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>::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 NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
 
  info->matVecMul3( vScale, vel, sc );
}

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

  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:	857
Committed:	Fri Nov 7 17:09:48 2003 UTC (20 years, 8 months ago) by mmeineke
File size:	7196 byte(s)
Log Message:	moved the velocity scale matrix calculation outside of the atom loop in the NPT family of integrators.
#	User	Rev	Content
1	gezelter	829	#include <math.h>
2	mmeineke	857
3	gezelter	576	#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	gezelter	576
13	gezelter	772	#ifdef IS_MPI
14			#include "mpiSimulation.hpp"
15			#endif
16	gezelter	576
17	gezelter	578	// Basic non-isotropic thermostating and barostating via the Melchionna
18	gezelter	576	// modification of the Hoover algorithm:
19			//
20			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
21	tim	837	// Molec. Phys., 78, 533.
22	gezelter	576	//
23			// and
24	tim	837	//
25	gezelter	576	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
26
27	tim	645	template<typename T> NPTf<T>::NPTf ( SimInfo theInfo, ForceFields the_ff):
28			T( theInfo, the_ff )
29	gezelter	576	{
30	tim	837	GenericData* data;
31			DoubleArrayData * etaValue;
32			vector<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	855
44			if( theInfo->useInitXSstate ){
45	tim	837	// retrieve eta array from simInfo if it exists
46			data = info->getProperty(ETAVALUE_ID);
47			if(data){
48			etaValue = dynamic_cast<DoubleArrayData*>(data);
49	mmeineke	855
50	tim	837	if(etaValue){
51	mmeineke	855	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	mmeineke	855	}
62	tim	837
63	mmeineke	780	}
64	gezelter	588
65	mmeineke	780	template<typename T> NPTf<T>::~NPTf() {
66	tim	767
67	mmeineke	780	// empty for now
68			}
69	tim	767
70	mmeineke	780	template<typename T> void NPTf<T>::resetIntegrator() {
71	tim	837
72	mmeineke	780	int i, j;
73	tim	837
74	mmeineke	780	for(i = 0; i < 3; i++)
75			for (j = 0; j < 3; j++)
76			eta[i][j] = 0.0;
77	tim	837
78	mmeineke	780	T::resetIntegrator();
79	gezelter	576	}
80
81	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaA() {
82	tim	837
83	mmeineke	780	int i, j;
84	tim	837
85	mmeineke	780	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	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
90			else
91			eta[i][j] += dt2 * instaVol * press[i][j] / (NkBT*tb2);
92			}
93			}
94	tim	837
95	mmeineke	780	for(i = 0; i < 3; i++)
96			for (j = 0; j < 3; j++)
97			oldEta[i][j] = eta[i][j];
98	tim	767	}
99
100	mmeineke	780	template<typename T> void NPTf<T>::evolveEtaB() {
101	tim	837
102	mmeineke	780	int i,j;
103	gezelter	772
104	mmeineke	780	for(i = 0; i < 3; i++)
105			for (j = 0; j < 3; j++)
106			prevEta[i][j] = eta[i][j];
107	mmeineke	778
108	mmeineke	780	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	780	(press[i][j] - targetPressure/p_convert) / (NkBT*tb2);
113			} else {
114			eta[i][j] = oldEta[i][j] + dt2 * instaVol * press[i][j] / (NkBT*tb2);
115			}
116			}
117			}
118			}
119	gezelter	600
120	mmeineke	857	template<typename T> void NPTf<T>::calcVelScale(void){
121	mmeineke	780	int i,j;
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	mmeineke	857	}
133	tim	837
134	mmeineke	857	template<typename T> void NPTf<T>::getVelScaleA(double sc[3], double vel[3]) {
135
136	mmeineke	780	info->matVecMul3( vScale, vel, sc );
137			}
138	gezelter	600
139	mmeineke	780	template<typename T> void NPTf<T>::getVelScaleB(double sc[3], int index ){
140	mmeineke	857	int j;
141	mmeineke	780	double myVel[3];
142			double vScale[3][3];
143	gezelter	600
144	mmeineke	780	for (j = 0; j < 3; j++)
145			myVel[j] = oldVel[3*index + j];
146	tim	767
147	mmeineke	780	info->matVecMul3( vScale, myVel, sc );
148			}
149	tim	767
150	tim	837	template<typename T> void NPTf<T>::getPosScale(double pos[3], double COM[3],
151	mmeineke	780	int index, double sc[3]){
152			int j;
153			double rj[3];
154	tim	767
155	mmeineke	780	for(j=0; j<3; j++)
156			rj[j] = ( oldPos[index*3+j] + pos[j]) / 2.0 - COM[j];
157	tim	767
158	mmeineke	780	info->matVecMul3( eta, rj, sc );
159			}
160	tim	767
161	mmeineke	780	template<typename T> void NPTf<T>::scaleSimBox( void ){
162	tim	767
163	mmeineke	780	int i,j,k;
164			double scaleMat[3][3];
