src/integrators/NPrT.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/NPrT.hpp"
#include "primitives/Molecule.hpp"
#include "utils/OOPSEConstant.hpp"
#include "utils/simError.h"

namespace oopse {
  NPrT::NPrT(SimInfo* info) : NPT(info) {
    Globals* simParams = info_->getSimParams();
    if (!simParams->haveTargetStress()) {
      sprintf(painCave.errMsg,
              "If you use the NPT integrator, you must set tauBarostat.\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    } else {
      targetStress= simParams->getTargetStress();
    }

  }
  void NPrT::evolveEtaA() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    double hz = hmat(2, 2);
    double Axy = hmat(0,0) * hmat(1, 1);
    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
    eta(0,0) -= Axy * (sx - targetStress) / (NkBT*tb2);
    eta(1,1) -= Axy * (sy - targetStress) / (NkBT*tb2);
    eta(2,2) += dt2 *  instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
    oldEta = eta;  
  }

  void NPrT::evolveEtaB() {
    Mat3x3d hmat = currentSnapshot_->getHmat();
    double hz = hmat(2, 2);
    double Axy = hmat(0,0) * hmat(1, 1);
    prevEta = eta;
    double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
    double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
    eta(0,0) -= Axy * (sx -targetStress) / (NkBT*tb2);
    eta(1,1) -= Axy * (sy -targetStress) / (NkBT*tb2);
    eta(2,2) = oldEta(2, 2) + dt2 *  instaVol *
            (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
  }

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

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

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

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

  void NPrT::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,
               "NPrT 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,
               "NPrT 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 NPrT::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 NPrT::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 NPrT::loadEta() {
    eta= currentSnapshot_->getEta();

