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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 11 months ago) by gezelter
File size:	4913 byte(s)
Log Message:	updated copyright notices
#	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	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	898	*/
42
43			#include "applications/hydrodynamics/BeadModel.hpp"
44
45	gezelter	1390	namespace OpenMD {
46	gezelter	944	bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
47
48	tim	898	if (sd_->isAtom()) {
49	gezelter	944	if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
50			sprintf( painCave.errMsg,
51			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
52	gezelter	1390	painCave.severity = OPENMD_ERROR;
53	gezelter	944	painCave.isFatal = 1;
54			simError();
55			return false;
56			}
57	tim	898	}
58			else if (sd_->isRigidBody()) {
59	gezelter	944	RigidBody* rb = static_cast<RigidBody*>(sd_);
60			std::vector<Atom*>::iterator ai;
61			Atom* atom;
62			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
63			if (!createSingleBead(atom, beads)) {
64			sprintf( painCave.errMsg,
65			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
66	gezelter	1390	painCave.severity = OPENMD_ERROR;
67	gezelter	944	painCave.isFatal = 1;
68			simError();
69			return false;
70	tim	898	}
71	gezelter	944	}
72			}
73	tim	898	return true;
74	gezelter	944	}
75
76			bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
77	tim	898	AtomType* atomType = atom->getAtomType();
78	gezelter	944
79	tim	898	if (atomType->isGayBerne()) {
80	gezelter	944	return false;
81	tim	898	} else if (atomType->isLennardJones()){
82	gezelter	944	GenericData* data = atomType->getPropertyByName("LennardJones");
83			if (data != NULL) {
84			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
85
86			if (ljData != NULL) {
87			LJParam ljParam = ljData->getData();
88			BeadParam currBead;
89			currBead.atomName = atom->getType();
90			currBead.pos = atom->getPos();
91			currBead.radius = ljParam.sigma/2.0;
92			beads.push_back(currBead);
93	tim	898	} else {
94	gezelter	944	sprintf( painCave.errMsg,
95			"Can not cast GenericData to LJParam\n");
96	gezelter	1390	painCave.severity = OPENMD_ERROR;
97	gezelter	944	painCave.isFatal = 1;
98			simError();
99			}
100			}
101	gezelter	946	} else {
102			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
103			if (obanum != 0) {
104			BeadParam currBead;
105			currBead.atomName = atom->getType();
106			currBead.pos = atom->getPos();
107			currBead.radius = etab.GetVdwRad(obanum);
108			std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
109			beads.push_back(currBead);
110			} else {
111			sprintf( painCave.errMsg,
112			"Could not find atom type in default element.txt\n");
113	gezelter	1390	painCave.severity = OPENMD_ERROR;
114	gezelter	946	painCave.isFatal = 1;
115			simError();
116	gezelter	944	}
117	gezelter	946	}
118			return true;
119	gezelter	944	}
120	tim	898	}