src/constraints/Shake.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 "constraints/Shake.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
namespace OpenMD {

  Shake::Shake(SimInfo* info) : info_(info), maxConsIteration_(10), 
                                consTolerance_(1.0e-6), doShake_(false),
                                currConstraintTime_(0.0)  {
    
    if (info_->getNGlobalConstraints() > 0)
      doShake_ = true;
    
    if (!doShake_) return;

    Globals* simParams = info_->getSimParams();

    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    if (simParams->haveConstraintTime()){
      constraintTime_ = simParams->getConstraintTime();
    } else {
      constraintTime_ = simParams->getStatusTime();
    }

    constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + 
      ".constraintForces";

    // create ConstraintWriter  
    constraintWriter_ = new ConstraintWriter(info_, 
                                             constraintOutputFile_.c_str());   

    if (!constraintWriter_){
      sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
      painCave.isFatal = 1;
      simError();
    }
  }
  
  void Shake::constraintR() {
    if (!doShake_) return;
    doConstraint(&Shake::constraintPairR);
  }
  void Shake::constraintF() {
    if (!doShake_) return;    
    doConstraint(&Shake::constraintPairF);

    if (currentSnapshot_->getTime() >= currConstraintTime_){
      Molecule* mol;
      SimInfo::MoleculeIterator mi;
      ConstraintPair* consPair;
      Molecule::ConstraintPairIterator cpi;
      std::list<ConstraintPair*> constraints;
      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
             consPair = mol->nextConstraintPair(cpi)) {
          
          constraints.push_back(consPair);
        }
      }
      
      constraintWriter_->writeConstraintForces(constraints);
      currConstraintTime_ += constraintTime_;
    }
  }

  void Shake::doConstraint(ConstraintPairFuncPtr func) {
    if (!doShake_) return;

    Molecule* mol;
    SimInfo::MoleculeIterator mi;
    ConstraintElem* consElem;
    Molecule::ConstraintElemIterator cei;
    ConstraintPair* consPair;
    Molecule::ConstraintPairIterator cpi;
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (consElem = mol->beginConstraintElem(cei); consElem != NULL; 
           consElem = mol->nextConstraintElem(cei)) {
        consElem->setMoved(true);
        consElem->setMoving(false);
      }
    }
    
    //main loop of constraint algorithm
    bool done = false;
    int iteration = 0;
    while(!done && iteration < maxConsIteration_){
      done = true;

      //loop over every constraint pair

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; 
             consPair = mol->nextConstraintPair(cpi)) {
          

          //dispatch constraint algorithm
          if(consPair->isMoved()) {
            int exeStatus = (this->*func)(consPair);

            switch(exeStatus){
            case consFail:
              sprintf(painCave.errMsg,
                      "Constraint failure in Shake::constrainA, "
                      "Constraint Fail\n");
              painCave.isFatal = 1;
              simError();                             
                            
              break;
            case consSuccess:
              // constrain the pair by moving two elements
              done = false;
              consPair->getConsElem1()->setMoving(true);
              consPair->getConsElem2()->setMoving(true);
              break;
            case consAlready:
              // current pair is already constrained, do not need to
              // move the elements
              break;
            default:          
              sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
                      "Error: unrecognized status");
              painCave.isFatal = 1;
              simError();                           
              break;
            }      
          }
        }
      }//end for(iter->first())


      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        for (consElem = mol->beginConstraintElem(cei); consElem != NULL; 
             consElem = mol->nextConstraintElem(cei)) {
          consElem->setMoved(consElem->getMoving());
          consElem->setMoving(false);
        }
      }

      iteration++;
    }//end while

    if (!done){
      sprintf(painCave.errMsg,
              "Constraint failure in Shake::constrainA, "
              "too many iterations: %d\n",
              iteration);
      painCave.isFatal = 1;
      simError();    
    }
  }

  /**
   * remove constraint force along the bond direction
   */
  int Shake::constraintPairR(ConstraintPair* consPair){

    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d pab = posA -posB;   

    //periodic boundary condition

    currentSnapshot_->wrapVector(pab);

    RealType pabsq = pab.lengthSquare();

    RealType rabsq = consPair->getConsDistSquare();
    RealType diffsq = rabsq - pabsq;

    // the original rattle code from alan tidesley
    if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
    
      Vector3d oldPosA = consElem1->getPrevPos();
      Vector3d oldPosB = consElem2->getPrevPos();      

      Vector3d rab = oldPosA - oldPosB;    

      currentSnapshot_->wrapVector(rab);

      RealType rpab = dot(rab, pab);
      RealType rpabsq = rpab * rpab;

      if (rpabsq < (rabsq * -diffsq)){
        return consFail;
      }

      RealType rma = 1.0 / consElem1->getMass();
      RealType rmb = 1.0 / consElem2->getMass();

      RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);

      Vector3d delta = rab * gab;

      //set atom1's position
      posA += rma * delta;    
      consElem1->setPos(posA);

