OOPSE/libmdtools/NPTf.cpp

#include <stdlib.h>
#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.

NPTf::NPTf ( SimInfo *theInfo, ForceFields* the_ff):
  NPT( theInfo, the_ff )
{
  GenericData* data;
  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;
    }
  }

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

NPTf::~NPTf() {

  // empty for now
}

void NPTf::resetIntegrator() {

  int i, j;

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

  NPT::resetIntegrator();
}

void NPTf::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] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
    }
  }

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

void NPTf::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] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
      }
    }
  }
}

void NPTf::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 );
}

void NPTf::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 );
}

void NPTf::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 );
}

void NPTf::scaleSimBox( void ){

  int i,j,k;
  double scaleMat[3][3];
  double eta2ij;
  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++){

      // 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,
             "NPTf 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 if (offDiagMax > 0.1) {
    sprintf( painCave.errMsg,
             "NPTf error: Attempting an off-diagonal 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);
  }
}

bool NPTf::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 );
}

double NPTf::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;

}

string NPTf::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;

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

  return parameters;

}
Revision:	850
Committed:	Mon Nov 3 22:07:17 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	7406 byte(s)
Log Message:	begun work on removing templates and most of standard template library from OOPSE.
#	User	Rev	Content
1	mmeineke	850	#include <stdlib.h>
2	gezelter	829	#include <math.h>
3	mmeineke	850
4	gezelter	576	#include "Atom.hpp"
5			#include "SRI.hpp"
6			#include "AbstractClasses.hpp"
7			#include "SimInfo.hpp"
8			#include "ForceFields.hpp"
9			#include "Thermo.hpp"
10			#include "ReadWrite.hpp"
11			#include "Integrator.hpp"
12	tim	837	#include "simError.h"
13	gezelter	576
14	gezelter	772	#ifdef IS_MPI
15			#include "mpiSimulation.hpp"
16			#endif
17	gezelter	576
18	gezelter	578	// Basic non-isotropic thermostating and barostating via the Melchionna
19	gezelter	576	// modification of the Hoover algorithm:
20			//
21			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
22	tim	837	// Molec. Phys., 78, 533.
23	gezelter	576	//
24			// and
25	tim	837	//
26	gezelter	576	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
27
28	mmeineke	849	NPTf::NPTf ( SimInfo theInfo, ForceFields the_ff):
29	mmeineke	850	NPT( theInfo, the_ff )
30	gezelter	576	{
31	tim	837	GenericData* data;
32	mmeineke	850	double *etaArray;
33	mmeineke	780	int i,j;
34	tim	837
35	mmeineke	780	for(i = 0; i < 3; i++){
36			for (j = 0; j < 3; j++){
37	tim	837
38	gezelter	588	eta[i][j] = 0.0;
39	mmeineke	780	oldEta[i][j] = 0.0;
40			}
41			}
42	tim	837
43	mmeineke	850	// retrieve eta array from simInfo if it exists
44			data = info->getProperty(ETAVALUE_ID);
45			if(data != NULL){
46
47			int test = data->getDarray(etaArray);
48
49			if( test == 9 ){
50
51			for(i = 0; i < 3; i++){
52			for (j = 0; j < 3; j++){
53			eta[i][j] = etaArray[3*i+j];
54			oldEta[i][j] = eta[i][j];
55			}
56			}
57			delete[] etaArray;
58	tim	837	}
59	mmeineke	850	else
60			std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test
61			<< ").\n"
62			<< " Simulation wil proceed with eta = 0;\n";
63			}
64	mmeineke	780	}
65	gezelter	588
66	mmeineke	849	NPTf::~NPTf() {
67	tim	767
68	mmeineke	780	// empty for now
