applications/hydrodynamics/BeadModel.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/BeadModel.hpp"

namespace OpenMD {
  bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
    
    if (sd_->isAtom()) {
      if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
        sprintf( painCave.errMsg,
                 "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();    
        return false;
      }
    }
    else if (sd_->isRigidBody()) {
      RigidBody* rb = static_cast<RigidBody*>(sd_);
      std::vector<Atom*>::iterator ai; 
      Atom* atom;
      for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
        if (!createSingleBead(atom, beads)) {
          sprintf( painCave.errMsg,
                   "BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();    
          return false;
        }
      }
    }    
    return true;
  }
  
  bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
    AtomType* atomType = atom->getAtomType();
    
    if (atomType->isGayBerne()) {
      return false;
    } 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();
          BeadParam currBead;
          currBead.atomName = atom->getType();
          currBead.pos = atom->getPos();
          currBead.radius = ljParam.sigma/2.0;
          beads.push_back(currBead);
        } 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) {
        BeadParam currBead;      
        currBead.atomName = atom->getType();
        currBead.pos = atom->getPos();        
        currBead.radius = etab.GetVdwRad(obanum);
        std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
        beads.push_back(currBead);
      } else {
        sprintf( painCave.errMsg,
                 "Could not find atom type in default element.txt\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }
    return true;    
  }
}
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
Original Path:	*trunk/src/applications/hydrodynamics/BeadModel.cpp*
File size:	4847 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	tim	898	/*
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	898	* 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	898	* 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	898	*/
41
42			#include "applications/hydrodynamics/BeadModel.hpp"
43
44	gezelter	1390	namespace OpenMD {
45	gezelter	944	bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
46
47	tim	898	if (sd_->isAtom()) {
48	gezelter	944	if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
49			sprintf( painCave.errMsg,
50			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
51	gezelter	1390	painCave.severity = OPENMD_ERROR;
52	gezelter	944	painCave.isFatal = 1;
53			simError();
54			return false;
55			}
56	tim	898	}
57			else if (sd_->isRigidBody()) {
58	gezelter	944	RigidBody* rb = static_cast<RigidBody*>(sd_);
59			std::vector<Atom*>::iterator ai;
60			Atom* atom;
61			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
62			if (!createSingleBead(atom, beads)) {
63			sprintf( painCave.errMsg,
64			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
65	gezelter	1390	painCave.severity = OPENMD_ERROR;
66	gezelter	944	painCave.isFatal = 1;
67			simError();
68			return false;
69	tim	898	}
70	gezelter	944	}
71			}
72	tim	898	return true;
73	gezelter	944	}
74
75			bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
76	tim	898	AtomType* atomType = atom->getAtomType();
77	gezelter	944
78	tim	898	if (atomType->isGayBerne()) {
79	gezelter	944	return false;
80	tim	898	} else if (atomType->isLennardJones()){
81	gezelter	944	GenericData* data = atomType->getPropertyByName("LennardJones");
82			if (data != NULL) {
83			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
84
85			if (ljData != NULL) {
86			LJParam ljParam = ljData->getData();
87			BeadParam currBead;
88			currBead.atomName = atom->getType();
89			currBead.pos = atom->getPos();
90			currBead.radius = ljParam.sigma/2.0;
91			beads.push_back(currBead);
92	tim	898	} else {
93	gezelter	944	sprintf( painCave.errMsg,
94			"Can not cast GenericData to LJParam\n");
95	gezelter	1390	painCave.severity = OPENMD_ERROR;
96	gezelter	944	painCave.isFatal = 1;
97			simError();
98			}
99			}
100	gezelter	946	} else {
101			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
102			if (obanum != 0) {
103			BeadParam currBead;
104			currBead.atomName = atom->getType();
105			currBead.pos = atom->getPos();
106			currBead.radius = etab.GetVdwRad(obanum);
107			std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
108			beads.push_back(currBead);
109			} else {
110			sprintf( painCave.errMsg,
111			"Could not find atom type in default element.txt\n");
112	gezelter	1390	painCave.severity = OPENMD_ERROR;
113	gezelter	946	painCave.isFatal = 1;
114			simError();
115	gezelter	944	}
116	gezelter	946	}
117			return true;
118	gezelter	944	}
119	tim	898	}