      //set atom2's position
      posB -= rmb * delta;
      consElem2->setPos(posB);

      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;
  }

  /**
   * remove constraint force along the bond direction
   */
  int Shake::constraintPairF(ConstraintPair* consPair){
    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

    Vector3d posA = consElem1->getPos();
    Vector3d posB = consElem2->getPos();

    Vector3d rab = posA - posB;

    currentSnapshot_->wrapVector(rab);

    Vector3d frcA = consElem1->getFrc();
    Vector3d frcB = consElem2->getFrc();

    RealType rma = 1.0 / consElem1->getMass();
    RealType rmb = 1.0 / consElem2->getMass();

    Vector3d fpab = frcA * rma - frcB * rmb;

    RealType gab = fpab.lengthSquare();
    if (gab < 1.0) gab = 1.0;
    
    RealType rabsq = rab.lengthSquare();
    RealType rfab = dot(rab, fpab);

    if (fabs(rfab) > sqrt(rabsq*gab) * consTolerance_){
      gab = -rfab / (rabsq * (rma + rmb));

      frcA += rab*gab;
      frcB -= rab*gab;
      
      consElem1->setFrc(frcA);
      consElem2->setFrc(frcB);

      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;
  }
}
Revision:	1989
Committed:	Fri Apr 18 20:07:09 2014 UTC (11 years ago) by gezelter
File size:	9564 byte(s)
Log Message:	Fixed the creation of constraintForces files on simulations which don't have constraints
#	User	Rev	Content
1	gezelter	1748	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1748	* [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 "constraints/Shake.hpp"
44			#include "primitives/Molecule.hpp"
45			#include "utils/simError.h"
46			namespace OpenMD {
47
48	gezelter	1983	Shake::Shake(SimInfo* info) : info_(info), maxConsIteration_(10),
49			consTolerance_(1.0e-6), doShake_(false),
50			currConstraintTime_(0.0) {
51	gezelter	1748
52	gezelter	1982	if (info_->getNGlobalConstraints() > 0)
53	gezelter	1748	doShake_ = true;
54
55	gezelter	1989	if (!doShake_) return;
56
57	gezelter	1982	Globals* simParams = info_->getSimParams();
58
59	gezelter	1748	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
60	gezelter	1982	if (simParams->haveConstraintTime()){
61			constraintTime_ = simParams->getConstraintTime();
62			} else {
63			constraintTime_ = simParams->getStatusTime();
64			}
65
66	gezelter	1983	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
67			".constraintForces";
68	gezelter	1982
69			// create ConstraintWriter
70	gezelter	1983	constraintWriter_ = new ConstraintWriter(info_,
71			constraintOutputFile_.c_str());
72	gezelter	1982
73			if (!constraintWriter_){
74			sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
75			painCave.isFatal = 1;
76			simError();
77			}
78	gezelter	1748	}
79
80			void Shake::constraintR() {
81			if (!doShake_) return;
82			doConstraint(&Shake::constraintPairR);
83			}
84			void Shake::constraintF() {
85			if (!doShake_) return;
86			doConstraint(&Shake::constraintPairF);
87	gezelter	1982
88			if (currentSnapshot_->getTime() >= currConstraintTime_){
89			Molecule* mol;
90			SimInfo::MoleculeIterator mi;
91			ConstraintPair* consPair;
92			Molecule::ConstraintPairIterator cpi;
93			std::list<ConstraintPair*> constraints;
94			for (mol = info_->beginMolecule(mi); mol != NULL;
95			mol = info_->nextMolecule(mi)) {
96			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
97			consPair = mol->nextConstraintPair(cpi)) {
98
99			constraints.push_back(consPair);
100			}
101			}
102
103			constraintWriter_->writeConstraintForces(constraints);
104			currConstraintTime_ += constraintTime_;
105			}
106	gezelter	1748	}
107
108			void Shake::doConstraint(ConstraintPairFuncPtr func) {
109			if (!doShake_) return;
110
111			Molecule* mol;
112			SimInfo::MoleculeIterator mi;
113			ConstraintElem* consElem;
114			Molecule::ConstraintElemIterator cei;
115			ConstraintPair* consPair;
116			Molecule::ConstraintPairIterator cpi;
117
118	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
119			mol = info_->nextMolecule(mi)) {
120			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
121			consElem = mol->nextConstraintElem(cei)) {
122	gezelter	1748	consElem->setMoved(true);
123			consElem->setMoving(false);
124			}
125			}
126
127			//main loop of constraint algorithm
128			bool done = false;
129			int iteration = 0;
130			while(!done && iteration < maxConsIteration_){
131			done = true;
132
133			//loop over every constraint pair
134
135	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
136			mol = info_->nextMolecule(mi)) {
137			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
138			consPair = mol->nextConstraintPair(cpi)) {
139
