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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "integrators/IntegratorCreator.hpp"
#include "integrators/NPTf.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"
#include "utils/simError.h"

namespace OpenMD {

  // 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/PhysicalConstants::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/PhysicalConstants::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) += thermostat.first;
        }
      }
    }
  }

  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)/(RealType)2.0 -COM;
    sc = eta * rj;
  }

  void NPTf::scaleSimBox(){

    int i;
    int j;
    int k;
    Mat3x3d scaleMat;
    RealType eta2ij;
    RealType 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 = snap->getHmat();
      hmat = hmat *scaleMat;
      snap->setHmat(hmat);
        
    }
  }

  bool NPTf::etaConverged() {
    int i;
    RealType 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 );
  }

  RealType NPTf::calcConservedQuantity(){
    
    thermostat = snap->getThermostat();
    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()*PhysicalConstants::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()*PhysicalConstants::kB *targetTemp;    
    
    RealType conservedQuantity;
    RealType totalEnergy;
    RealType thermostat_kinetic;
    RealType thermostat_potential;
    RealType barostat_kinetic;
    RealType barostat_potential;
    RealType trEta;

    totalEnergy = thermo.getTotalEnergy();
    
    thermostat_kinetic = fkBT * tt2 * thermostat.first * 
      thermostat.first /(2.0 * PhysicalConstants::energyConvert);

    thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;

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

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

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

    return conservedQuantity;

  }

  void NPTf::loadEta() {
    eta= snap->getBarostat();

    //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() {
    snap->setBarostat(eta);
  }

