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;
    

    if (info_->getSimParams()->haveDt()) {
      dt_ = info_->getSimParams()->getDt();
    } else {
      sprintf(painCave.errMsg,
              "Integrator Error: dt is not set\n");
      painCave.isFatal = 1;
      simError();
    }    
    currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
  }

  void Rattle::constraintA() {
    if (!doRattle_) return;
    doConstraint(&Rattle::constraintPairA);
  }
  void Rattle::constraintB() {
    if (!doRattle_) return;    
    doConstraint(&Rattle::constraintPairB);
  }

  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:	1979
Committed:	Sat Apr 5 20:56:01 2014 UTC (11 years, 6 months ago) by gezelter
File size:	8479 byte(s)
Log Message:	* Changed the stdDev printouts in RNEMD stats to the 95% confidence intervals * Added the ability to specify non-bonded constraints in a molecule * Added the ability to do selection offsets in the pAngle staticProps module
#	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
54	if (info_->getSimParams()->haveDt()) {
55	dt_ = info_->getSimParams()->getDt();
56	} else {
57	sprintf(painCave.errMsg,
58	"Integrator Error: dt is not set\n");
59	painCave.isFatal = 1;
60	simError();
61	}
62	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
63	}
64
65	void Rattle::constraintA() {
66	if (!doRattle_) return;
67	doConstraint(&Rattle::constraintPairA);
68	}
69	void Rattle::constraintB() {
70	if (!doRattle_) return;
71	doConstraint(&Rattle::constraintPairB);
72	}
73
74	void Rattle::doConstraint(ConstraintPairFuncPtr func) {
75	if (!doRattle_) return;
76
77	Molecule* mol;
78	SimInfo::MoleculeIterator mi;
79	ConstraintElem* consElem;
80	Molecule::ConstraintElemIterator cei;
81	ConstraintPair* consPair;
82	Molecule::ConstraintPairIterator cpi;
83
84	for (mol = info_->beginMolecule(mi); mol != NULL;
85	mol = info_->nextMolecule(mi)) {
86	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
87	consElem = mol->nextConstraintElem(cei)) {
88	consElem->setMoved(true);
89	consElem->setMoving(false);
90	}
91	}
92
93	//main loop of constraint algorithm
94	bool done = false;
95	int iteration = 0;
96	while(!done && iteration < maxConsIteration_){
97	done = true;
98
99	//loop over every constraint pair
100
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
107	//dispatch constraint algorithm
108	if(consPair->isMoved()) {
109	int exeStatus = (this->*func)(consPair);
110
111	switch(exeStatus){
112	case consFail:
113	sprintf(painCave.errMsg,
114	"Constraint failure in Rattle::constrainA, "
115	"Constraint Fail\n");
116	painCave.isFatal = 1;
117	simError();
118
119	break;
120	case consSuccess:
121	// constrain the pair by moving two elements
122	done = false;
123	consPair->getConsElem1()->setMoving(true);
124	consPair->getConsElem2()->setMoving(true);
125	break;
126	case consAlready:
127	// current pair is already constrained, do not need to
128	// move the elements
129	break;
130	default:
131	sprintf(painCave.errMsg, "ConstraintAlgorithm::doConstraint() "
132	"Error: unrecognized status");
133	painCave.isFatal = 1;
134	simError();
135	break;
136	}
137	}
138	}
139	}//end for(iter->first())
140
141
142	for (mol = info_->beginMolecule(mi); mol != NULL;
143	mol = info_->nextMolecule(mi)) {
144	for (consElem = mol->beginConstraintElem(cei); consElem != NULL;
145	consElem = mol->nextConstraintElem(cei)) {
146	consElem->setMoved(consElem->getMoving());
147	consElem->setMoving(false);
148	}
149	}
150
151	iteration++;
152	}//end while
153
154	if (!done){
155	sprintf(painCave.errMsg,
156	"Constraint failure in Rattle::constrainA, "
157	"too many iterations: %d\n",
158	iteration);
159	painCave.isFatal = 1;
160	simError();
161	}
162	}
163
164	int Rattle::constraintPairA(ConstraintPair* consPair){
165
166	ConstraintElem* consElem1 = consPair->getConsElem1();
167	ConstraintElem* consElem2 = consPair->getConsElem2();
168
169	Vector3d posA = consElem1->getPos();
170	Vector3d posB = consElem2->getPos();
171
172	Vector3d pab = posA -posB;
173
174	//periodic boundary condition
175
176	currentSnapshot_->wrapVector(pab);
177
178	RealType pabsq = pab.lengthSquare();
179
180	RealType rabsq = consPair->getConsDistSquare();
181	RealType diffsq = rabsq - pabsq;
182
183	// the original rattle code from alan tidesley
184	if (fabs(diffsq) > (consTolerance_ * rabsq * 2)){
185
186	Vector3d oldPosA = consElem1->getPrevPos();
187	Vector3d oldPosB = consElem2->getPrevPos();
188
189	Vector3d rab = oldPosA - oldPosB;
190
191	currentSnapshot_->wrapVector(rab);
192
193	RealType rpab = dot(rab, pab);
194	RealType rpabsq = rpab * rpab;
195
196	if (rpabsq < (rabsq * -diffsq)){
197	return consFail;
198	}
199
200	RealType rma = 1.0 / consElem1->getMass();
201	RealType rmb = 1.0 / consElem2->getMass();
202
203	RealType gab = diffsq / (2.0 * (rma + rmb) * rpab);
204
205	Vector3d delta = rab * gab;
206
207	//set atom1's position
208	posA += rma * delta;
209	consElem1->setPos(posA);
210
211	//set atom2's position
212	posB -= rmb * delta;
213	consElem2->setPos(posB);
214
215	delta /= dt_;
216
217	//set atom1's velocity
218	Vector3d velA = consElem1->getVel();
219	velA += rma * delta;
220	consElem1->setVel(velA);
221
222	//set atom2's velocity
223	Vector3d velB = consElem2->getVel();
224	velB -= rmb * delta;
225	consElem2->setVel(velB);
226
227	// report the constraint force back to the constraint pair:
228	consPair->setConstraintForce(gab);
229	return consSuccess;
230	}
231	else
232	return consAlready;
233
234	}
235
236
237	int Rattle::constraintPairB(ConstraintPair* consPair){
238	ConstraintElem* consElem1 = consPair->getConsElem1();
239	ConstraintElem* consElem2 = consPair->getConsElem2();
240
241
242	Vector3d velA = consElem1->getVel();
243	Vector3d velB = consElem2->getVel();
244
245	Vector3d dv = velA - velB;
246
247	Vector3d posA = consElem1->getPos();
248	Vector3d posB = consElem2->getPos();
249
250	Vector3d rab = posA - posB;
251
252	currentSnapshot_->wrapVector(rab);
253
254	RealType rma = 1.0 / consElem1->getMass();
255	RealType rmb = 1.0 / consElem2->getMass();
256
257	RealType rvab = dot(rab, dv);
258
259	RealType gab = -rvab / ((rma + rmb) * consPair->getConsDistSquare());
260
261	if (fabs(gab) > consTolerance_){
262	Vector3d delta = rab * gab;
263
264	velA += rma * delta;
265	consElem1->setVel(velA);
266
267	velB -= rmb * delta;
268	consElem2->setVel(velB);
269
270	// report the constraint force back to the constraint pair:
271	consPair->setConstraintForce(gab);
272	return consSuccess;
273	}
274	else
275	return consAlready;
276
277	}
278
279	}