src/visitors/AtomVisitor.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 <cstring>
#include "visitors/AtomVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
#include "types/MultipoleAdapter.hpp"
#include "types/GayBerneAdapter.hpp"

namespace OpenMD {

  BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() {
    storageLayout_ = info->getStorageLayout(); 
  }    
  
  void BaseAtomVisitor::visit(RigidBody *rb) {
    //vector<Atom*> myAtoms;
    //vector<Atom*>::iterator atomIter;

    //myAtoms = rb->getAtoms();

    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    //  (*atomIter)->accept(this);
  }

  void BaseAtomVisitor::setVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");

    //if visited property is not existed, add it as new property
    if (data == NULL) {
      data = new GenericData();
      data->setID("VISITED");
      atom->addProperty(data);
    }
  }

  bool BaseAtomVisitor::isVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");
    return data == NULL ? false : true;
  }

  //------------------------------------------------------------------------//
        
  void DefaultAtomVisitor::visit(Atom *atom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    AtomType* atype = atom->getAtomType();
              
    if (isVisited(atom))
      return;
    
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = atom->getType();
    atomInfo->pos = atom->getPos();
    atomInfo->vel = atom->getVel();
    atomInfo->frc = atom->getFrc();
    atomInfo->vec = V3Zero;
    atomInfo->hasVelocity = true;
    atomInfo->hasForce = true;
        
    FixedChargeAdapter fca = FixedChargeAdapter(atype);
    if ( fca.isFixedCharge() ) {
      atomInfo->hasCharge = true;
      atomInfo->charge = fca.getCharge();
    }
          
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
    if ( fqa.isFluctuatingCharge() ) {
      atomInfo->hasCharge = true;
      atomInfo->charge += atom->getFlucQPos();
    }
    
    if ((storageLayout_ & DataStorage::dslElectricField) && 
        (atype->isElectrostatic())) {
      atomInfo->hasElectricField = true;
      atomInfo->eField = atom->getElectricField();
    }

    atomData = new AtomData;
    atomData->setID("ATOMDATA");   
    atomData->addAtomInfo(atomInfo);
    
    atom->addProperty(atomData);
    
    setVisited(atom);
  }
  
  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    AtomType* atype = datom->getAtomType();

    if (isVisited(datom))
      return;
    
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = datom->getType();
    atomInfo->pos = datom->getPos();
    atomInfo->vel = datom->getVel();
    atomInfo->frc = datom->getFrc();
    atomInfo->hasVelocity = true;
    atomInfo->hasForce = true;

    FixedChargeAdapter fca = FixedChargeAdapter(atype);
    if ( fca.isFixedCharge() ) {
      atomInfo->hasCharge = true;
      atomInfo->charge = fca.getCharge();
    }
          
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
    if ( fqa.isFluctuatingCharge() ) {
      atomInfo->hasCharge = true;
      atomInfo->charge += datom->getFlucQPos();
    }

    if ((storageLayout_ & DataStorage::dslElectricField) && 
        (atype->isElectrostatic())) {
      atomInfo->hasElectricField = true;
      atomInfo->eField = datom->getElectricField();
    }

    GayBerneAdapter gba = GayBerneAdapter(atype);
    MultipoleAdapter ma = MultipoleAdapter(atype);
    
    if (gba.isGayBerne()) {
      atomInfo->hasVector = true;
      atomInfo->vec = datom->getA().transpose()*V3Z;
    } else if (ma.isDipole()) {
      atomInfo->hasVector = true;
      atomInfo->vec = datom->getDipole();
    } else if (ma.isQuadrupole()) {
      atomInfo->hasVector = true;
      atomInfo->vec = datom->getA().transpose()*V3Z;
    }

    atomData = new AtomData;
    atomData->setID("ATOMDATA");   
    atomData->addAtomInfo(atomInfo);

    datom->addProperty(atomData);

    setVisited(datom);
  }

  const std::string DefaultAtomVisitor::toString() {
    char   buffer[65535];
    std::string result;

    sprintf(buffer,
            "--------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer,
            "Visitor Description: copy atom infomation into atom data\n");
    result += buffer;

    sprintf(buffer,
            "--------------------------------------------------------------\n");
    result += buffer;

