OOPSE/libmdtools/NPTf.cpp

#include <stdlib.h>
#include <math.h>
#include <string.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];

//   std::cerr << "velScaleB chi = " << chi << "\n";

  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 > 1.01) || (smallScale < 0.99)) {
    sprintf( painCave.errMsg,
             "NPTf error: Attempting a Box scaling of more than 1 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 > 0.01) {
    sprintf( painCave.errMsg,
             "NPTf error: Attempting an off-diagonal Box scaling of more than 1 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;

  return conservedQuantity;

}

char* NPTf::getAdditionalParameters(void){

  sprintf(addParamBuffer,
          "\t%G\t%G;"
          "\t%G\t%G\t%G;"
          "\t%G\t%G\t%G;"
          "\t%G\t%G\t%G;",
          chi, integralOfChidt,
          eta[0][0], eta[0][1], eta[0][2],
          eta[1][0], eta[1][1], eta[1][2],
          eta[2][0], eta[2][1], eta[2][2]
          );

  return addParamBuffer;
}
Revision:	852
Committed:	Thu Nov 6 18:20:47 2003 UTC (21 years, 8 months ago) by mmeineke
File size:	7128 byte(s)
Log Message:	fixed the "Sudden Death" bug. The box was not switching between orthorhombic and non-orthorhombic wrapping correctly. we added a fabs() to the check.which should fix it.
#	User	Rev	Content
1	mmeineke	850	#include <stdlib.h>
2	gezelter	829	#include <math.h>
3	mmeineke	851	#include <string.h>
4	mmeineke	850
5	gezelter	576	#include "Atom.hpp"
6			#include "SRI.hpp"
7			#include "AbstractClasses.hpp"
8			#include "SimInfo.hpp"
9			#include "ForceFields.hpp"
10			#include "Thermo.hpp"
11			#include "ReadWrite.hpp"
12			#include "Integrator.hpp"
13	tim	837	#include "simError.h"
14	gezelter	576
15	gezelter	772	#ifdef IS_MPI
16			#include "mpiSimulation.hpp"
17			#endif
18	gezelter	576
19	gezelter	578	// Basic non-isotropic thermostating and barostating via the Melchionna
20	gezelter	576	// modification of the Hoover algorithm:
21			//
22			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
23	tim	837	// Molec. Phys., 78, 533.
24	gezelter	576	//
25			// and
26	tim	837	//
27	gezelter	576	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
28
29	mmeineke	849	NPTf::NPTf ( SimInfo theInfo, ForceFields the_ff):
30	mmeineke	850	NPT( theInfo, the_ff )
31	gezelter	576	{
32	tim	837	GenericData* data;
33	mmeineke	850	double *etaArray;
34	mmeineke	780	int i,j;
35	tim	837
36	mmeineke	780	for(i = 0; i < 3; i++){
37			for (j = 0; j < 3; j++){
38	tim	837
39	gezelter	588	eta[i][j] = 0.0;
40	mmeineke	780	oldEta[i][j] = 0.0;
41			}
42			}
43	tim	837
44	mmeineke	850	// retrieve eta array from simInfo if it exists
45			data = info->getProperty(ETAVALUE_ID);
46			if(data != NULL){
47
48			int test = data->getDarray(etaArray);
49
50			if( test == 9 ){
51
52			for(i = 0; i < 3; i++){
53			for (j = 0; j < 3; j++){
54			eta[i][j] = etaArray[3*i+j];
55			oldEta[i][j] = eta[i][j];
56			}
57			}
58			delete[] etaArray;
59	tim	837	}
60	mmeineke	850	else
61			std::cerr << "NPTf error: etaArray is not length 9 (actual = " << test
62			<< ").\n"
63			<< " Simulation wil proceed with eta = 0;\n";
64			}
65	mmeineke	780	}
66	gezelter	588
67	mmeineke	849	NPTf::~NPTf() {
68	tim	767
69	mmeineke	780	// empty for now
70			}
71	tim	767
72	mmeineke	849	void NPTf::resetIntegrator() {
73	tim	837
74	mmeineke	780	int i, j;
75	tim	837
76	mmeineke	780	for(i = 0; i < 3; i++)
77			for (j = 0; j < 3; j++)
78			eta[i][j] = 0.0;
79	tim	837
80	mmeineke	850	NPT::resetIntegrator();
81	gezelter	576	}
82
83	mmeineke	849	void NPTf::evolveEtaA() {
