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Comparing trunk/src/applications/hydrodynamics/ShapeBuilder.cpp (file contents):
Revision 944 by gezelter, Tue Apr 25 02:06:12 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #include "applications/hydrodynamics/ShapeBuilder.hpp"
42 < #include "applications/hydrodynamics/Spheric.hpp"
43 < #include "applications/hydrodynamics/Ellipsoid.hpp"
42 > #include "hydrodynamics/Sphere.hpp"
43 > #include "hydrodynamics/Ellipsoid.hpp"
44   #include "applications/hydrodynamics/CompositeShape.hpp"
45 < namespace oopse {
45 > namespace OpenMD {
46    
47    Shape* ShapeBuilder::createShape(StuntDouble* sd) {
48      Shape* currShape = NULL;
# Line 66 | Line 66 | namespace oopse {
66          
67          if (ljData != NULL) {
68            LJParam ljParam = ljData->getData();
69 <          currShape = new Spheric(atom->getPos(), ljParam.sigma/2.0);
69 >          currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
70          } else {
71            sprintf( painCave.errMsg,
72                     "Can not cast GenericData to LJParam\n");
73 <          painCave.severity = OOPSE_ERROR;
73 >          painCave.severity = OPENMD_ERROR;
74            painCave.isFatal = 1;
75            simError();          
76          }      
77        }
78 <    } else if (atomType->isEAM()) {
79 <      GenericData* data = atomType->getPropertyByName("EAM");
80 <      if (data != NULL) {
81 <        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
82 <        
83 <        if (eamData != NULL) {
84 <          EAMParam eamParam = eamData->getData();
85 <          currShape = new Spheric(atom->getPos(), eamParam.rcut);
86 <        } else {
87 <          sprintf( painCave.errMsg,
88 <                   "Can not cast GenericData to EAMParam\n");
89 <          painCave.severity = OOPSE_ERROR;
90 <          painCave.isFatal = 1;
91 <          simError();          
92 <        }      
78 >    } else {
79 >      int obanum = etab.GetAtomicNum((atom->getType()).c_str());
80 >      if (obanum != 0) {
81 >        currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
82 >      } else {
83 >        sprintf( painCave.errMsg,
84 >                 "Could not find atom type in default element.txt\n");
85 >        painCave.severity = OPENMD_ERROR;
86 >        painCave.isFatal = 1;
87 >        simError();          
88        }
89 <    }    
89 >    }
90      return currShape;
91    }
92    
# Line 107 | Line 102 | namespace oopse {
102          
103          if (gayBerneData != NULL) {  
104            GayBerneParam gayBerneParam = gayBerneData->getData();
105 <          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_sigma/2.0, gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, datom->getA());
105 >          currShape = new Ellipsoid(datom->getPos(), gayBerneParam.GB_l/2.0,
106 >                                    gayBerneParam.GB_d/2.0, datom->getA());
107          } else {
108            sprintf( painCave.errMsg,
109                     "Can not cast GenericData to GayBerneParam\n");
110 <          painCave.severity = OOPSE_ERROR;
110 >          painCave.severity = OPENMD_ERROR;
111            painCave.isFatal = 1;
112            simError();  
113          }
114        } else {
115          sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
116 <        painCave.severity = OOPSE_ERROR;
116 >        painCave.severity = OPENMD_ERROR;
117          painCave.isFatal = 1;
118          simError();    
119        }            
# Line 128 | Line 124 | namespace oopse {
124          
125          if (ljData != NULL) {
126            LJParam ljParam = ljData->getData();
127 <          currShape = new Spheric(datom->getPos(), ljParam.sigma/2.0);
127 >          currShape = new Sphere(datom->getPos(), ljParam.sigma/2.0);
128          } else {
129            sprintf( painCave.errMsg,
130                     "Can not cast GenericData to LJParam\n");
131 <          painCave.severity = OOPSE_ERROR;
131 >          painCave.severity = OPENMD_ERROR;
132            painCave.isFatal = 1;
133            simError();          
134          }      
135 <      } else if (atomType->isEAM()) {
136 <        GenericData* data = atomType->getPropertyByName("EAM");
137 <        if (data != NULL) {
138 <          EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);          
139 <          if (eamData != NULL) {
140 <            EAMParam eamParam = eamData->getData();
141 <            currShape = new Spheric(datom->getPos(), eamParam.rcut);
142 <          } else {
143 <            sprintf( painCave.errMsg,
144 <                     "Can not cast GenericData to EAMParam\n");
149 <            painCave.severity = OOPSE_ERROR;
150 <            painCave.isFatal = 1;
151 <            simError();          
152 <          }      
135 >      } else {
136 >        int obanum = etab.GetAtomicNum((datom->getType()).c_str());
137 >        if (obanum != 0) {
138 >          currShape = new Sphere(datom->getPos(), etab.GetVdwRad(obanum));
139 >        } else {
140 >          sprintf( painCave.errMsg,
141 >                   "Could not find atom type in default element.txt\n");
142 >          painCave.severity = OPENMD_ERROR;
143 >          painCave.isFatal = 1;
144 >          simError();          
145          }
146 <      }
146 >      }      
147      }
148      return currShape;
149    }

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