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]  Vardeman & Gezelter, in progress (2009).                        
 */
#include "applications/hydrodynamics/ShapeBuilder.hpp"
#include "hydrodynamics/Sphere.hpp"
#include "hydrodynamics/Ellipsoid.hpp"
#include "applications/hydrodynamics/CompositeShape.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;
    if (atomType->isLennardJones()){
      GenericData* data = atomType->getPropertyByName("LennardJones");
      if (data != NULL) {
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        
        if (ljData != NULL) {
          LJParam ljParam = ljData->getData();
          currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to LJParam\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }       
      }
    } 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;
    if (atomType->isGayBerne()) {
      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
      
      GenericData* data = dAtomType->getPropertyByName("GayBerne");
      if (data != NULL) {
        GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
        
        if (gayBerneData != NULL) {  
          GayBerneParam gayBerneParam = gayBerneData->getData();
          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0, 
                                    gayBerneParam.GB_d/2.0, datom->getA());
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to GayBerneParam\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();   
        }
      } else {
        sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();    
      }            
    } else if (atomType->isLennardJones()) {
      GenericData* data = atomType->getPropertyByName("LennardJones");
      if (data != NULL) {
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        
        if (ljData != NULL) {
          LJParam ljParam = ljData->getData();
          currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to LJParam\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }       
      } 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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	6802 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	906	*/
41			#include "applications/hydrodynamics/ShapeBuilder.hpp"
42	gezelter	972	#include "hydrodynamics/Sphere.hpp"
43			#include "hydrodynamics/Ellipsoid.hpp"
44	tim	906	#include "applications/hydrodynamics/CompositeShape.hpp"
45	gezelter	1390	namespace OpenMD {
46	gezelter	944
47			Shape* ShapeBuilder::createShape(StuntDouble* sd) {
48	tim	906	Shape* currShape = NULL;
49	gezelter	944	if (sd->isDirectionalAtom()) {
50			currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
51			} else if (sd->isAtom()) {
52			currShape = internalCreateShape(static_cast<Atom*>(sd));
53			} else if (sd->isRigidBody()) {
54			currShape = internalCreateShape(static_cast<RigidBody*>(sd));
55			}
56			return currShape;
57			}
58
59			Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
60	tim	906	AtomType* atomType = atom->getAtomType();
61			Shape* currShape = NULL;
62			if (atomType->isLennardJones()){
63	gezelter	944	GenericData* data = atomType->getPropertyByName("LennardJones");
64			if (data != NULL) {
65			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
66
67			if (ljData != NULL) {
68			LJParam ljParam = ljData->getData();
69	gezelter	972	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
70	tim	906	} else {
71	gezelter	944	sprintf( painCave.errMsg,
72			"Can not cast GenericData to LJParam\n");
73	gezelter	1390	painCave.severity = OPENMD_ERROR;
74	gezelter	944	painCave.isFatal = 1;
75			simError();
76			}
77			}
78	gezelter	946	} else {
79			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
80			if (obanum != 0) {
81	gezelter	972	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
82	gezelter	946	} else {
83			sprintf( painCave.errMsg,
84			"Could not find atom type in default element.txt\n");
85	gezelter	1390	painCave.severity = OPENMD_ERROR;
86	gezelter	946	painCave.isFatal = 1;
87			simError();
88	gezelter	944	}
89	gezelter	946	}
90	tim	906	return currShape;
91	gezelter	944	}
92
93			Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
94	tim	906	AtomType* atomType = datom->getAtomType();
95			Shape* currShape = NULL;
96			if (atomType->isGayBerne()) {
97	gezelter	944	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
98
99			GenericData* data = dAtomType->getPropertyByName("GayBerne");
100			if (data != NULL) {
101			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
102
103			if (gayBerneData != NULL) {
104			GayBerneParam gayBerneParam = gayBerneData->getData();
105	xsun	1208	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0,
106			gayBerneParam.GB_d/2.0, datom->getA());
107	tim	906	} else {
108	gezelter	944	sprintf( painCave.errMsg,
109			"Can not cast GenericData to GayBerneParam\n");
110	gezelter	1390	painCave.severity = OPENMD_ERROR;
111	gezelter	944	painCave.isFatal = 1;
112			simError();
113			}
114			} else {
115			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
116	gezelter	1390	painCave.severity = OPENMD_ERROR;
117	gezelter	944	painCave.isFatal = 1;
118			simError();
119			}
120			} else if (atomType->isLennardJones()) {
121			GenericData* data = atomType->getPropertyByName("LennardJones");
122			if (data != NULL) {
123			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
124
125			if (ljData != NULL) {
126			LJParam ljParam = ljData->getData();
127	gezelter	972	currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
128	gezelter	944	} else {
129			sprintf( painCave.errMsg,
130			"Can not cast GenericData to LJParam\n");
131	gezelter	1390	painCave.severity = OPENMD_ERROR;
132	gezelter	944	painCave.isFatal = 1;
133			simError();
134			}
135	gezelter	946	} else {
136			int obanum = etab.GetAtomicNum((datom->getType()).c_str());
137			if (obanum != 0) {
138	gezelter	972	currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
139	gezelter	946	} else {
140			sprintf( painCave.errMsg,
141			"Could not find atom type in default element.txt\n");
142	gezelter	1390	painCave.severity = OPENMD_ERROR;
143	gezelter	946	painCave.isFatal = 1;
144			simError();
145	tim	909	}
146	gezelter	946	}
147	tim	906	}
148			return currShape;
149	gezelter	944	}
150	tim	906
151	gezelter	944	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
152
153			std::vector<Atom*>::iterator ai;
154			CompositeShape* compositeShape = new CompositeShape;
155			Atom* atom;
156			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
157			Shape* currShape = NULL;
158			if (atom->isDirectionalAtom()){
159			currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
160			}else if (atom->isAtom()){
161			currShape = internalCreateShape(static_cast<Atom*>(atom));
162			}
163			if (currShape != NULL)
164			compositeShape->addShape(currShape);
165			}
166
167			return compositeShape;
168			}
169	tim	906	}