84	tim	837
85	mmeineke	780	int i, j;
86	tim	837
87	mmeineke	780	for(i = 0; i < 3; i ++){
88			for(j = 0; j < 3; j++){
89			if( i == j)
90	tim	837	eta[i][j] += dt2 * instaVol *
91	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
92			else
93			eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
94			}
95			}
96	tim	837
97	mmeineke	780	for(i = 0; i < 3; i++)
98			for (j = 0; j < 3; j++)
99			oldEta[i][j] = eta[i][j];
100	tim	767	}
101
102	mmeineke	849	void NPTf::evolveEtaB() {
103	tim	837
104	mmeineke	780	int i,j;
105	gezelter	772
106	mmeineke	780	for(i = 0; i < 3; i++)
107			for (j = 0; j < 3; j++)
108			prevEta[i][j] = eta[i][j];
109	mmeineke	778
110	mmeineke	780	for(i = 0; i < 3; i ++){
111			for(j = 0; j < 3; j++){
112			if( i == j) {
113	tim	837	eta[i][j] = oldEta[i][j] + dt2 * instaVol *
114	mmeineke	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
115			} else {
116			eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
117			}
118			}
119			}
120			}
121	gezelter	600
122	mmeineke	849	void NPTf::getVelScaleA(double sc[3], double vel[3]) {
123	mmeineke	780	int i,j;
124			double vScale[3][3];
125	gezelter	576
126	gezelter	588	for (i = 0; i < 3; i++ ) {
127			for (j = 0; j < 3; j++ ) {
128	tim	767	vScale[i][j] = eta[i][j];
129	tim	837
130	gezelter	588	if (i == j) {
131	tim	837	vScale[i][j] += chi;
132			}
133	gezelter	588	}
134			}
135	tim	837
136	mmeineke	780	info->matVecMul3( vScale, vel, sc );
137			}
138	gezelter	600
139	mmeineke	849	void NPTf::getVelScaleB(double sc[3], int index ){
140	mmeineke	780	int i,j;
141			double myVel[3];
142			double vScale[3][3];
143	gezelter	600
144	mmeineke	851	// std::cerr << "velScaleB chi = " << chi << "\n";
145
146	mmeineke	780	for (i = 0; i < 3; i++ ) {
147			for (j = 0; j < 3; j++ ) {
148			vScale[i][j] = eta[i][j];
149	tim	837
150	mmeineke	780	if (i == j) {
151	tim	837	vScale[i][j] += chi;
152			}
153	tim	767	}
154			}
155	tim	837
156	mmeineke	780	for (j = 0; j < 3; j++)
157			myVel[j] = oldVel[3*index + j];
158	tim	767
159	mmeineke	780	info->matVecMul3( vScale, myVel, sc );
160			}
161	tim	767
162	mmeineke	849	void NPTf::getPosScale(double pos[3], double COM[3],
163	mmeineke	852	int index, double sc[3]){
164	mmeineke	780	int j;
165			double rj[3];
166	tim	767
167	mmeineke	780	for(j=0; j<3; j++)
168			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
169	tim	767
170	mmeineke	780	info->matVecMul3( eta, rj, sc );
171			}
172	tim	767
173	mmeineke	849	void NPTf::scaleSimBox( void ){
174	tim	767
175	mmeineke	780	int i,j,k;
176			double scaleMat[3][3];
177			double eta2ij;
178			double bigScale, smallScale, offDiagMax;
179			double hm[3][3], hmnew[3][3];
180	tim	767
181	mmeineke	780
182	tim	837
183	gezelter	577	// Scale the box after all the positions have been moved:
184	tim	837
185	gezelter	578	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
186			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
187	tim	837
188	gezelter	617	bigScale = 1.0;
189			smallScale = 1.0;
190			offDiagMax = 0.0;
191	tim	837
192	gezelter	578	for(i=0; i<3; i++){
193			for(j=0; j<3; j++){
194	tim	837
195	gezelter	588	// Calculate the matrix Product of the eta array (we only need
196			// the ij element right now):
197	tim	837
198	gezelter	588	eta2ij = 0.0;
199	gezelter	578	for(k=0; k<3; k++){
200	gezelter	588	eta2ij += eta[i][k] * eta[k][j];
201	gezelter	578	}
202	tim	837
203	gezelter	588	scaleMat[i][j] = 0.0;
204			// identity matrix (see above):
205			if (i == j) scaleMat[i][j] = 1.0;
206			// Taylor expansion for the exponential truncated at second order:
