OOPSE/libmdtools/NPTf.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> NPTf<T>::NPTf ( 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> NPTf<T>::~NPTf() {

  // empty for now
}

template<typename T> void NPTf<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 NPTf<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] += 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];
}

template<typename T> void NPTf<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] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
      }
    }
  }
}

template<typename T> void NPTf<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 NPTf<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 NPTf<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 NPTf<T>::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);
  }
}

template<typename T> bool NPTf<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 NPTf<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;

  return conservedQuantity;

}

template<typename T> string NPTf<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:	7322 byte(s)
Log Message:	added the following parameters to BASS: * useInitialExtendedSystemState * orthoBoxTolerance * useIntiTime => useInitialTime
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	gezelter	576	#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	576
12	gezelter	772	#ifdef IS_MPI
13			#include "mpiSimulation.hpp"
14			#endif
15	gezelter	576
16	gezelter	578	// Basic non-isotropic thermostating and barostating via the Melchionna
17	gezelter	576	// 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	576	//
22			// and
23	tim	837	//
24	gezelter	576	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
25
26	tim	645	template<typename T> NPTf<T>::NPTf ( SimInfo theInfo, ForceFields the_ff):
27			T( theInfo, the_ff )
28	gezelter	576	{
29	tim	837	GenericData* data;
30			DoubleArrayData * etaValue;
31			vector<double> etaArray;
32	mmeineke	780	int i,j;
33	tim	837
34	mmeineke	780	for(i = 0; i < 3; i++){
35			for (j = 0; j < 3; j++){
36	tim	837
37	gezelter	588	eta[i][j] = 0.0;
38	mmeineke	780	oldEta[i][j] = 0.0;
39			}
40			}
41	tim	837
42	mmeineke	855
43			if( theInfo->useInitXSstate ){
44	tim	837	// retrieve eta array from simInfo if it exists
45			data = info->getProperty(ETAVALUE_ID);
46			if(data){
47			etaValue = dynamic_cast<DoubleArrayData*>(data);
48	mmeineke	855
49	tim	837	if(etaValue){
50	mmeineke	855	etaArray = etaValue->getData();
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	tim	837	}
59			}
60	mmeineke	855	}
61	tim	837
62	mmeineke	780	}
63	gezelter	588
64	mmeineke	780	template<typename T> NPTf<T>::~NPTf() {
65	tim	767
66	mmeineke	780	// empty for now
67			}
68	tim	767
69	mmeineke	780	template<typename T> void NPTf<T>::resetIntegrator() {
70	tim	837
71	mmeineke	780	int i, j;
72	tim	837
73	mmeineke	780	for(i = 0; i < 3; i++)
74			for (j = 0; j < 3; j++)
75			eta[i][j] = 0.0;
76	tim	837
77	mmeineke	780	T::resetIntegrator();
78	gezelter	576	}
79
80	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaA() {
81	tim	837
82	mmeineke	780	int i, j;
83	tim	837
84	mmeineke	780	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	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
89			else
90			eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
91			}
92			}
93	tim	837
94	mmeineke	780	for(i = 0; i < 3; i++)
95			for (j = 0; j < 3; j++)
96			oldEta[i][j] = eta[i][j];
97	tim	767	}
98
99	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaB() {
100	tim	837
101	mmeineke	780	int i,j;
102	gezelter	772
103	mmeineke	780	for(i = 0; i < 3; i++)
104			for (j = 0; j < 3; j++)
105			prevEta[i][j] = eta[i][j];
106	mmeineke	778
107	mmeineke	780	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	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
112			} else {
113			eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
114			}
115			}
116			}
117			}
118	gezelter	600
119	mmeineke	780	template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
120			int i,j;
121			double vScale[3][3];
122	gezelter	576
123	gezelter	588	for (i = 0; i < 3; i++ ) {
124			for (j = 0; j < 3; j++ ) {
125	tim	767	vScale[i][j] = eta[i][j];
126	tim	837
127	gezelter	588	if (i == j) {
128	tim	837	vScale[i][j] += chi;
129			}
130	gezelter	588	}
131			}
132	tim	837
133	mmeineke	780	info->matVecMul3( vScale, vel, sc );
134			}
135	gezelter	600
136	mmeineke	780	template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
137			int i,j;
138			double myVel[3];
139			double vScale[3][3];
140	gezelter	600
141	mmeineke	780	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	780	if (i == j) {
146	tim	837	vScale[i][j] += chi;
147			}
148	tim	767	}
149			}
150	tim	837
151	mmeineke	780	for (j = 0; j < 3; j++)
152			myVel[j] = oldVel[3*index + j];
153	tim	767
154	mmeineke	780	info->matVecMul3( vScale, myVel, sc );
155			}
156	tim	767
157	tim	837	template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