165			double eta2ij;
166			double bigScale, smallScale, offDiagMax;
167			double hm[3][3], hmnew[3][3];
168	tim	767
169	mmeineke	780
170	tim	837
171	gezelter	577	// Scale the box after all the positions have been moved:
172	tim	837
173	gezelter	578	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
174			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
175	tim	837
176	gezelter	617	bigScale = 1.0;
177			smallScale = 1.0;
178			offDiagMax = 0.0;
179	tim	837
180	gezelter	578	for(i=0; i<3; i++){
181			for(j=0; j<3; j++){
182	tim	837
183	gezelter	588	// Calculate the matrix Product of the eta array (we only need
184			// the ij element right now):
185	tim	837
186	gezelter	588	eta2ij = 0.0;
187	gezelter	578	for(k=0; k<3; k++){
188	gezelter	588	eta2ij += eta[i][k] * eta[k][j];
189	gezelter	578	}
190	tim	837
191	gezelter	588	scaleMat[i][j] = 0.0;
192			// identity matrix (see above):
193			if (i == j) scaleMat[i][j] = 1.0;
194			// Taylor expansion for the exponential truncated at second order:
195			scaleMat[i][j] += dteta[i][j] + 0.5dtdteta2ij;
196	gezelter	617
197			if (i != j)
198	tim	837	if (fabs(scaleMat[i][j]) > offDiagMax)
199	gezelter	617	offDiagMax = fabs(scaleMat[i][j]);
200	gezelter	578	}
201	gezelter	617
202			if (scaleMat[i][i] > bigScale) bigScale = scaleMat[i][i];
203			if (scaleMat[i][i] < smallScale) smallScale = scaleMat[i][i];
204	gezelter	578	}
205	tim	837
206	mmeineke	853	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
207	gezelter	617	sprintf( painCave.errMsg,
208	mmeineke	853	"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
209	gezelter	617	" Check your tauBarostat, as it is probably too small!\n\n"
210			" scaleMat = [%lf\t%lf\t%lf]\n"
211			" [%lf\t%lf\t%lf]\n"
212			" [%lf\t%lf\t%lf]\n",
213			scaleMat[0][0],scaleMat[0][1],scaleMat[0][2],
214			scaleMat[1][0],scaleMat[1][1],scaleMat[1][2],
215			scaleMat[2][0],scaleMat[2][1],scaleMat[2][2]);
216			painCave.isFatal = 1;
217			simError();
218	mmeineke	853	} else if (offDiagMax > 0.01) {
219	gezelter	617	sprintf( painCave.errMsg,
220	mmeineke	853	"NPTf error: Attempting an off-diagonal 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			} else {
231			info->getBoxM(hm);
232			info->matMul3(hm, scaleMat, hmnew);
233			info->setBoxM(hmnew);
234			}
235	gezelter	576	}
236
237	mmeineke	780	template<typename T> bool NPTf<T>::etaConverged() {
238			int i;
239			double diffEta, sumEta;
240	gezelter	600
241	mmeineke	780	sumEta = 0;
242	tim	767	for(i = 0; i < 3; i++)
243	tim	837	sumEta += pow(prevEta[i][i] - eta[i][i], 2);
244
245	mmeineke	780	diffEta = sqrt( sumEta / 3.0 );
246	tim	837
247	mmeineke	780	return ( diffEta <= etaTolerance );
248	gezelter	576	}
249
250	mmeineke	780	template<typename T> double NPTf<T>::getConservedQuantity(void){
251	tim	837
252	tim	763	double conservedQuantity;
253	mmeineke	782	double totalEnergy;
254	gezelter	772	double thermostat_kinetic;
255			double thermostat_potential;
256			double barostat_kinetic;
257			double barostat_potential;
258			double trEta;
259			double a[3][3], b[3][3];
260	tim	763
261	mmeineke	782	totalEnergy = tStats->getTotalE();
262	tim	763
263	tim	837	thermostat_kinetic = fkBT * tt2 * chi * chi /
264	gezelter	772	(2.0 * eConvert);
265	tim	763
266	gezelter	772	thermostat_potential = fkBT* integralOfChidt / eConvert;
267	tim	763
268	gezelter	772	info->transposeMat3(eta, a);
269			info->matMul3(a, eta, b);
270			trEta = info->matTrace3(b);
271	tim	767
272	tim	837	barostat_kinetic = NkBT * tb2 * trEta /
273	gezelter	772	(2.0 * eConvert);
274	tim	837
275			barostat_potential = (targetPressure * tStats->getVolume() / p_convert) /
276	gezelter	772	eConvert;
277	tim	767
278	mmeineke	782	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
279	gezelter	772	barostat_kinetic + barostat_potential;
280	tim	837
281			return conservedQuantity;
282
283	tim	763	}
284	tim	837
285			template<typename T> string NPTf<T>::getAdditionalParameters(void){
286			string parameters;
287			const int BUFFERSIZE = 2000; // size of the read buffer
288			char buffer[BUFFERSIZE];
289
290	mmeineke	853	sprintf(buffer,"\t%G\t%G;", chi, integralOfChidt);
291	tim	837	parameters += buffer;
292
293			for(int i = 0; i < 3; i++){
294	mmeineke	853	sprintf(buffer,"\t%G\t%G\t%G;", eta[i][0], eta[i][1], eta[i][2]);
295	tim	837	parameters += buffer;
296			}
297
298			return parameters;
299
300			}