src/integrators/NPTf.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NPTf.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {

  // 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.

  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/OOPSEConstant::pressureConvert) / (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;
    int 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/OOPSEConstant::pressureConvert) / (NkBT*tb2);
        } else {
          eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2);
        }
      }
    }

  
  }

  void NPTf::calcVelScale(){

    for (int i = 0; i < 3; i++ ) {
      for (int j = 0; j < 3; j++ ) {
        vScale(i, j) = eta(i, j);

        if (i == j) {
          vScale(i, j) += chi;
        }
      }
    }
  }

  void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){
    sc = vScale * vel;
  }

  void NPTf::getVelScaleB(Vector3d& sc, int index ) {
    sc = vScale * oldVel[index];
  }

  void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {

    /**@todo */
    Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
    sc = eta * rj;
  }

  void NPTf::scaleSimBox(){

    int i;
    int j;
    int k;
    Mat3x3d scaleMat;
    double eta2ij;
    double bigScale, smallScale, offDiagMax;
    Mat3x3d hm;
    Mat3x3d hmnew;


    // 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"
               "      eta = [%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),
               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));
      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"
               "      eta = [%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),
               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));
      painCave.isFatal = 1;
      simError();
    } else {

      Mat3x3d hmat = currentSnapshot_->getHmat();
      hmat = hmat *scaleMat;
      currentSnapshot_->setHmat(hmat);
        
    }
  }

  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::calcConservedQuantity(){

    chi= currentSnapshot_->getChi();
    integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
    loadEta();
    
    // We need NkBT a lot, so just set it here: This is the RAW number
    // of integrableObjects, so no subtraction or addition of constraints or
    // orientational degrees of freedom:
    NkBT = info_->getNGlobalIntegrableObjects()*OOPSEConstant::kB *targetTemp;

    // fkBT is used because the thermostat operates on more degrees of freedom
    // than the barostat (when there are particles with orientational degrees
    // of freedom).  
    fkBT = info_->getNdf()*OOPSEConstant::kB *targetTemp;    
    
    double conservedQuantity;
    double totalEnergy;
    double thermostat_kinetic;
    double thermostat_potential;
    double barostat_kinetic;
    double barostat_potential;
    double trEta;

    totalEnergy = thermo.getTotalE();

    thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);

    thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;

    SquareMatrix<double, 3> tmp = eta.transpose() * eta;
    trEta = tmp.trace();
    
    barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);

    barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;

    conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
      barostat_kinetic + barostat_potential;

    return conservedQuantity;

  }

  void NPTf::loadEta() {
    eta= currentSnapshot_->getEta();

    //if (!eta.isDiagonal()) {
    //    sprintf( painCave.errMsg,
    //             "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
    //    painCave.isFatal = 1;
    //    simError();
    //}
  }