    return result;
  }
} //namespace OpenMD
Revision:	1873
Committed:	Fri May 10 16:09:34 2013 UTC (12 years, 5 months ago) by gezelter
File size:	6938 byte(s)
Log Message:	Fixed a bug when there's no electric field being calculated.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#include <cstring>
44	tim	3	#include "visitors/AtomVisitor.hpp"
45			#include "primitives/DirectionalAtom.hpp"
46			#include "primitives/RigidBody.hpp"
47	gezelter	1871	#include "types/FixedChargeAdapter.hpp"
48			#include "types/FluctuatingChargeAdapter.hpp"
49	gezelter	1787	#include "types/MultipoleAdapter.hpp"
50			#include "types/GayBerneAdapter.hpp"
51	gezelter	2
52	gezelter	1390	namespace OpenMD {
53	gezelter	1873
54			BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() {
55			storageLayout_ = info->getStorageLayout();
56			}
57
58	gezelter	507	void BaseAtomVisitor::visit(RigidBody *rb) {
59			//vector<Atom*> myAtoms;
60			//vector<Atom*>::iterator atomIter;
61	tim	132
62	gezelter	507	//myAtoms = rb->getAtoms();
63	gezelter	2
64	gezelter	507	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
65			// (*atomIter)->accept(this);
66			}
67	gezelter	2
68	gezelter	507	void BaseAtomVisitor::setVisited(Atom *atom) {
69	gezelter	246	GenericData *data;
70			data = atom->getPropertyByName("VISITED");
71	gezelter	2
72	gezelter	246	//if visited property is not existed, add it as new property
73			if (data == NULL) {
74	gezelter	507	data = new GenericData();
75			data->setID("VISITED");
76			atom->addProperty(data);
77	gezelter	246	}
78	gezelter	507	}
79	gezelter	2
80	gezelter	507	bool BaseAtomVisitor::isVisited(Atom *atom) {
81	gezelter	246	GenericData *data;
82			data = atom->getPropertyByName("VISITED");
83			return data == NULL ? false : true;
84	gezelter	507	}
85	gezelter	2
86	gezelter	1455	//------------------------------------------------------------------------//
87
88	gezelter	507	void DefaultAtomVisitor::visit(Atom *atom) {
89	gezelter	246	AtomData *atomData;
90			AtomInfo *atomInfo;
91	gezelter	1871	AtomType* atype = atom->getAtomType();
92
93	gezelter	246	if (isVisited(atom))
94	gezelter	507	return;
95	gezelter	1455
96	gezelter	246	atomInfo = new AtomInfo;
97	gezelter	407	atomInfo->atomTypeName = atom->getType();
98	gezelter	1871	atomInfo->pos = atom->getPos();
99			atomInfo->vel = atom->getVel();
100			atomInfo->frc = atom->getFrc();
101			atomInfo->vec = V3Zero;
102	gezelter	1456	atomInfo->hasVelocity = true;
103			atomInfo->hasForce = true;
104	gezelter	1871
105			FixedChargeAdapter fca = FixedChargeAdapter(atype);
106			if ( fca.isFixedCharge() ) {
107			atomInfo->hasCharge = true;
108			atomInfo->charge = fca.getCharge();
109			}
110
111			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
112			if ( fqa.isFluctuatingCharge() ) {
113			atomInfo->hasCharge = true;
114			atomInfo->charge += atom->getFlucQPos();
115			}
116	gezelter	1873
117			if ((storageLayout_ & DataStorage::dslElectricField) &&
118			(atype->isElectrostatic())) {
119	gezelter	1871	atomInfo->hasElectricField = true;
120			atomInfo->eField = atom->getElectricField();
121			}
122
123			atomData = new AtomData;
124			atomData->setID("ATOMDATA");
125	gezelter	246	atomData->addAtomInfo(atomInfo);
126	gezelter	1455
127	gezelter	246	atom->addProperty(atomData);
128	gezelter	1455
129	gezelter	246	setVisited(atom);
130	gezelter	507	}
131	gezelter	1455
132	gezelter	507	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
133	gezelter	246	AtomData *atomData;
134			AtomInfo *atomInfo;
135	gezelter	1871	AtomType* atype = datom->getAtomType();
136	gezelter	2
137	gezelter	246	if (isVisited(datom))
138	gezelter	507	return;
139	gezelter	1456
140	gezelter	1871	atomInfo = new AtomInfo;
141			atomInfo->atomTypeName = datom->getType();
142			atomInfo->pos = datom->getPos();
143			atomInfo->vel = datom->getVel();
144			atomInfo->frc = datom->getFrc();
145			atomInfo->hasVelocity = true;
146			atomInfo->hasForce = true;
147	gezelter	1787
148	gezelter	1871	FixedChargeAdapter fca = FixedChargeAdapter(atype);
149			if ( fca.isFixedCharge() ) {
150			atomInfo->hasCharge = true;
151			atomInfo->charge = fca.getCharge();
152			}
153
154			FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
155			if ( fqa.isFluctuatingCharge() ) {
156			atomInfo->hasCharge = true;
157			atomInfo->charge += datom->getFlucQPos();
158			}
159
160	gezelter	1873	if ((storageLayout_ & DataStorage::dslElectricField) &&
161			(atype->isElectrostatic())) {
162	gezelter	1871	atomInfo->hasElectricField = true;
163			atomInfo->eField = datom->getElectricField();
164			}
165
166			GayBerneAdapter gba = GayBerneAdapter(atype);
167			MultipoleAdapter ma = MultipoleAdapter(atype);
168	gezelter	1787
169			if (gba.isGayBerne()) {
170	gezelter	1871	atomInfo->hasVector = true;
171			atomInfo->vec = datom->getA().transpose()*V3Z;
172	gezelter	1787	} else if (ma.isDipole()) {
173	gezelter	1871	atomInfo->hasVector = true;
174			atomInfo->vec = datom->getDipole();
175	gezelter	1814	} else if (ma.isQuadrupole()) {
176	gezelter	1871	atomInfo->hasVector = true;
177			atomInfo->vec = datom->getA().transpose()*V3Z;
178	tim	989	}
179	gezelter	2
180	gezelter	1872	atomData = new AtomData;
181			atomData->setID("ATOMDATA");
182	gezelter	246	atomData->addAtomInfo(atomInfo);
183	gezelter	1872
184	gezelter	246	datom->addProperty(atomData);
185
186			setVisited(datom);
187	gezelter	507	}
188	gezelter	2
189	gezelter	507	const std::string DefaultAtomVisitor::toString() {
190	gezelter	246	char buffer[65535];
191			std::string result;
192	gezelter	2
193	gezelter	246	sprintf(buffer,
194	gezelter	1871	"--------------------------------------------------------------\n");
195	gezelter	246	result += buffer;
196	gezelter	2
197	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
198			result += buffer;
199	gezelter	2
200	gezelter	246	sprintf(buffer,
201			"Visitor Description: copy atom infomation into atom data\n");
202			result += buffer;
203	gezelter	2
204	gezelter	246	sprintf(buffer,
205	gezelter	1871	"--------------------------------------------------------------\n");
206	gezelter	246	result += buffer;
207	gezelter	2
208	gezelter	246	return result;
209	gezelter	507	}
210	gezelter	1390	} //namespace OpenMD