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"
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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 11 months ago) by gezelter
File size:	6868 byte(s)
Log Message:	updated copyright notices
#	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	1390	namespace OpenMD {
47	gezelter	944
48			Shape* ShapeBuilder::createShape(StuntDouble* sd) {
49	tim	906	Shape* currShape = NULL;
50	gezelter	944	if (sd->isDirectionalAtom()) {
51			currShape = internalCreateShape(static_cast<DirectionalAtom*>(sd));
52			} else if (sd->isAtom()) {
53			currShape = internalCreateShape(static_cast<Atom*>(sd));
54			} else if (sd->isRigidBody()) {
55			currShape = internalCreateShape(static_cast<RigidBody*>(sd));
56			}
57			return currShape;
58			}
59
60			Shape* ShapeBuilder::internalCreateShape(Atom* atom) {
61	tim	906	AtomType* atomType = atom->getAtomType();
62			Shape* currShape = NULL;
63			if (atomType->isLennardJones()){
64	gezelter	944	GenericData* data = atomType->getPropertyByName("LennardJones");
65			if (data != NULL) {
66			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
67
68			if (ljData != NULL) {
69			LJParam ljParam = ljData->getData();
70	gezelter	972	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
71	tim	906	} else {
72	gezelter	944	sprintf( painCave.errMsg,
73			"Can not cast GenericData to LJParam\n");
74	gezelter	1390	painCave.severity = OPENMD_ERROR;
75	gezelter	944	painCave.isFatal = 1;
76			simError();
77			}
78			}
79	gezelter	946	} else {
80			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
81			if (obanum != 0) {
82	gezelter	972	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
83	gezelter	946	} else {
84			sprintf( painCave.errMsg,
85			"Could not find atom type in default element.txt\n");
86	gezelter	1390	painCave.severity = OPENMD_ERROR;
87	gezelter	946	painCave.isFatal = 1;
88			simError();
89	gezelter	944	}
90	gezelter	946	}
91	tim	906	return currShape;
92	gezelter	944	}
93
94			Shape* ShapeBuilder::internalCreateShape(DirectionalAtom* datom) {
95	tim	906	AtomType* atomType = datom->getAtomType();
96			Shape* currShape = NULL;
97			if (atomType->isGayBerne()) {
98	gezelter	944	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
99
100			GenericData* data = dAtomType->getPropertyByName("GayBerne");
101			if (data != NULL) {
102			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
103
104			if (gayBerneData != NULL) {
105			GayBerneParam gayBerneParam = gayBerneData->getData();
106	xsun	1208	currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0,
107			gayBerneParam.GB_d/2.0, datom->getA());
108	tim	906	} else {
109	gezelter	944	sprintf( painCave.errMsg,
110			"Can not cast GenericData to GayBerneParam\n");
111	gezelter	1390	painCave.severity = OPENMD_ERROR;
112	gezelter	944	painCave.isFatal = 1;
113			simError();
114			}
115			} else {
116			sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
117	gezelter	1390	painCave.severity = OPENMD_ERROR;
118	gezelter	944	painCave.isFatal = 1;
119			simError();
120			}
121			} else if (atomType->isLennardJones()) {
122			GenericData* data = atomType->getPropertyByName("LennardJones");
123			if (data != NULL) {
124			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
125
126			if (ljData != NULL) {
127			LJParam ljParam = ljData->getData();
128	gezelter	972	currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
129	gezelter	944	} else {
130			sprintf( painCave.errMsg,
131			"Can not cast GenericData to LJParam\n");
132	gezelter	1390	painCave.severity = OPENMD_ERROR;
133	gezelter	944	painCave.isFatal = 1;
134			simError();
135			}
136	gezelter	946	} else {
137			int obanum = etab.GetAtomicNum((datom->getType()).c_str());
138			if (obanum != 0) {
139	gezelter	972	currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
140	gezelter	946	} else {
141			sprintf( painCave.errMsg,
142			"Could not find atom type in default element.txt\n");
143	gezelter	1390	painCave.severity = OPENMD_ERROR;
144	gezelter	946	painCave.isFatal = 1;
145			simError();
146	tim	909	}
147	gezelter	946	}
148	tim	906	}
149			return currShape;
150	gezelter	944	}
151	tim	906
152	gezelter	944	Shape* ShapeBuilder::internalCreateShape(RigidBody* rb) {
153
154			std::vector<Atom*>::iterator ai;
155			CompositeShape* compositeShape = new CompositeShape;
156			Atom* atom;
157			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
158			Shape* currShape = NULL;
159			if (atom->isDirectionalAtom()){
160			currShape = internalCreateShape(static_cast<DirectionalAtom*>(atom));
161			}else if (atom->isAtom()){
162			currShape = internalCreateShape(static_cast<Atom*>(atom));
163			}
164			if (currShape != NULL)
165			compositeShape->addShape(currShape);
166			}
167
168			return compositeShape;
169			}
170	tim	906	}