207			scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
208	gezelter	617
209			if (i != j)
210	tim	837	if (fabs(scaleMat[i][j]) > offDiagMax)
211	gezelter	617	offDiagMax = fabs(scaleMat[i][j]);
212	gezelter	578	}
213	gezelter	617
214			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
215			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
216	gezelter	578	}
217	tim	837
218	mmeineke	852	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
219	gezelter	617	sprintf( painCave.errMsg,
220	mmeineke	852	"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
221	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
222			" scaleMat = [%lf\t%lf\t%lf]\n"
223			" [%lf\t%lf\t%lf]\n"
224			" [%lf\t%lf\t%lf]\n",
225			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
226			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
227			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
228			painCave.isFatal = 1;
229			simError();
230	mmeineke	852	} else if (offDiagMax > 0.01) {
231	gezelter	617	sprintf( painCave.errMsg,
232	mmeineke	852	"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
233	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
234			" scaleMat = [%lf\t%lf\t%lf]\n"
235			" [%lf\t%lf\t%lf]\n"
236			" [%lf\t%lf\t%lf]\n",
237			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
238			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
239			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
240			painCave.isFatal = 1;
241			simError();
242			} else {
243			info->getBoxM(hm);
244			info->matMul3(hm, scaleMat, hmnew);
245			info->setBoxM(hmnew);
246			}
247	gezelter	576	}
248
249	mmeineke	849	bool NPTf::etaConverged() {
250	mmeineke	780	int i;
251			double diffEta, sumEta;
252	gezelter	600
253	mmeineke	780	sumEta = 0;
254	tim	767	for(i = 0; i < 3; i++)
255	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
256
257	mmeineke	780	diffEta = sqrt( sumEta / 3.0 );
258	tim	837
259	mmeineke	780	return ( diffEta <= etaTolerance );
260	gezelter	576	}
261
262	mmeineke	849	double NPTf::getConservedQuantity(void){
263	tim	837
264	tim	763	double conservedQuantity;
265	mmeineke	782	double totalEnergy;
266	gezelter	772	double thermostat_kinetic;
267			double thermostat_potential;
268			double barostat_kinetic;
269			double barostat_potential;
270			double trEta;
271			double a[3][3], b[3][3];
272	tim	763
273	mmeineke	782	totalEnergy = tStats->getTotalE();
274	tim	763
275	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
276	gezelter	772	(2.0 * eConvert);
277	tim	763
278	gezelter	772	thermostat_potential = fkBT* integralOfChidt / eConvert;
279	tim	763
280	gezelter	772	info->transposeMat3(eta, a);
281			info->matMul3(a, eta, b);
282			trEta = info->matTrace3(b);
283	tim	767
284	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
285	gezelter	772	(2.0 * eConvert);
286	tim	837
287			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
288	gezelter	772	eConvert;
289	tim	767
290	mmeineke	782	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
291	gezelter	772	barostat_kinetic + barostat_potential;
292	tim	837
293			return conservedQuantity;
294
295	tim	763	}
296	tim	837
297	mmeineke	851	char* NPTf::getAdditionalParameters(void){
298	tim	837
299	mmeineke	851	sprintf(addParamBuffer,
300			"\t%G\t%G;"
301			"\t%G\t%G\t%G;"
302			"\t%G\t%G\t%G;"
303			"\t%G\t%G\t%G;",
304			chi, integralOfChidt,
305			eta[0][0], eta[0][1], eta[0][2],
306			eta[1][0], eta[1][1], eta[1][2],
307			eta[2][0], eta[2][1], eta[2][2]
308			);
309	tim	837
310	mmeineke	851	return addParamBuffer;
311	tim	837	}