}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	9315 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
2	* 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "brains/SimInfo.hpp"
44	#include "brains/Thermo.hpp"
45	#include "integrators/IntegratorCreator.hpp"
46	#include "integrators/NPTf.hpp"
47	#include "primitives/Molecule.hpp"
48	#include "utils/PhysicalConstants.hpp"
49	#include "utils/simError.h"
50
51	namespace OpenMD {
52
53	// Basic non-isotropic thermostating and barostating via the Melchionna
54	// modification of the Hoover algorithm:
55	//
56	// Melchionna, S., Ciccotti, G., and Holian, B. L., 1993,
57	// Molec. Phys., 78, 533.
58	//
59	// and
60	//
61	// Hoover, W. G., 1986, Phys. Rev. A, 34, 2499.
62
63	void NPTf::evolveEtaA() {
64
65	int i, j;
66
67	for(i = 0; i < 3; i ++){
68	for(j = 0; j < 3; j++){
69	if( i == j) {
70	eta(i, j) += dt2 * instaVol * (press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
71	} else {
72	eta(i, j) += dt2 * instaVol * press(i, j) / (NkBT*tb2);
73	}
74	}
75	}
76
77	for(i = 0; i < 3; i++) {
78	for (j = 0; j < 3; j++) {
79	oldEta(i, j) = eta(i, j);
80	}
81	}
82
83	}
84
85	void NPTf::evolveEtaB() {
86
87	int i;
88	int j;
89
90	for(i = 0; i < 3; i++) {
91	for (j = 0; j < 3; j++) {
92	prevEta(i, j) = eta(i, j);
93	}
94	}
95
96	for(i = 0; i < 3; i ++){
97	for(j = 0; j < 3; j++){
98	if( i == j) {
99	eta(i, j) = oldEta(i, j) + dt2 * instaVol *
100	(press(i, j) - targetPressure/PhysicalConstants::pressureConvert) / (NkBT*tb2);
101	} else {
102	eta(i, j) = oldEta(i, j) + dt2 * instaVol * press(i, j) / (NkBT*tb2);
103	}
104	}
105	}
106
107
108	}
109
110	void NPTf::calcVelScale(){
111
112	for (int i = 0; i < 3; i++ ) {
113	for (int j = 0; j < 3; j++ ) {
114	vScale(i, j) = eta(i, j);
115
116	if (i == j) {
117	vScale(i, j) += thermostat.first;
118	}
119	}
120	}
121	}
122
123	void NPTf::getVelScaleA(Vector3d& sc, const Vector3d& vel){
124	sc = vScale * vel;
125	}
126
127	void NPTf::getVelScaleB(Vector3d& sc, int index ) {
128	sc = vScale * oldVel[index];
129	}
130
131	void NPTf::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
132
133	/*@todo /
134	Vector3d rj = (oldPos[index] + pos)/(RealType)2.0 -COM;
135	sc = eta * rj;
136	}
137
138	void NPTf::scaleSimBox(){
139
140	int i;
141	int j;
142	int k;
143	Mat3x3d scaleMat;
144	RealType eta2ij;
145	RealType bigScale, smallScale, offDiagMax;
146	Mat3x3d hm;
147	Mat3x3d hmnew;
148
149
150
151	// Scale the box after all the positions have been moved:
152
153	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
154	// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
155
156	bigScale = 1.0;
157	smallScale = 1.0;
158	offDiagMax = 0.0;
159
160	for(i=0; i<3; i++){
161	for(j=0; j<3; j++){
162
163	// Calculate the matrix Product of the eta array (we only need
164	// the ij element right now):
165
166	eta2ij = 0.0;
167	for(k=0; k<3; k++){
168	eta2ij += eta(i, k) * eta(k, j);
169	}
170
171	scaleMat(i, j) = 0.0;
172	// identity matrix (see above):
173	if (i == j) scaleMat(i, j) = 1.0;
174	// Taylor expansion for the exponential truncated at second order:
175	scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
176
177
178	if (i != j)
179	if (fabs(scaleMat(i, j)) > offDiagMax)
180	offDiagMax = fabs(scaleMat(i, j));
181	}
182
183	if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
184	if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
185	}
186
187	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
188	sprintf( painCave.errMsg,
189	"NPTf error: Attempting a Box scaling of more than 1 percent.\n"
190	" Check your tauBarostat, as it is probably too small!\n\n"
191	" scaleMat = [%lf\t%lf\t%lf]\n"
192	" [%lf\t%lf\t%lf]\n"
193	" [%lf\t%lf\t%lf]\n"
194	" eta = [%lf\t%lf\t%lf]\n"
195	" [%lf\t%lf\t%lf]\n"
196	" [%lf\t%lf\t%lf]\n",
197	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
198	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
199	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
200	eta(0, 0),eta(0, 1),eta(0, 2),
201	eta(1, 0),eta(1, 1),eta(1, 2),
202	eta(2, 0),eta(2, 1),eta(2, 2));
203	painCave.isFatal = 1;
204	simError();
205	} else if (offDiagMax > 0.01) {
206	sprintf( painCave.errMsg,
207	"NPTf error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
208	" Check your tauBarostat, as it is probably too small!\n\n"
209	" scaleMat = [%lf\t%lf\t%lf]\n"
210	" [%lf\t%lf\t%lf]\n"
211	" [%lf\t%lf\t%lf]\n"
212	" eta = [%lf\t%lf\t%lf]\n"
213	" [%lf\t%lf\t%lf]\n"
214	" [%lf\t%lf\t%lf]\n",
215	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
216	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
217	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
218	eta(0, 0),eta(0, 1),eta(0, 2),
219	eta(1, 0),eta(1, 1),eta(1, 2),
220	eta(2, 0),eta(2, 1),eta(2, 2));
221	painCave.isFatal = 1;
222	simError();
223	} else {
224
225	Mat3x3d hmat = snap->getHmat();
226	hmat = hmat *scaleMat;
227	snap->setHmat(hmat);
228
229	}
230	}
231
232	bool NPTf::etaConverged() {
233	int i;
234	RealType diffEta, sumEta;
235
236	sumEta = 0;
237	for(i = 0; i < 3; i++) {
238	sumEta += pow(prevEta(i, i) - eta(i, i), 2);
239	}
240
241	diffEta = sqrt( sumEta / 3.0 );
242
243	return ( diffEta <= etaTolerance );
244	}
245
246	RealType NPTf::calcConservedQuantity(){
247
248	thermostat = snap->getThermostat();
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()PhysicalConstants::kB targetTemp;
255
256	// 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()PhysicalConstants::kB targetTemp;
260
261	RealType conservedQuantity;
262	RealType totalEnergy;
263	RealType thermostat_kinetic;
264	RealType thermostat_potential;
265	RealType barostat_kinetic;
266	RealType barostat_potential;
267	RealType trEta;
268
269	totalEnergy = thermo.getTotalEnergy();
270
271	thermostat_kinetic = fkBT * tt2 * thermostat.first *
272	thermostat.first /(2.0 * PhysicalConstants::energyConvert);
273
274	thermostat_potential = fkBT* thermostat.second / PhysicalConstants::energyConvert;
275
276	SquareMatrix<RealType, 3> tmp = eta.transpose() * eta;
277	trEta = tmp.trace();
278
279	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * PhysicalConstants::energyConvert);
280
281	barostat_potential = (targetPressure * thermo.getVolume() / PhysicalConstants::pressureConvert) /PhysicalConstants::energyConvert;
282
283	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
284	barostat_kinetic + barostat_potential;
285
286	return conservedQuantity;
287
288	}
289
290	void NPTf::loadEta() {
291	eta= snap->getBarostat();
292
293	//if (!eta.isDiagonal()) {
294	// sprintf( painCave.errMsg,
295	// "NPTf error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
296	// painCave.isFatal = 1;
297	// simError();
298	//}
299	}
300
301	void NPTf::saveEta() {
302	snap->setBarostat(eta);
303	}
304
305	}