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

  Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) {
    
    if (info_->getNConstraints() > 0)
      doRattle_ = true;
    
    Globals* simParams = info_->getSimParams();

    if (simParams->haveDt()) {
      dt_ = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }    
    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 Rattle::constraintA() {
    if (!doRattle_) return;
    doConstraint(&Rattle::constraintPairA);
  }
  void Rattle::constraintB() {
    if (!doRattle_) return;    
    doConstraint(&Rattle::constraintPairB);

    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 Rattle::doConstraint(ConstraintPairFuncPtr func) {
    if (!doRattle_) 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 Rattle::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 Rattle::constrainA, "
              "too many iterations: %d\n",
              iteration);
      painCave.isFatal = 1;
      simError();    
    }
  }

  int Rattle::constraintPairA(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);

      delta /= dt_;
    
      //set atom1's velocity
      Vector3d velA = consElem1->getVel();
      velA += rma * delta;
      consElem1->setVel(velA);

      //set atom2's velocity
      Vector3d velB = consElem2->getVel();
      velB -= rmb * delta;
      consElem2->setVel(velB);
      
      // report the constraint force back to the constraint pair:
      consPair->setConstraintForce(gab);
      return consSuccess;
    }
    else
      return consAlready;
  
  }


  int Rattle::constraintPairB(ConstraintPair* consPair){
    ConstraintElem* consElem1 = consPair->getConsElem1();
    ConstraintElem* consElem2 = consPair->getConsElem2();

  
    Vector3d velA = consElem1->getVel();
    Vector3d velB = consElem2->getVel();

    Vector3d dv = velA - velB;

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

    Vector3d rab = posA - posB;

    currentSnapshot_->wrapVector(rab);

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

    RealType rvab = dot(rab, dv);

    RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());

    if (fabs(gab) > consTolerance_){
      Vector3d delta = rab * gab;
      
      velA += rma * delta;
      consElem1->setVel(velA);
      
      velB -= rmb * delta;
      consElem2->setVel(velB);