  void NPTf::saveEta() {
    currentSnapshot_->setEta(eta);
  }

}
Revision:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years, 6 months ago) by gezelter
File size:	9168 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	tim	3	#include "brains/SimInfo.hpp"
43			#include "brains/Thermo.hpp"
44	gezelter	246	#include "integrators/IntegratorCreator.hpp"
45			#include "integrators/NPTf.hpp"
46			#include "primitives/Molecule.hpp"
47			#include "utils/OOPSEConstant.hpp"
48	tim	3	#include "utils/simError.h"
49	gezelter	2
50	gezelter	246	namespace oopse {
51	gezelter	2
52	gezelter	507	// Basic non-isotropic thermostating and barostating via the Melchionna
53			// modification of the Hoover algorithm:
54			//
55			// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
56			// Molec. Phys., 78, 533.
57			//
58			// and
59			//
60			// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
61	gezelter	2
62	gezelter	507	void NPTf::evolveEtaA() {
63	gezelter	2
64	gezelter	507	int i, j;
65	gezelter	2
66	gezelter	246	for(i = 0; i < 3; i ++){
67	gezelter	507	for(j = 0; j < 3; j++){
68			if( i == j) {
69			eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
70			} else {
71			eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2);
72			}
73			}
74	gezelter	2	}
75	gezelter	246
76			for(i = 0; i < 3; i++) {
77	gezelter	507	for (j = 0; j < 3; j++) {
78	gezelter	246	oldEta(i, j) = eta(i, j);
79	gezelter	507	}
80	gezelter	2	}
81	gezelter	246
82	gezelter	507	}
83	gezelter	2
84	gezelter	507	void NPTf::evolveEtaB() {
85	gezelter	2
86	gezelter	246	int i;
87			int j;
88	gezelter	2
89	gezelter	246	for(i = 0; i < 3; i++) {
90	gezelter	507	for (j = 0; j < 3; j++) {
91			prevEta(i, j) = eta(i, j);
92			}
93	gezelter	246	}
94	gezelter	2
95	gezelter	246	for(i = 0; i < 3; i ++){
96	gezelter	507	for(j = 0; j < 3; j++){
97			if( i == j) {
98			eta(i, j) = oldEta(i, j) + dt2 * instaVol *
99			(press(i, j) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
100			} else {
101			eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2);
102			}
103			}
104	gezelter	246	}
105	gezelter	2
106
107	gezelter	507	}
108	gezelter	2
109	gezelter	507	void NPTf::calcVelScale(){
110	gezelter	2
111	gezelter	507	for (int i = 0; i < 3; i++ ) {
112			for (int j = 0; j < 3; j++ ) {
113			vScale(i, j) = eta(i, j);
114	gezelter	2
115	gezelter	507	if (i == j) {
116			vScale(i, j) += chi;
117			}
118	gezelter	2	}
119			}
120			}
121
122	gezelter	507	void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){
123	gezelter	246	sc = vScale * vel;
124	gezelter	507	}
125	gezelter	2
126	gezelter	507	void NPTf::getVelScaleB(Vector3d& sc, int index ) {
127			sc = vScale * oldVel[index];
128			}
129	gezelter	2
130	gezelter	507	void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
131	gezelter	2
132	gezelter	246	/*@todo /
133			Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
134			sc = eta * rj;
135	gezelter	507	}
136	gezelter	2
137	gezelter	507	void NPTf::scaleSimBox(){
138	gezelter	2
139	gezelter	507	int i;
140			int j;
141			int k;
142			Mat3x3d scaleMat;
143			double eta2ij;
144			double bigScale, smallScale, offDiagMax;
145			Mat3x3d hm;
146			Mat3x3d hmnew;
147	gezelter	2
148
149
150	gezelter	507	// Scale the box after all the positions have been moved:
151	gezelter	2
152	gezelter	507	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
153			// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
154	gezelter	2
155	gezelter	507	bigScale = 1.0;
156			smallScale = 1.0;
157			offDiagMax = 0.0;
158	gezelter	2
159	gezelter	507	for(i=0; i<3; i++){
160			for(j=0; j<3; j++){
161	gezelter	2
162	gezelter	507	// Calculate the matrix Product of the eta array (we only need
163			// the ij element right now):
164	gezelter	2
165	gezelter	507	eta2ij = 0.0;
166			for(k=0; k<3; k++){
167			eta2ij += eta(i, k) * eta(k, j);
168			}
169	gezelter	2
170	gezelter	507	scaleMat(i, j) = 0.0;
171			// identity matrix (see above):
172			if (i == j) scaleMat(i, j) = 1.0;
173			// Taylor expansion for the exponential truncated at second order:
174			scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
175	gezelter	2
176
177	gezelter	507	if (i != j)
178			if (fabs(scaleMat(i, j)) > offDiagMax)
179			offDiagMax = fabs(scaleMat(i, j));
180			}
181
182			if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
