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() {
    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() {

    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:	2233
Committed:	Thu May 19 04:28:26 2005 UTC (19 years, 1 month ago) by tim
File size:	9270 byte(s)
Log Message:	adding NPAT and NPrT integrators
#	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	double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
66	double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
67	eta(0,0) -= Axy * (sx - targetStress) / (NkBT*tb2);
68	eta(1,1) -= Axy * (sy - targetStress) / (NkBT*tb2);
69	eta(2,2) += dt2 * instaVol * (press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
70	oldEta = eta;
71	}
72
73	void NPrT::evolveEtaB() {
74
75	prevEta = eta;
76	double sx = -hz * (press(0, 0) - targetPressure/OOPSEConstant::pressureConvert);
77	double sy = -hz * (press(1, 1) - targetPressure/OOPSEConstant::pressureConvert);
78	eta(0,0) -= Axy * (sx -targetStress) / (NkBT*tb2);
79	eta(1,1) -= Axy * (sy -targetStress) / (NkBT*tb2);
80	eta(2,2) = oldEta(2, 2) + dt2 * instaVol *
81	(press(2, 2) - targetPressure/OOPSEConstant::pressureConvert) / (NkBT*tb2);
82	}
83
84	void NPrT::calcVelScale(){
85
86	for (int i = 0; i < 3; i++ ) {
87	for (int j = 0; j < 3; j++ ) {
88	vScale(i, j) = eta(i, j);
89
90	if (i == j) {
91	vScale(i, j) += chi;
92	}
93	}
94	}
95	}
96
97	void NPrT::getVelScaleA(Vector3d& sc, const Vector3d& vel){
98	sc = vScale * vel;
99	}
100
101	void NPrT::getVelScaleB(Vector3d& sc, int index ) {
102	sc = vScale * oldVel[index];
103	}
104
105	void NPrT::getPosScale(const Vector3d& pos, const Vector3d& COM, int index, Vector3d& sc) {
106
107	/*@todo /
108	Vector3d rj = (oldPos[index] + pos)/2.0 -COM;
109	sc = eta * rj;
110	}
111
112	void NPrT::scaleSimBox(){
113
114	int i;
115	int j;
116	int k;
117	Mat3x3d scaleMat;
118	double eta2ij;
119	double bigScale, smallScale, offDiagMax;
120	Mat3x3d hm;
121	Mat3x3d hmnew;
122
123
124
125	// Scale the box after all the positions have been moved:
126
127	// Use a taylor expansion for eta products: Hmat = Hmat . exp(dt * etaMat)
128	// Hmat = Hmat . ( Ident + dt * etaMat + dt^2 * etaMat*etaMat / 2)
129
130	bigScale = 1.0;
131	smallScale = 1.0;
132	offDiagMax = 0.0;
133
134	for(i=0; i<3; i++){
135	for(j=0; j<3; j++){
136
137	// Calculate the matrix Product of the eta array (we only need
138	// the ij element right now):
139
140	eta2ij = 0.0;
141	for(k=0; k<3; k++){
142	eta2ij += eta(i, k) * eta(k, j);
143	}
144
145	scaleMat(i, j) = 0.0;
146	// identity matrix (see above):
147	if (i == j) scaleMat(i, j) = 1.0;
148	// Taylor expansion for the exponential truncated at second order:
149	scaleMat(i, j) += dteta(i, j) + 0.5dtdteta2ij;
150
151
152	if (i != j)
153	if (fabs(scaleMat(i, j)) > offDiagMax)
154	offDiagMax = fabs(scaleMat(i, j));
155	}
156
157	if (scaleMat(i, i) > bigScale) bigScale = scaleMat(i, i);
158	if (scaleMat(i, i) < smallScale) smallScale = scaleMat(i, i);
159	}
160
161	if ((bigScale > 1.01) \|\| (smallScale < 0.99)) {
162	sprintf( painCave.errMsg,
163	"NPrT error: Attempting a Box scaling of more than 1 percent.\n"
164	" Check your tauBarostat, as it is probably too small!\n\n"
165	" scaleMat = [%lf\t%lf\t%lf]\n"
166	" [%lf\t%lf\t%lf]\n"
167	" [%lf\t%lf\t%lf]\n"
168	" eta = [%lf\t%lf\t%lf]\n"
169	" [%lf\t%lf\t%lf]\n"
170	" [%lf\t%lf\t%lf]\n",
