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), 
                                  currConstraintTime_(0.0) {
    
    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:	1983
Committed:	Tue Apr 15 20:36:19 2014 UTC (11 years, 6 months ago) by gezelter
File size:	9843 byte(s)
Log Message:	Fixes for ConstraintWriter in parallel, some cppcheck cleanup starting preparation for 2.2 release
#	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),
49	consTolerance_(1.0e-6), doRattle_(false),
50	currConstraintTime_(0.0) {
51
52	if (info_->getNGlobalConstraints() > 0)
53	doRattle_ = true;
54
55	Globals* simParams = info_->getSimParams();
56
57	if (simParams->haveDt()) {
58	dt_ = simParams->getDt();
59	} else {
60	sprintf(painCave.errMsg,
61	"Rattle Error: dt is not set\n");
62	painCave.isFatal = 1;
63	simError();
64	}
65
66	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
67	if (simParams->haveConstraintTime()){
68	constraintTime_ = simParams->getConstraintTime();
69	} else {
70	constraintTime_ = simParams->getStatusTime();
71	}
72
73	constraintOutputFile_ = getPrefix(info_->getFinalConfigFileName()) +
74	".constraintForces";
75
76	// create ConstraintWriter
77	constraintWriter_ = new ConstraintWriter(info_,
78	constraintOutputFile_.c_str());
79
80	if (!constraintWriter_){
81	sprintf(painCave.errMsg, "Failed to create ConstraintWriter\n");
82	painCave.isFatal = 1;
83	simError();
84	}
85	}
86
87	void Rattle::constraintA() {
88	if (!doRattle_) return;
89	doConstraint(&Rattle::constraintPairA);
90	}
91	void Rattle::constraintB() {
92	if (!doRattle_) return;
93	doConstraint(&Rattle::constraintPairB);
94
95	if (currentSnapshot_->getTime() >= currConstraintTime_){
96	Molecule* mol;
97	SimInfo::MoleculeIterator mi;
98	ConstraintPair* consPair;
99	Molecule::ConstraintPairIterator cpi;
100	std::list<ConstraintPair*> constraints;
101	for (mol = info_->beginMolecule(mi); mol != NULL;
102	mol = info_->nextMolecule(mi)) {
103	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
104	consPair = mol->nextConstraintPair(cpi)) {
105
106	constraints.push_back(consPair);
107	}
108	}
109	constraintWriter_->writeConstraintForces(constraints);
110	currConstraintTime_ += constraintTime_;
111	}
112	}
113
114	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
115	if (!doRattle_) return;
116
117	Molecule* mol;
118	SimInfo::MoleculeIterator mi;
119	ConstraintElem* consElem;
120	Molecule::ConstraintElemIterator cei;
121	ConstraintPair* consPair;
122	Molecule::ConstraintPairIterator cpi;
123
124	for (mol = info_->beginMolecule(mi); mol != NULL;
125	mol = info_->nextMolecule(mi)) {
126	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
127	consElem = mol->nextConstraintElem(cei)) {
128	consElem->setMoved(true);
129	consElem->setMoving(false);
130	}
131	}
132
133	//main loop of constraint algorithm
134	bool done = false;
135	int iteration = 0;
136	while(!done && iteration < maxConsIteration_){
137	done = true;
138
139	//loop over every constraint pair
140
141	for (mol = info_->beginMolecule(mi); mol != NULL;
142	mol = info_->nextMolecule(mi)) {
143	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL;
144	consPair = mol->nextConstraintPair(cpi)) {
145
146
147	//dispatch constraint algorithm
148	if(consPair->isMoved()) {
149	int exeStatus = (this->*func)(consPair);
150
151	switch(exeStatus){
152	case consFail:
153	sprintf(painCave.errMsg,
154	"Constraint failure in Rattle::constrainA, "
155	"Constraint Fail\n");
156	painCave.isFatal = 1;
157	simError();
158
159	break;
160	case consSuccess:
161	// constrain the pair by moving two elements
162	done = false;
163	consPair->getConsElem1()->setMoving(true);
164	consPair->getConsElem2()->setMoving(true);