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

  }

}
Revision:	1981
Committed:	Mon Apr 14 18:32:51 2014 UTC (11 years, 6 months ago) by gezelter
File size:	9698 byte(s)
Log Message:	Added the ConstraintWriter
#	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 "constraints/Rattle.hpp"
44	#include "primitives/Molecule.hpp"
45	#include "utils/simError.h"
46	namespace OpenMD {
47
48	Rattle::Rattle(SimInfo* info) : info_(info), maxConsIteration_(10), consTolerance_(1.0e-6), doRattle_(false) {
49
50	if (info_->getNConstraints() > 0)
51	doRattle_ = true;
52
53	Globals* simParams = info_->getSimParams();
54
55	if (simParams->haveDt()) {
56	dt_ = simParams->getDt();
57	} else {
58	sprintf(painCave.errMsg,
59	"Integrator Error: dt is not set\n");
60	painCave.isFatal = 1;
61	simError();
62	}
63	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
64	if (simParams->haveConstraintTime()){
65	constraintTime_ = simParams->getConstraintTime();
66	} else {
67	constraintTime_ = simParams->getStatusTime();
68	}
69
70	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
71
72	// create ConstraintWriter
73	constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
74
75	if (!constraintWriter_){
76	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
77	painCave.isFatal = 1;
78	simError();
79	}
80	}
81
82	void Rattle::constraintA() {
83	if (!doRattle_) return;
84	doConstraint(&Rattle::constraintPairA);
85	}
86	void Rattle::constraintB() {
87	if (!doRattle_) return;
88	doConstraint(&Rattle::constraintPairB);
89
90	if (currentSnapshot_->getTime() >= currConstraintTime_){
91	Molecule* mol;
92	SimInfo::MoleculeIterator mi;
93	ConstraintPair* consPair;
94	Molecule::ConstraintPairIterator cpi;
95	std::list<ConstraintPair*> constraints;
96	for (mol = info_->beginMolecule(mi); mol != NULL;
97	mol = info_->nextMolecule(mi)) {
98	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
99	consPair = mol->nextConstraintPair(cpi)) {
100
101	constraints.push_back(consPair);
102	}
103	}
104
105	constraintWriter_->writeConstraintForces(constraints);
106	currConstraintTime_ += constraintTime_;
107	}
108	}
109
110	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
111	if (!doRattle_) return;
112
113	Molecule* mol;
114	SimInfo::MoleculeIterator mi;
115	ConstraintElem* consElem;
116	Molecule::ConstraintElemIterator cei;
117	ConstraintPair* consPair;
118	Molecule::ConstraintPairIterator cpi;
119
120	for (mol = info_->beginMolecule(mi); mol != NULL;
121	mol = info_->nextMolecule(mi)) {
122	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
123	consElem = mol->nextConstraintElem(cei)) {
124	consElem->setMoved(true);
125	consElem->setMoving(false);
126	}
127	}
128
129	//main loop of constraint algorithm
130	bool done = false;
131	int iteration = 0;
132	while(!done && iteration < maxConsIteration_){
133	done = true;
134
135	//loop over every constraint pair
136
137	for (mol = info_->beginMolecule(mi); mol != NULL;
138	mol = info_->nextMolecule(mi)) {
139	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
140	consPair = mol->nextConstraintPair(cpi)) {
141
142
143	//dispatch constraint algorithm
144	if(consPair->isMoved()) {
145	int exeStatus = (this->*func)(consPair);
146
147	switch(exeStatus){
148	case consFail:
149	sprintf(painCave.errMsg,
150	"Constraint failure in Rattle::constrainA, "
151	"Constraint Fail\n");
152	painCave.isFatal = 1;
153	simError();
154
155	break;
156	case consSuccess:
157	// constrain the pair by moving two elements
158	done = false;
159	consPair->getConsElem1()->setMoving(true);
160	consPair->getConsElem2()->setMoving(true);
161	break;
162	case consAlready:
163	// current pair is already constrained, do not need to
164	// move the elements
165	break;
166	default:
167	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
168	"Error: unrecognized status");
169	painCave.isFatal = 1;
170	simError();
171	break;
172	}
173	}
174	}
175	}//end for(iter->first())
176
177
178	for (mol = info_->beginMolecule(mi); mol != NULL;
179	mol = info_->nextMolecule(mi)) {
180	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
181	consElem = mol->nextConstraintElem(cei)) {
182	consElem->setMoved(consElem->getMoving());
183	consElem->setMoving(false);
184	}
185	}
186
187	iteration++;
188	}//end while
189
190	if (!done){
191	sprintf(painCave.errMsg,
192	"Constraint failure in Rattle::constrainA, "
193	"too many iterations: %d\n",
194	iteration);
195	painCave.isFatal = 1;
196	simError();
197	}
198	}
199
200	int Rattle::constraintPairA(ConstraintPair* consPair){
201
202	ConstraintElem* consElem1 = consPair->getConsElem1();
203	ConstraintElem* consElem2 = consPair->getConsElem2();
204
205	Vector3d posA = consElem1->getPos();
206	Vector3d posB = consElem2->getPos();
207
208	Vector3d pab = posA -posB;
209
210	//periodic boundary condition
211
212	currentSnapshot_->wrapVector(pab);
213
214	RealType pabsq = pab.lengthSquare();
215
216	RealType rabsq = consPair->getConsDistSquare();
217	RealType diffsq = rabsq - pabsq;
218
219	// the original rattle code from alan tidesley
220	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
221
222	Vector3d oldPosA = consElem1->getPrevPos();
223	Vector3d oldPosB = consElem2->getPrevPos();
224
225	Vector3d rab = oldPosA - oldPosB;
226
227	currentSnapshot_->wrapVector(rab);
228
229	RealType rpab = dot(rab, pab);
230	RealType rpabsq = rpab * rpab;
231
232	if (rpabsq < (rabsq * -diffsq)){
233	return consFail;
234	}
235
236	RealType rma = 1.0 / consElem1->getMass();
237	RealType rmb = 1.0 / consElem2->getMass();
238
239	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
240
241	Vector3d delta = rab * gab;
242
243	//set atom1's position
244	posA += rma * delta;
245	consElem1->setPos(posA);
246
247	//set atom2's position
248	posB -= rmb * delta;
249	consElem2->setPos(posB);
250
251	delta /= dt_;
252
253	//set atom1's velocity
254	Vector3d velA = consElem1->getVel();
255	velA += rma * delta;
256	consElem1->setVel(velA);
257
258	//set atom2's velocity
259	Vector3d velB = consElem2->getVel();
260	velB -= rmb * delta;
261	consElem2->setVel(velB);
262
263	// report the constraint force back to the constraint pair:
264	consPair->setConstraintForce(gab);
265	return consSuccess;
266	}
267	else
268	return consAlready;
269
270	}
271
272
273	int Rattle::constraintPairB(ConstraintPair* consPair){
274	ConstraintElem* consElem1 = consPair->getConsElem1();
275	ConstraintElem* consElem2 = consPair->getConsElem2();
276
277
278	Vector3d velA = consElem1->getVel();
279	Vector3d velB = consElem2->getVel();
280
281	Vector3d dv = velA - velB;
282
283	Vector3d posA = consElem1->getPos();
284	Vector3d posB = consElem2->getPos();
285
286	Vector3d rab = posA - posB;
287
288	currentSnapshot_->wrapVector(rab);
289
290	RealType rma = 1.0 / consElem1->getMass();
291	RealType rmb = 1.0 / consElem2->getMass();
292
293	RealType rvab = dot(rab, dv);
294
295	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
296
297	if (fabs(gab) > consTolerance_){
298	Vector3d delta = rab * gab;
299
300	velA += rma * delta;
301	consElem1->setVel(velA);
302
303	velB -= rmb * delta;
304	consElem2->setVel(velB);
305
306	// report the constraint force back to the constraint pair:
307	consPair->setConstraintForce(gab);
308	return consSuccess;
309	}
310	else
311	return consAlready;
312
313	}
314
315	}