183			if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
184	gezelter	2	}
185
186	gezelter	507	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
187			sprintf( painCave.errMsg,
188			"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
189			" Check your tauBarostat, as it is probably too small!\n\n"
190			" scaleMat = [%lf\t%lf\t%lf]\n"
191			" [%lf\t%lf\t%lf]\n"
192			" [%lf\t%lf\t%lf]\n"
193			" eta = [%lf\t%lf\t%lf]\n"
194			" [%lf\t%lf\t%lf]\n"
195			" [%lf\t%lf\t%lf]\n",
196			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
197			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
198			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
199			eta(0, 0),eta(0, 1),eta(0, 2),
200			eta(1, 0),eta(1, 1),eta(1, 2),
201			eta(2, 0),eta(2, 1),eta(2, 2));
202			painCave.isFatal = 1;
203			simError();
204			} else if (offDiagMax > 0.01) {
205			sprintf( painCave.errMsg,
206			"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
207			" Check your tauBarostat, as it is probably too small!\n\n"
208			" scaleMat = [%lf\t%lf\t%lf]\n"
209			" [%lf\t%lf\t%lf]\n"
210			" [%lf\t%lf\t%lf]\n"
211			" eta = [%lf\t%lf\t%lf]\n"
212			" [%lf\t%lf\t%lf]\n"
213			" [%lf\t%lf\t%lf]\n",
214			scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
215			scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
216			scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
217			eta(0, 0),eta(0, 1),eta(0, 2),
218			eta(1, 0),eta(1, 1),eta(1, 2),
219			eta(2, 0),eta(2, 1),eta(2, 2));
220			painCave.isFatal = 1;
221			simError();
222			} else {
223	gezelter	2
224	gezelter	507	Mat3x3d hmat = currentSnapshot_->getHmat();
225			hmat = hmat *scaleMat;
226			currentSnapshot_->setHmat(hmat);
227	gezelter	246
228	gezelter	507	}
229	gezelter	2	}
230
231	gezelter	507	bool NPTf::etaConverged() {
232	gezelter	246	int i;
233			double diffEta, sumEta;
234	gezelter	2
235	gezelter	246	sumEta = 0;
236			for(i = 0; i < 3; i++) {
237	gezelter	507	sumEta += pow(prevEta(i, i) - eta(i, i), 2);
238	gezelter	246	}
239
240			diffEta = sqrt( sumEta / 3.0 );
241	gezelter	2
242	gezelter	246	return ( diffEta <= etaTolerance );
243	gezelter	507	}
244	gezelter	2
245	gezelter	507	double NPTf::calcConservedQuantity(){
246	gezelter	2
247	gezelter	246	chi= currentSnapshot_->getChi();
248			integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
249			loadEta();
250
251			// We need NkBT a lot, so just set it here: This is the RAW number
252			// of integrableObjects, so no subtraction or addition of constraints or
253			// orientational degrees of freedom:
254			NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
255	gezelter	2
256	gezelter	246	// fkBT is used because the thermostat operates on more degrees of freedom
257			// than the barostat (when there are particles with orientational degrees
258			// of freedom).
259			fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
260
261			double conservedQuantity;
262			double totalEnergy;
263			double thermostat_kinetic;
264			double thermostat_potential;
265			double barostat_kinetic;
266			double barostat_potential;
267			double trEta;
268	gezelter	2
269	gezelter	246	totalEnergy = thermo.getTotalE();
270	gezelter	2
271	gezelter	246	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
272	gezelter	2
273	gezelter	246	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
274	gezelter	2
275	gezelter	246	SquareMatrix<double, 3> tmp = eta.transpose() * eta;
276			trEta = tmp.trace();
277
278			barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
279	gezelter	2
280	gezelter	246	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
281	gezelter	2
282	gezelter	246	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
283	gezelter	507	barostat_kinetic + barostat_potential;
284	gezelter	2
285	gezelter	246	return conservedQuantity;
286	gezelter	2
287	gezelter	507	}
288	gezelter	2
289	gezelter	507	void NPTf::loadEta() {
290	gezelter	246	eta= currentSnapshot_->getEta();
291	gezelter	2
292	gezelter	246	//if (!eta.isDiagonal()) {
293			// sprintf( painCave.errMsg,
294			// "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
295			// painCave.isFatal = 1;
296			// simError();
297			//}
298	gezelter	507	}
299	gezelter	2
300	gezelter	507	void NPTf::saveEta() {
301	gezelter	246	currentSnapshot_->setEta(eta);
302	gezelter	507	}
303	gezelter	2
304			}