165	break;
166	case consAlready:
167	// current pair is already constrained, do not need to
168	// move the elements
169	break;
170	default:
171	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
172	"Error: unrecognized status");
173	painCave.isFatal = 1;
174	simError();
175	break;
176	}
177	}
178	}
179	}//end for(iter->first())
180
181
182	for (mol = info_->beginMolecule(mi); mol != NULL;
183	mol = info_->nextMolecule(mi)) {
184	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
185	consElem = mol->nextConstraintElem(cei)) {
186	consElem->setMoved(consElem->getMoving());
187	consElem->setMoving(false);
188	}
189	}
190
191	iteration++;
192	}//end while
193
194	if (!done){
195	sprintf(painCave.errMsg,
196	"Constraint failure in Rattle::constrainA, "
197	"too many iterations: %d\n",
198	iteration);
199	painCave.isFatal = 1;
200	simError();
201	}
202	}
203
204	int Rattle::constraintPairA(ConstraintPair* consPair){
205
206	ConstraintElem* consElem1 = consPair->getConsElem1();
207	ConstraintElem* consElem2 = consPair->getConsElem2();
208
209	Vector3d posA = consElem1->getPos();
210	Vector3d posB = consElem2->getPos();
211
212	Vector3d pab = posA -posB;
213
214	//periodic boundary condition
215
216	currentSnapshot_->wrapVector(pab);
217
218	RealType pabsq = pab.lengthSquare();
219
220	RealType rabsq = consPair->getConsDistSquare();
221	RealType diffsq = rabsq - pabsq;
222
223	// the original rattle code from alan tidesley
224	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
225
226	Vector3d oldPosA = consElem1->getPrevPos();
227	Vector3d oldPosB = consElem2->getPrevPos();
228
229	Vector3d rab = oldPosA - oldPosB;
230
231	currentSnapshot_->wrapVector(rab);
232
233	RealType rpab = dot(rab, pab);
234	RealType rpabsq = rpab * rpab;
235
236	if (rpabsq < (rabsq * -diffsq)){
237	return consFail;
238	}
239
240	RealType rma = 1.0 / consElem1->getMass();
241	RealType rmb = 1.0 / consElem2->getMass();
242
243	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
244
245	Vector3d delta = rab * gab;
246
247	//set atom1's position
248	posA += rma * delta;
249	consElem1->setPos(posA);
250
251	//set atom2's position
252	posB -= rmb * delta;
253	consElem2->setPos(posB);
254
255	delta /= dt_;
256
257	//set atom1's velocity
258	Vector3d velA = consElem1->getVel();
259	velA += rma * delta;
260	consElem1->setVel(velA);
261
262	//set atom2's velocity
263	Vector3d velB = consElem2->getVel();
264	velB -= rmb * delta;
265	consElem2->setVel(velB);
266
267	// report the constraint force back to the constraint pair:
268	consPair->setConstraintForce(gab);
269	return consSuccess;
270	}
271	else
272	return consAlready;
273
274	}
275
276
277	int Rattle::constraintPairB(ConstraintPair* consPair){
278	ConstraintElem* consElem1 = consPair->getConsElem1();
279	ConstraintElem* consElem2 = consPair->getConsElem2();
280
281
282	Vector3d velA = consElem1->getVel();
283	Vector3d velB = consElem2->getVel();
284
285	Vector3d dv = velA - velB;
286
287	Vector3d posA = consElem1->getPos();
288	Vector3d posB = consElem2->getPos();
289
290	Vector3d rab = posA - posB;
291
292	currentSnapshot_->wrapVector(rab);
293
294	RealType rma = 1.0 / consElem1->getMass();
295	RealType rmb = 1.0 / consElem2->getMass();
296
297	RealType rvab = dot(rab, dv);
298
299	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
300
301	if (fabs(gab) > consTolerance_){
302	Vector3d delta = rab * gab;
303
304	velA += rma * delta;
305	consElem1->setVel(velA);
306
307	velB -= rmb * delta;
308	consElem2->setVel(velB);
309
310	// report the constraint force back to the constraint pair:
311	consPair->setConstraintForce(gab);
312	return consSuccess;
313	}
314	else
315	return consAlready;
316
317	}
318
319	}