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_->getNGlobalConstraints() > 0)
      doRattle_ = true;
    
    Globals* simParams = info_->getSimParams();

    if (simParams->haveDt()) {
      dt_ = simParams->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Rattle 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:	1982
Committed:	Tue Apr 15 12:12:23 2014 UTC (11 years, 6 months ago) by gezelter
File size:	9701 byte(s)
Log Message:	Migrated ConstraintWriter calls into Shake
#	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_->getNGlobalConstraints() > 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	"Rattle Error: dt is not set\n");
60	painCave.isFatal = 1;
61	simError();
62	}
63
64	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
65	if (simParams->haveConstraintTime()){
66	constraintTime_ = simParams->getConstraintTime();
67	} else {
68	constraintTime_ = simParams->getStatusTime();
69	}
70
71	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) + ".constraintForces";
72
73	// create ConstraintWriter
74	constraintWriter_ = new ConstraintWriter(info_, constraintOutputFile_.c_str());
75
76	if (!constraintWriter_){
77	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
78	painCave.isFatal = 1;
79	simError();
80	}
81	}
82
83	void Rattle::constraintA() {
84	if (!doRattle_) return;
85	doConstraint(&Rattle::constraintPairA);
86	}
87	void Rattle::constraintB() {
88	if (!doRattle_) return;
89	doConstraint(&Rattle::constraintPairB);
90
91	if (currentSnapshot_->getTime() >= currConstraintTime_){
92	Molecule* mol;
93	SimInfo::MoleculeIterator mi;
94	ConstraintPair* consPair;
95	Molecule::ConstraintPairIterator cpi;
96	std::list<ConstraintPair*> constraints;
97	for (mol = info_->beginMolecule(mi); mol != NULL;
98	mol = info_->nextMolecule(mi)) {
99	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
100	consPair = mol->nextConstraintPair(cpi)) {
101
102	constraints.push_back(consPair);
103	}
104	}
105
106	constraintWriter_->writeConstraintForces(constraints);
107	currConstraintTime_ += constraintTime_;
108	}
109	}
110
111	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
112	if (!doRattle_) return;
113
114	Molecule* mol;
115	SimInfo::MoleculeIterator mi;
116	ConstraintElem* consElem;
117	Molecule::ConstraintElemIterator cei;
118	ConstraintPair* consPair;
119	Molecule::ConstraintPairIterator cpi;
120
121	for (mol = info_->beginMolecule(mi); mol != NULL;
122	mol = info_->nextMolecule(mi)) {
123	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
124	consElem = mol->nextConstraintElem(cei)) {
125	consElem->setMoved(true);
126	consElem->setMoving(false);
127	}
128	}
129
130	//main loop of constraint algorithm
131	bool done = false;
132	int iteration = 0;
133	while(!done && iteration < maxConsIteration_){
134	done = true;
135
136	//loop over every constraint pair
137
138	for (mol = info_->beginMolecule(mi); mol != NULL;
139	mol = info_->nextMolecule(mi)) {
140	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
141	consPair = mol->nextConstraintPair(cpi)) {
142
143
144	//dispatch constraint algorithm
145	if(consPair->isMoved()) {
146	int exeStatus = (this->*func)(consPair);
147
148	switch(exeStatus){
149	case consFail:
150	sprintf(painCave.errMsg,
151	"Constraint failure in Rattle::constrainA, "
152	"Constraint Fail\n");
153	painCave.isFatal = 1;
154	simError();
155
156	break;
157	case consSuccess:
158	// constrain the pair by moving two elements
159	done = false;
160	consPair->getConsElem1()->setMoving(true);
161	consPair->getConsElem2()->setMoving(true);
162	break;
163	case consAlready:
164	// current pair is already constrained, do not need to
165	// move the elements
166	break;
167	default:
168	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
169	"Error: unrecognized status");
170	painCave.isFatal = 1;
171	simError();
172	break;
173	}
174	}
175	}
176	}//end for(iter->first())
177
178
179	for (mol = info_->beginMolecule(mi); mol != NULL;
180	mol = info_->nextMolecule(mi)) {
181	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
182	consElem = mol->nextConstraintElem(cei)) {
183	consElem->setMoved(consElem->getMoving());
184	consElem->setMoving(false);
185	}
186	}
187
188	iteration++;
189	}//end while
190
191	if (!done){
192	sprintf(painCave.errMsg,
193	"Constraint failure in Rattle::constrainA, "
194	"too many iterations: %d\n",
195	iteration);
196	painCave.isFatal = 1;
197	simError();
198	}
199	}
200
201	int Rattle::constraintPairA(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
252	delta /= dt_;
253
254	//set atom1's velocity
255	Vector3d velA = consElem1->getVel();
256	velA += rma * delta;
257	consElem1->setVel(velA);
258
259	//set atom2's velocity
260	Vector3d velB = consElem2->getVel();
261	velB -= rmb * delta;
262	consElem2->setVel(velB);
263
264	// report the constraint force back to the constraint pair:
265	consPair->setConstraintForce(gab);
266	return consSuccess;
267	}
268	else
269	return consAlready;
270
271	}
272
273
274	int Rattle::constraintPairB(ConstraintPair* consPair){
275	ConstraintElem* consElem1 = consPair->getConsElem1();
276	ConstraintElem* consElem2 = consPair->getConsElem2();
277
278
279	Vector3d velA = consElem1->getVel();
280	Vector3d velB = consElem2->getVel();
281
282	Vector3d dv = velA - velB;
283
284	Vector3d posA = consElem1->getPos();
285	Vector3d posB = consElem2->getPos();
286
287	Vector3d rab = posA - posB;
288
289	currentSnapshot_->wrapVector(rab);
290
291	RealType rma = 1.0 / consElem1->getMass();
292	RealType rmb = 1.0 / consElem2->getMass();
293
294	RealType rvab = dot(rab, dv);
295
296	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
297
298	if (fabs(gab) > consTolerance_){
299	Vector3d delta = rab * gab;
300
301	velA += rma * delta;
302	consElem1->setVel(velA);
303
304	velB -= rmb * delta;
305	consElem2->setVel(velB);
306
307	// report the constraint force back to the constraint pair:
308	consPair->setConstraintForce(gab);
309	return consSuccess;
310	}
311	else
312	return consAlready;
313
314	}
315
316	}