applications/hydrodynamics/ShapeBuilder.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include "applications/hydrodynamics/ShapeBuilder.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.hpp"
#include "types/LennardJonesAdapter.hpp"
#include "types/GayBerneAdapter.hpp"

namespace OpenMD {
  
  Shape* ShapeBuilder::createShape(StuntDouble* sd) {
    Shape* currShape = NULL;
    if (sd->isDirectionalAtom()) {
      currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
    } else if (sd->isAtom()) {
      currShape = internalCreateShape(static_cast<Atom*>(sd));
    } else if (sd->isRigidBody()) {
      currShape = internalCreateShape(static_cast<RigidBody*>(sd));
    }       
    return currShape;   
  }
  
  Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
    AtomType* atomType = atom->getAtomType();
    Shape* currShape = NULL;
    LennardJonesAdapter lja = LennardJonesAdapter(atomType);
    if (lja.isLennardJones()){      
      currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
    } else {
      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
      if (obanum != 0) {
        currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
      } else {
        sprintf( painCave.errMsg,
                 "Could not find atom type in default element.txt\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }
    return currShape;
  }
  
  Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
    AtomType* atomType = datom->getAtomType();
    Shape* currShape = NULL;
    LennardJonesAdapter lja = LennardJonesAdapter(atomType);
    GayBerneAdapter gba = GayBerneAdapter(atomType);
    if (gba.isGayBerne()) {
      currShape = new Ellipsoid(datom->getPos(), gba.getL()/2.0, 
                                gba.getD()/2.0, datom->getA());
    } else if (lja.isLennardJones()) {
      currShape = new Sphere(datom->getPos(), lja.getSigma()/2.0);
    } else {
      int obanum = etab.GetAtomicNum((datom->getType()).c_str());
      if (obanum != 0) {
        currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
      } else {
        sprintf( painCave.errMsg,
                 "Could not find atom type in default element.txt\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }        
    return currShape;
  }

  Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
    
    std::vector<Atom*>::iterator ai; 
    CompositeShape* compositeShape = new CompositeShape;
    Atom* atom;
    for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
      Shape* currShape = NULL;
      if (atom->isDirectionalAtom()){
        currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
      }else if (atom->isAtom()){
        currShape =  internalCreateShape(static_cast<Atom*>(atom));
      }
      if (currShape != NULL)
        compositeShape->addShape(currShape);
    }
    
    return compositeShape;
  }  
}
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (13 years, 5 months ago) by gezelter
File size:	5239 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	User	Rev	Content
1	tim	906	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	906	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	906	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (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	tim	906	*/
42			#include "applications/hydrodynamics/ShapeBuilder.hpp"
43	gezelter	972	#include "hydrodynamics/Sphere.hpp"
44			#include "hydrodynamics/Ellipsoid.hpp"
45	tim	906	#include "applications/hydrodynamics/CompositeShape.hpp"
46	gezelter	1710	#include "types/LennardJonesAdapter.hpp"
47			#include "types/GayBerneAdapter.hpp"
48
49	gezelter	1390	namespace OpenMD {
50	gezelter	944
51			Shape* ShapeBuilder::createShape(StuntDouble* sd) {
52	tim	906	Shape* currShape = NULL;
53	gezelter	944	if (sd->isDirectionalAtom()) {
54			currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
55			} else if (sd->isAtom()) {
56			currShape = internalCreateShape(static_cast<Atom*>(sd));
57			} else if (sd->isRigidBody()) {
58			currShape = internalCreateShape(static_cast<RigidBody*>(sd));
59			}
60			return currShape;
61			}
62
63			Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
64	tim	906	AtomType* atomType = atom->getAtomType();
65			Shape* currShape = NULL;
66	gezelter	1710	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
67			if (lja.isLennardJones()){
68			currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
69	gezelter	946	} else {
70			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
71			if (obanum != 0) {
72	gezelter	972	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
73	gezelter	946	} else {
74			sprintf( painCave.errMsg,
75			"Could not find atom type in default element.txt\n");
76	gezelter	1390	painCave.severity = OPENMD_ERROR;
77	gezelter	946	painCave.isFatal = 1;
78			simError();
79	gezelter	944	}
80	gezelter	946	}
81	tim	906	return currShape;
82	gezelter	944	}
83
84			Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
85	tim	906	AtomType* atomType = datom->getAtomType();
86			Shape* currShape = NULL;
87	gezelter	1710	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
88			GayBerneAdapter gba = GayBerneAdapter(atomType);
89			if (gba.isGayBerne()) {
90			currShape = new Ellipsoid(datom->getPos(), gba.getL()/2.0,
91			gba.getD()/2.0, datom->getA());
92			} else if (lja.isLennardJones()) {
93			currShape = new Sphere(datom->getPos(), lja.getSigma()/2.0);
94			} else {
95			int obanum = etab.GetAtomicNum((datom->getType()).c_str());
96			if (obanum != 0) {
97			currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
98	gezelter	944	} else {
99	gezelter	1710	sprintf( painCave.errMsg,
100			"Could not find atom type in default element.txt\n");
101	gezelter	1390	painCave.severity = OPENMD_ERROR;
102	gezelter	944	painCave.isFatal = 1;
103	gezelter	1710	simError();
104			}
105			}
106	tim	906	return currShape;
107	gezelter	944	}
108	tim	906
109	gezelter	944	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
110
111			std::vector<Atom*>::iterator ai;
112			CompositeShape* compositeShape = new CompositeShape;
113			Atom* atom;
114			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
115			Shape* currShape = NULL;
116			if (atom->isDirectionalAtom()){
117			currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
118			}else if (atom->isAtom()){
119			currShape = internalCreateShape(static_cast<Atom*>(atom));
120			}
121			if (currShape != NULL)
122			compositeShape->addShape(currShape);
123			}
124
125			return compositeShape;
126			}
127	tim	906	}