69			}
70	tim	767
71	mmeineke	849	void NPTf::resetIntegrator() {
72	tim	837
73	mmeineke	780	int i, j;
74	tim	837
75	mmeineke	780	for(i = 0; i < 3; i++)
76			for (j = 0; j < 3; j++)
77			eta[i][j] = 0.0;
78	tim	837
79	mmeineke	850	NPT::resetIntegrator();
80	gezelter	576	}
81
82	mmeineke	849	void NPTf::evolveEtaA() {
83	tim	837
84	mmeineke	780	int i, j;
85	tim	837
86	mmeineke	780	for(i = 0; i < 3; i ++){
87			for(j = 0; j < 3; j++){
88			if( i == j)
89	tim	837	eta[i][j] += dt2 * instaVol *
90	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
91			else
92			eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
93			}
94			}
95	tim	837
96	mmeineke	780	for(i = 0; i < 3; i++)
97			for (j = 0; j < 3; j++)
98			oldEta[i][j] = eta[i][j];
99	tim	767	}
100
101	mmeineke	849	void NPTf::evolveEtaB() {
102	tim	837
103	mmeineke	780	int i,j;
104	gezelter	772
105	mmeineke	780	for(i = 0; i < 3; i++)
106			for (j = 0; j < 3; j++)
107			prevEta[i][j] = eta[i][j];
108	mmeineke	778
109	mmeineke	780	for(i = 0; i < 3; i ++){
110			for(j = 0; j < 3; j++){
111			if( i == j) {
112	tim	837	eta[i][j] = oldEta[i][j] + dt2 * instaVol *
113	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
114			} else {
115			eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
116			}
117			}
118			}
119			}
120	gezelter	600
121	mmeineke	849	void NPTf::getVelScaleA(double sc[3], double vel[3]) {
122	mmeineke	780	int i,j;
123			double vScale[3][3];
124	gezelter	576
125	gezelter	588	for (i = 0; i < 3; i++ ) {
126			for (j = 0; j < 3; j++ ) {
127	tim	767	vScale[i][j] = eta[i][j];
128	tim	837
129	gezelter	588	if (i == j) {
130	tim	837	vScale[i][j] += chi;
131			}
132	gezelter	588	}
133			}
134	tim	837
135	mmeineke	780	info->matVecMul3( vScale, vel, sc );
136			}
137	gezelter	600
138	mmeineke	849	void NPTf::getVelScaleB(double sc[3], int index ){
139	mmeineke	780	int i,j;
140			double myVel[3];
141			double vScale[3][3];
142	gezelter	600
143	mmeineke	780	for (i = 0; i < 3; i++ ) {
144			for (j = 0; j < 3; j++ ) {
145			vScale[i][j] = eta[i][j];
146	tim	837
147	mmeineke	780	if (i == j) {
148	tim	837	vScale[i][j] += chi;
149			}
150	tim	767	}
151			}
152	tim	837
153	mmeineke	780	for (j = 0; j < 3; j++)
154			myVel[j] = oldVel[3*index + j];
155	tim	767
156	mmeineke	780	info->matVecMul3( vScale, myVel, sc );
157			}
158	tim	767
159	mmeineke	849	void NPTf::getPosScale(double pos[3], double COM[3],
160	mmeineke	780	int index, double sc[3]){
161			int j;
162			double rj[3];
163	tim	767
164	mmeineke	780	for(j=0; j<3; j++)
165			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
166	tim	767
167	mmeineke	780	info->matVecMul3( eta, rj, sc );
168			}
169	tim	767
170	mmeineke	849	void NPTf::scaleSimBox( void ){
171	tim	767
172	mmeineke	780	int i,j,k;
173			double scaleMat[3][3];
174			double eta2ij;
175			double bigScale, smallScale, offDiagMax;
176			double hm[3][3], hmnew[3][3];
177	tim	767
178	mmeineke	780
179	tim	837
180	gezelter	577	// Scale the box after all the positions have been moved:
181	tim	837
182	gezelter	578	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
183			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
184	tim	837
185	gezelter	617	bigScale = 1.0;
186			smallScale = 1.0;
187			offDiagMax = 0.0;
188	tim	837
189	gezelter	578	for(i=0; i<3; i++){
190			for(j=0; j<3; j++){
191	tim	837
192	gezelter	588	// Calculate the matrix Product of the eta array (we only need
193			// the ij element right now):
194	tim	837
195	gezelter	588	eta2ij = 0.0;
196	gezelter	578	for(k=0; k<3; k++){
197	gezelter	588	eta2ij += eta[i][k] * eta[k][j];
198	gezelter	578	}
199	tim	837
200	gezelter	588	scaleMat[i][j] = 0.0;
201			// identity matrix (see above):
202			if (i == j) scaleMat[i][j] = 1.0;
203			// Taylor expansion for the exponential truncated at second order:
204			scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
205	gezelter	617
206			if (i != j)