171	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
172	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
173	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
174	eta(0, 0),eta(0, 1),eta(0, 2),
175	eta(1, 0),eta(1, 1),eta(1, 2),
176	eta(2, 0),eta(2, 1),eta(2, 2));
177	painCave.isFatal = 1;
178	simError();
179	} else if (offDiagMax > 0.01) {
180	sprintf( painCave.errMsg,
181	"NPrT error: Attempting an off-diagonal Box scaling of more than 1 percent.\n"
182	" Check your tauBarostat, as it is probably too small!\n\n"
183	" scaleMat = [%lf\t%lf\t%lf]\n"
184	" [%lf\t%lf\t%lf]\n"
185	" [%lf\t%lf\t%lf]\n"
186	" eta = [%lf\t%lf\t%lf]\n"
187	" [%lf\t%lf\t%lf]\n"
188	" [%lf\t%lf\t%lf]\n",
189	scaleMat(0, 0),scaleMat(0, 1),scaleMat(0, 2),
190	scaleMat(1, 0),scaleMat(1, 1),scaleMat(1, 2),
191	scaleMat(2, 0),scaleMat(2, 1),scaleMat(2, 2),
192	eta(0, 0),eta(0, 1),eta(0, 2),
193	eta(1, 0),eta(1, 1),eta(1, 2),
194	eta(2, 0),eta(2, 1),eta(2, 2));
195	painCave.isFatal = 1;
196	simError();
197	} else {
198
199	Mat3x3d hmat = currentSnapshot_->getHmat();
200	hmat = hmat *scaleMat;
201	currentSnapshot_->setHmat(hmat);
202
203	}
204	}
205
206	bool NPrT::etaConverged() {
207	int i;
208	double diffEta, sumEta;
209
210	sumEta = 0;
211	for(i = 0; i < 3; i++) {
212	sumEta += pow(prevEta(i, i) - eta(i, i), 2);
213	}
214
215	diffEta = sqrt( sumEta / 3.0 );
216
217	return ( diffEta <= etaTolerance );
218	}
219
220	double NPrT::calcConservedQuantity(){
221
222	chi= currentSnapshot_->getChi();
223	integralOfChidt = currentSnapshot_->getIntegralOfChiDt();
224	loadEta();
225
226	// We need NkBT a lot, so just set it here: This is the RAW number
227	// of integrableObjects, so no subtraction or addition of constraints or
228	// orientational degrees of freedom:
229	NkBT = info_->getNGlobalIntegrableObjects()OOPSEConstant::kB targetTemp;
230
231	// fkBT is used because the thermostat operates on more degrees of freedom
232	// than the barostat (when there are particles with orientational degrees
233	// of freedom).
234	fkBT = info_->getNdf()OOPSEConstant::kB targetTemp;
235
236	double conservedQuantity;
237	double totalEnergy;
238	double thermostat_kinetic;
239	double thermostat_potential;
240	double barostat_kinetic;
241	double barostat_potential;
242	double trEta;
243
244	totalEnergy = thermo.getTotalE();
245
246	thermostat_kinetic = fkBT * tt2 * chi * chi /(2.0 * OOPSEConstant::energyConvert);
247
248	thermostat_potential = fkBT* integralOfChidt / OOPSEConstant::energyConvert;
249
250	SquareMatrix<double, 3> tmp = eta.transpose() * eta;
251	trEta = tmp.trace();
252
253	barostat_kinetic = NkBT * tb2 * trEta /(2.0 * OOPSEConstant::energyConvert);
254
255	barostat_potential = (targetPressure * thermo.getVolume() / OOPSEConstant::pressureConvert) /OOPSEConstant::energyConvert;
256
257	conservedQuantity = totalEnergy + thermostat_kinetic + thermostat_potential +
258	barostat_kinetic + barostat_potential;
259
260	return conservedQuantity;
261
262	}
263
264	void NPrT::loadEta() {
265	eta= currentSnapshot_->getEta();
266
267	//if (!eta.isDiagonal()) {
268	// sprintf( painCave.errMsg,
269	// "NPrT error: the diagonal elements of eta matrix are not the same or etaMat is not a diagonal matrix");
270	// painCave.isFatal = 1;
271	// simError();
272	//}
273	}
274
275	void NPrT::saveEta() {
276	currentSnapshot_->setEta(eta);
277	}
278
279	}
280
281