158	mmeineke	780	int index, double sc[3]){
159			int j;
160			double rj[3];
161	tim	767
162	mmeineke	780	for(j=0; j<3; j++)
163			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
164	tim	767
165	mmeineke	780	info->matVecMul3( eta, rj, sc );
166			}
167	tim	767
168	mmeineke	780	template<typename T> void NPTf<T>::scaleSimBox( void ){
169	tim	767
170	mmeineke	780	int i,j,k;
171			double scaleMat[3][3];
172			double eta2ij;
173			double bigScale, smallScale, offDiagMax;
174			double hm[3][3], hmnew[3][3];
175	tim	767
176	mmeineke	780
177	tim	837
178	gezelter	577	// Scale the box after all the positions have been moved:
179	tim	837
180	gezelter	578	// 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	gezelter	617	bigScale = 1.0;
184			smallScale = 1.0;
185			offDiagMax = 0.0;
186	tim	837
187	gezelter	578	for(i=0; i<3; i++){
188			for(j=0; j<3; j++){
189	tim	837
190	gezelter	588	// Calculate the matrix Product of the eta array (we only need
191			// the ij element right now):
192	tim	837
193	gezelter	588	eta2ij = 0.0;
194	gezelter	578	for(k=0; k<3; k++){
195	gezelter	588	eta2ij += eta[i][k] * eta[k][j];
196	gezelter	578	}
197	tim	837
198	gezelter	588	scaleMat[i][j] = 0.0;
199			// identity matrix (see above):
200			if (i == j) scaleMat[i][j] = 1.0;
201			// Taylor expansion for the exponential truncated at second order:
202			scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
203	gezelter	617
204			if (i != j)
205	tim	837	if (fabs(scaleMat[i][j]) > offDiagMax)
206	gezelter	617	offDiagMax = fabs(scaleMat[i][j]);
207	gezelter	578	}
208	gezelter	617
209			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
210			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
211	gezelter	578	}
212	tim	837
213	mmeineke	853	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
214	gezelter	617	sprintf( painCave.errMsg,
215	mmeineke	853	"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
216	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
217			" scaleMat = [%lf\t%lf\t%lf]\n"
218			" [%lf\t%lf\t%lf]\n"
219			" [%lf\t%lf\t%lf]\n",
220			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
221			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
222			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
223			painCave.isFatal = 1;
224			simError();
225	mmeineke	853	} else if (offDiagMax > 0.01) {
226	gezelter	617	sprintf( painCave.errMsg,
227	mmeineke	853	"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
228	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
229			" scaleMat = [%lf\t%lf\t%lf]\n"
230			" [%lf\t%lf\t%lf]\n"
231			" [%lf\t%lf\t%lf]\n",
232			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
233			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
234			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
235			painCave.isFatal = 1;
236			simError();
237			} else {
238			info->getBoxM(hm);
239			info->matMul3(hm, scaleMat, hmnew);
240			info->setBoxM(hmnew);
241			}
242	gezelter	576	}
243
244	mmeineke	780	template<typename T> bool NPTf<T>::etaConverged() {
245			int i;
246			double diffEta, sumEta;
247	gezelter	600
248	mmeineke	780	sumEta = 0;
249	tim	767	for(i = 0; i < 3; i++)
250	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
251
252	mmeineke	780	diffEta = sqrt( sumEta / 3.0 );
253	tim	837
254	mmeineke	780	return ( diffEta <= etaTolerance );
255	gezelter	576	}
256
257	mmeineke	780	template<typename T> double NPTf<T>::getConservedQuantity(void){
258	tim	837
259	tim	763	double conservedQuantity;
260	mmeineke	782	double totalEnergy;
261	gezelter	772	double thermostat_kinetic;
262			double thermostat_potential;
263			double barostat_kinetic;
264			double barostat_potential;
265			double trEta;
266			double a[3][3], b[3][3];
267	tim	763
268	mmeineke	782	totalEnergy = tStats->getTotalE();
269	tim	763
270	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
271	gezelter	772	(2.0 * eConvert);
272	tim	763
273	gezelter	772	thermostat_potential = fkBT* integralOfChidt / eConvert;
274	tim	763
275	gezelter	772	info->transposeMat3(eta, a);
276			info->matMul3(a, eta, b);
277			trEta = info->matTrace3(b);
278	tim	767
279	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
280	gezelter	772	(2.0 * eConvert);
281	tim	837
282			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
283	gezelter	772	eConvert;
284	tim	767
285	mmeineke	782	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
286	gezelter	772	barostat_kinetic + barostat_potential;
287	tim	837
288			return conservedQuantity;
289
290	tim	763	}
291	tim	837
292			template<typename T> string NPTf<T>::getAdditionalParameters(void){
293			string parameters;
294			const int BUFFERSIZE = 2000; // size of the read buffer
295			char buffer[BUFFERSIZE];
296
297	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
298	tim	837	parameters += buffer;
299
300			for(int i = 0; i < 3; i++){
301	mmeineke	853	sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
302	tim	837	parameters += buffer;
303			}
304
305			return parameters;
306
307			}