207	tim	837	if (fabs(scaleMat[i][j]) > offDiagMax)
208	gezelter	617	offDiagMax = fabs(scaleMat[i][j]);
209	gezelter	578	}
210	gezelter	617
211			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
212			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
213	gezelter	578	}
214	tim	837
215	gezelter	617	if ((bigScale > 1.1) \|\| (smallScale < 0.9)) {
216			sprintf( painCave.errMsg,
217			"NPTf error: Attempting a Box scaling of more than 10 percent.\n"
218			" Check your tauBarostat, as it is probably too small!\n\n"
219			" scaleMat = [%lf\t%lf\t%lf]\n"
220			" [%lf\t%lf\t%lf]\n"
221			" [%lf\t%lf\t%lf]\n",
222			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
223			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
224			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
225			painCave.isFatal = 1;
226			simError();
227			} else if (offDiagMax > 0.1) {
228			sprintf( painCave.errMsg,
229			"NPTf error: Attempting an off-diagonal Box scaling of more than 10 percent.\n"
230			" Check your tauBarostat, as it is probably too small!\n\n"
231			" scaleMat = [%lf\t%lf\t%lf]\n"
232			" [%lf\t%lf\t%lf]\n"
233			" [%lf\t%lf\t%lf]\n",
234			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
235			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
236			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
237			painCave.isFatal = 1;
238			simError();
239			} else {
240			info->getBoxM(hm);
241			info->matMul3(hm, scaleMat, hmnew);
242			info->setBoxM(hmnew);
243			}
244	gezelter	576	}
245
246	mmeineke	849	bool NPTf::etaConverged() {
247	mmeineke	780	int i;
248			double diffEta, sumEta;
249	gezelter	600
250	mmeineke	780	sumEta = 0;
251	tim	767	for(i = 0; i < 3; i++)
252	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
253
254	mmeineke	780	diffEta = sqrt( sumEta / 3.0 );
255	tim	837
256	mmeineke	780	return ( diffEta <= etaTolerance );
257	gezelter	576	}
258
259	mmeineke	849	double NPTf::getConservedQuantity(void){
260	tim	837
261	tim	763	double conservedQuantity;
262	mmeineke	782	double totalEnergy;
263	gezelter	772	double thermostat_kinetic;
264			double thermostat_potential;
265			double barostat_kinetic;
266			double barostat_potential;
267			double trEta;
268			double a[3][3], b[3][3];
269	tim	763
270	mmeineke	782	totalEnergy = tStats->getTotalE();
271	tim	763
272	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
273	gezelter	772	(2.0 * eConvert);
274	tim	763
275	gezelter	772	thermostat_potential = fkBT* integralOfChidt / eConvert;
276	tim	763
277	gezelter	772	info->transposeMat3(eta, a);
278			info->matMul3(a, eta, b);
279			trEta = info->matTrace3(b);
280	tim	767
281	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
282	gezelter	772	(2.0 * eConvert);
283	tim	837
284			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
285	gezelter	772	eConvert;
286	tim	767
287	mmeineke	782	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
288	gezelter	772	barostat_kinetic + barostat_potential;
289	tim	837
290	mmeineke	780	// cout.width(8);
291			// cout.precision(8);
292	tim	767
293	tim	837	// cerr << info->getTime() << "\t" << Energy << "\t" << thermostat_kinetic <<
294			// "\t" << thermostat_potential << "\t" << barostat_kinetic <<
295	mmeineke	780	// "\t" << barostat_potential << "\t" << conservedQuantity << endl;
296	gezelter	772
297	tim	837	return conservedQuantity;
298
299	tim	763	}
300	tim	837
301	mmeineke	849	string NPTf::getAdditionalParameters(void){
302	tim	837	string parameters;
303			const int BUFFERSIZE = 2000; // size of the read buffer
304			char buffer[BUFFERSIZE];
305
306	mmeineke	847	sprintf(buffer,"\t%lf\t%lf;", chi, integralOfChidt);
307	tim	837	parameters += buffer;
308
309			for(int i = 0; i < 3; i++){
310	mmeineke	847	sprintf(buffer,"\t%lf\t%lf\t%lf;", eta[3i], eta[3i+1], eta[3*i+2]);
311	tim	837	parameters += buffer;
312			}
313
314			return parameters;
315
316			}