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

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

}


Revision:	2234
Committed:	Thu May 19 15:49:53 2005 UTC (19 years, 1 month ago) by tim
File size:	9504 byte(s)
Log Message:	fix bug in NPAT and NPrT
#	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. 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	#include "brains/SimInfo.hpp"
43	#include "brains/Thermo.hpp"
44	#include "integrators/IntegratorCreator.hpp"
45	#include "integrators/NPrT.hpp"
46	#include "primitives/Molecule.hpp"
47	#include "utils/OOPSEConstant.hpp"
48	#include "utils/simError.h"
49
50	namespace oopse {
51	NPrT::NPrT(SimInfo* info) : NPT(info) {
52	Globals* simParams = info_->getSimParams();
53	if (!simParams->haveTargetStress()) {
54	sprintf(painCave.errMsg,
55	"If you use the NPT integrator, you must set tauBarostat.\n");
56	painCave.severity = OOPSE_ERROR;
57	painCave.isFatal = 1;
58	simError();
59	} else {
60	targetStress= simParams->getTargetStress();
61	}
62
63	}
64	void NPrT::evolveEtaA() {
65	Mat3x3d hmat = currentSnapshot_->getHmat();
66	double hz = hmat(2, 2);
67	double Axy = hmat(0,0) * hmat(1, 1);
68	double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
69	double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
70	eta(0,0) -= Axy * (sx - targetStress) / (NkBT*tb2);
71	eta(1,1) -= Axy * (sy - targetStress) / (NkBT*tb2);
72	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
73	oldEta = eta;
74	}
75
76	void NPrT::evolveEtaB() {
77	Mat3x3d hmat = currentSnapshot_->getHmat();
78	double hz = hmat(2, 2);
79	double Axy = hmat(0,0) * hmat(1, 1);
80	prevEta = eta;
81	double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
82	double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
83	eta(0,0) -= Axy * (sx -targetStress) / (NkBT*tb2);
84	eta(1,1) -= Axy * (sy -targetStress) / (NkBT*tb2);
85	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
86	(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
87	}
88
89	void NPrT::calcVelScale(){
90
91	for (int i = 0; i < 3; i++ ) {
92	for (int j = 0; j < 3; j++ ) {
93	vScale(i, j) = eta(i, j);
94
95	if (i == j) {
96	vScale(i, j) += chi;
97	}
98	}
99	}
100	}
101
102	void NPrT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
103	sc = vScale * vel;
104	}
105
106	void NPrT::getVelScaleB(Vector3d& sc, int index ) {
107	sc = vScale * oldVel[index];
108	}
109
110	void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
111
112	/*@todo /
113	Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
114	sc = eta * rj;
115	}
116
117	void NPrT::scaleSimBox(){
118
119	int i;
120	int j;
121	int k;
122	Mat3x3d scaleMat;
123	double eta2ij;
124	double bigScale, smallScale, offDiagMax;
125	Mat3x3d hm;
126	Mat3x3d hmnew;
127
128
129
130	// Scale the box after all the positions have been moved:
131
132	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
133	// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
134
135	bigScale = 1.0;
136	smallScale = 1.0;
137	offDiagMax = 0.0;
138
139	for(i=0; i<3; i++){
140	for(j=0; j<3; j++){
141
142	// Calculate the matrix Product of the eta array (we only need
143	// the ij element right now):
144
145	eta2ij = 0.0;
146	for(k=0; k<3; k++){
147	eta2ij += eta(i, k) * eta(k, j);
148	}
149
150	scaleMat(i, j) = 0.0;
151	// identity matrix (see above):
152	if (i == j) scaleMat(i, j) = 1.0;
153	// Taylor expansion for the exponential truncated at second order:
154	scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
155
156
157	if (i != j)
158	if (fabs(scaleMat(i, j)) > offDiagMax)
159	offDiagMax = fabs(scaleMat(i, j));
160	}
161
162	if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
163	if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
164	}
165
166	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
167	sprintf( painCave.errMsg,
168	"NPrT error: Attempting a Box scaling of more than 1 percent.\n"
169	" Check your tauBarostat, as it is probably too small!\n\n"
170	" scaleMat = [%lf\t%lf\t%lf]\n"
171	" [%lf\t%lf\t%lf]\n"
172	" [%lf\t%lf\t%lf]\n"
173	" eta = [%lf\t%lf\t%lf]\n"
174	" [%lf\t%lf\t%lf]\n"
175	" [%lf\t%lf\t%lf]\n",
176	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
177	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
178	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
179	eta(0, 0),eta(0, 1),eta(0, 2),
180	eta(1, 0),eta(1, 1),eta(1, 2),
181	eta(2, 0),eta(2, 1),eta(2, 2));
182	painCave.isFatal = 1;
183	simError();
184	} else if (offDiagMax > 0.01) {
185	sprintf( painCave.errMsg,
186	"NPrT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
187	" Check your tauBarostat, as it is probably too small!\n\n"
188	" scaleMat = [%lf\t%lf\t%lf]\n"
189	" [%lf\t%lf\t%lf]\n"
190	" [%lf\t%lf\t%lf]\n"
191	" eta = [%lf\t%lf\t%lf]\n"
192	" [%lf\t%lf\t%lf]\n"
193	" [%lf\t%lf\t%lf]\n",
194	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
195	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
196	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
197	eta(0, 0),eta(0, 1),eta(0, 2),
198	eta(1, 0),eta(1, 1),eta(1, 2),
199	eta(2, 0),eta(2, 1),eta(2, 2));
200	painCave.isFatal = 1;
201	simError();
202	} else {
203
204	Mat3x3d hmat = currentSnapshot_->getHmat();
205	hmat = hmat *scaleMat;
206	currentSnapshot_->setHmat(hmat);
207
208	}
209	}
210
211	bool NPrT::etaConverged() {
212	int i;
213	double diffEta, sumEta;
214
215	sumEta = 0;
216	for(i = 0; i < 3; i++) {
217	sumEta += pow(prevEta(i, i) - eta(i, i), 2);
218	}
219
220	diffEta = sqrt( sumEta / 3.0 );
221
222	return ( diffEta <= etaTolerance );
223	}
224
225	double NPrT::calcConservedQuantity(){
226
227	chi= currentSnapshot_->getChi();
228	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
229	loadEta();
230
231	// We need NkBT a lot, so just set it here: This is the RAW number
232	// of integrableObjects, so no subtraction or addition of constraints or
233	// orientational degrees of freedom:
234	NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
235
236	// fkBT is used because the thermostat operates on more degrees of freedom
237	// than the barostat (when there are particles with orientational degrees
238	// of freedom).
239	fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
240
241	double conservedQuantity;
242	double totalEnergy;
243	double thermostat_kinetic;
244	double thermostat_potential;
245	double barostat_kinetic;
246	double barostat_potential;
247	double trEta;
248
249	totalEnergy = thermo.getTotalE();
250
251	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
252
253	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
254
255	SquareMatrix<double, 3> tmp = eta.transpose() * eta;
256	trEta = tmp.trace();
257
258	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
259
260	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
261
262	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
263	barostat_kinetic + barostat_potential;
264
265	return conservedQuantity;
266
267	}
268
269	void NPrT::loadEta() {
270	eta= currentSnapshot_->getEta();
271
272	//if (!eta.isDiagonal()) {
273	// sprintf( painCave.errMsg,
274	// "NPrT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
275	// painCave.isFatal = 1;
276	// simError();
277	//}
278	}
279
280	void NPrT::saveEta() {
281	currentSnapshot_->setEta(eta);
282	}
283
284	}
285
286