim	837
194	mmeineke	812	for(i=0;i<3;i++){
195	tim	837
196	mmeineke	812	// calculate the scaleFactors
197	tim	837
198	mmeineke	812	scaleFactor = exp(dt*eta[i][i]);
199	tim	837
200	mmeineke	812	scaleMat[i][i] = scaleFactor;
201
202			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
203			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
204			}
205
206			// for(i=0; i<3; i++){
207			// for(j=0; j<3; j++){
208	tim	837
209	mmeineke	812	// // Calculate the matrix Product of the eta array (we only need
210			// // the ij element right now):
211	tim	837
212	mmeineke	812	// eta2ij = 0.0;
213			// for(k=0; k<3; k++){
214			// eta2ij += eta[i][k] * eta[k][j];
215			// }
216	tim	837
217	mmeineke	812	// scaleMat[i][j] = 0.0;
218			// // identity matrix (see above):
219			// if (i == j) scaleMat[i][j] = 1.0;
220			// // Taylor expansion for the exponential truncated at second order:
221			// scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
222
223			// if (i != j)
224	tim	837	// if (fabs(scaleMat[i][j]) > offDiagMax)
225	mmeineke	812	// offDiagMax = fabs(scaleMat[i][j]);
226			// }
227
228			// if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
229			// if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
230			// }
231	tim	837
232	mmeineke	812	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
233			sprintf( painCave.errMsg,
234			"NPTxyz error: Attempting a Box scaling of more than 10 percent.\n"
235			" Check your tauBarostat, as it is probably too small!\n\n"
236			" scaleMat = [%lf\t%lf\t%lf]\n"
237			" [%lf\t%lf\t%lf]\n"
238			" [%lf\t%lf\t%lf]\n",
239			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
240			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
241			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
242			painCave.isFatal = 1;
243			simError();
244			} else {
245			info->getBoxM(hm);
246			info->matMul3(hm, scaleMat, hmnew);
247			info->setBoxM(hmnew);
248			}
249			}
250
251			template<typename T> bool NPTxyz<T>::etaConverged() {
252			int i;
253			double diffEta, sumEta;
254
255			sumEta = 0;
256			for(i = 0; i < 3; i++)
257	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
258
259	mmeineke	812	diffEta = sqrt( sumEta / 3.0 );
260	tim	837
261	mmeineke	812	return ( diffEta <= etaTolerance );
262			}
263
264			template<typename T> double NPTxyz<T>::getConservedQuantity(void){
265	tim	837
266	mmeineke	812	double conservedQuantity;
267			double totalEnergy;
268			double thermostat_kinetic;
269			double thermostat_potential;
270			double barostat_kinetic;
271			double barostat_potential;
272			double trEta;
273			double a[3][3], b[3][3];
274
275			totalEnergy = tStats->getTotalE();
276
277	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
278	mmeineke	812	(2.0 * eConvert);
279
280			thermostat_potential = fkBT* integralOfChidt / eConvert;
281
282			info->transposeMat3(eta, a);
283			info->matMul3(a, eta, b);
284			trEta = info->matTrace3(b);
285
286	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
287	mmeineke	812	(2.0 * eConvert);
288	tim	837
289			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
290	mmeineke	812	eConvert;
291
292			conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
293			barostat_kinetic + barostat_potential;
294	tim	837
295	mmeineke	812	// cout.width(8);
296			// cout.precision(8);
297
298	tim	837	// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
299			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
300	mmeineke	812	// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
301
302	tim	837	return conservedQuantity;
303
304	mmeineke	812	}
305	tim	837
306			template<typename T> string NPTxyz<T>::getAdditionalParameters(void){
307			string parameters;
308			const int BUFFERSIZE = 2000; // size of the read buffer
309			char buffer[BUFFERSIZE];
310
311	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
312	tim	837	parameters += buffer;
313
314			for(int i = 0; i < 3; i++){
315	mmeineke	853	sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
316	tim	837	parameters += buffer;
317			}
318
319			return parameters;
320
321			}