140	gezelter	1748
141			//dispatch constraint algorithm
142			if(consPair->isMoved()) {
143			int exeStatus = (this->*func)(consPair);
144
145			switch(exeStatus){
146			case consFail:
147			sprintf(painCave.errMsg,
148	gezelter	1982	"Constraint failure in Shake::constrainA, "
149			"Constraint Fail\n");
150	gezelter	1748	painCave.isFatal = 1;
151			simError();
152
153			break;
154			case consSuccess:
155	gezelter	1982	// constrain the pair by moving two elements
156	gezelter	1748	done = false;
157			consPair->getConsElem1()->setMoving(true);
158			consPair->getConsElem2()->setMoving(true);
159			break;
160			case consAlready:
161	gezelter	1982	// current pair is already constrained, do not need to
162			// move the elements
163	gezelter	1748	break;
164			default:
165	gezelter	1982	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
166			"Error: unrecognized status");
167	gezelter	1748	painCave.isFatal = 1;
168			simError();
169			break;
170			}
171			}
172			}
173			}//end for(iter->first())
174
175
176	gezelter	1982	for (mol = info_->beginMolecule(mi); mol != NULL;
177			mol = info_->nextMolecule(mi)) {
178			for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
179			consElem = mol->nextConstraintElem(cei)) {
180	gezelter	1748	consElem->setMoved(consElem->getMoving());
181			consElem->setMoving(false);
182			}
183			}
184
185			iteration++;
186			}//end while
187
188			if (!done){
189			sprintf(painCave.errMsg,
190	gezelter	1982	"Constraint failure in Shake::constrainA, "
191			"too many iterations: %d\n",
192	gezelter	1748	iteration);
193			painCave.isFatal = 1;
194			simError();
195			}
196			}
197
198			/**
199			* remove constraint force along the bond direction
200			*/
201			int Shake::constraintPairR(ConstraintPair* consPair){
202
203			ConstraintElem* consElem1 = consPair->getConsElem1();
204			ConstraintElem* consElem2 = consPair->getConsElem2();
205
206			Vector3d posA = consElem1->getPos();
207			Vector3d posB = consElem2->getPos();
208
209			Vector3d pab = posA -posB;
210
211			//periodic boundary condition
212
213			currentSnapshot_->wrapVector(pab);
214
215			RealType pabsq = pab.lengthSquare();
216
217			RealType rabsq = consPair->getConsDistSquare();
218			RealType diffsq = rabsq - pabsq;
219
220			// the original rattle code from alan tidesley
221			if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
222
223			Vector3d oldPosA = consElem1->getPrevPos();
224			Vector3d oldPosB = consElem2->getPrevPos();
225
226			Vector3d rab = oldPosA - oldPosB;
227
228			currentSnapshot_->wrapVector(rab);
229
230			RealType rpab = dot(rab, pab);
231			RealType rpabsq = rpab * rpab;
232
233			if (rpabsq < (rabsq * -diffsq)){
234			return consFail;
235			}
236
237			RealType rma = 1.0 / consElem1->getMass();
238			RealType rmb = 1.0 / consElem2->getMass();
239
240			RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
241
242			Vector3d delta = rab * gab;
243
244			//set atom1's position
245			posA += rma * delta;
246			consElem1->setPos(posA);
247
248			//set atom2's position
249			posB -= rmb * delta;
250			consElem2->setPos(posB);
251	gezelter	1982
252			// report the constraint force back to the constraint pair:
253			consPair->setConstraintForce(gab);
254	gezelter	1748	return consSuccess;
255			}
256			else
257			return consAlready;
258			}
259
260			/**
261			* remove constraint force along the bond direction
262			*/
263			int Shake::constraintPairF(ConstraintPair* consPair){
264			ConstraintElem* consElem1 = consPair->getConsElem1();
265			ConstraintElem* consElem2 = consPair->getConsElem2();
266
267			Vector3d posA = consElem1->getPos();
268			Vector3d posB = consElem2->getPos();
269
270			Vector3d rab = posA - posB;
271
272			currentSnapshot_->wrapVector(rab);
273
274			Vector3d frcA = consElem1->getFrc();
275			Vector3d frcB = consElem2->getFrc();
276
277			RealType rma = 1.0 / consElem1->getMass();
278			RealType rmb = 1.0 / consElem2->getMass();
279
280			Vector3d fpab = frcA * rma - frcB * rmb;
281
282			RealType gab = fpab.lengthSquare();
283			if (gab < 1.0) gab = 1.0;
284
285			RealType rabsq = rab.lengthSquare();
286			RealType rfab = dot(rab, fpab);
287
288			if (fabs(rfab) > sqrt(rabsqgab) consTolerance_){
289			gab = -rfab / (rabsq * (rma + rmb));
290
291			frcA += rab*gab;
292			frcB -= rab*gab;
293
294			consElem1->setFrc(frcA);
295			consElem2->setFrc(frcB);
296
297	gezelter	1982	// report the constraint force back to the constraint pair:
298			consPair->setConstraintForce(gab);
299	gezelter	1748	return consSuccess;
300			}
301			else
302			return consAlready;
303			}
304			}