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"
#include "types/LennardJonesAdapter.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();
    LennardJonesAdapter lja = LennardJonesAdapter(atomType);
    if (atomType->isGayBerne()) {
      return false;
    } else if (lja.isLennardJones()){
      BeadParam currBead;
      currBead.atomName = atom->getType();
      currBead.pos = atom->getPos();
      currBead.radius = lja.getSigma()/2.0;
      beads.push_back(currBead);
    } 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:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (13 years, 5 months ago) by gezelter
File size:	4477 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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	gezelter	1710	#include "types/LennardJonesAdapter.hpp"
45	tim	898
46	gezelter	1390	namespace OpenMD {
47	gezelter	944	bool BeadModel::createBeads(std::vector<BeadParam>& beads) {
48
49	tim	898	if (sd_->isAtom()) {
50	gezelter	944	if (!createSingleBead(static_cast<Atom*>(sd_), beads)) {
51			sprintf( painCave.errMsg,
52			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
53	gezelter	1390	painCave.severity = OPENMD_ERROR;
54	gezelter	944	painCave.isFatal = 1;
55			simError();
56			return false;
57			}
58	tim	898	}
59			else if (sd_->isRigidBody()) {
60	gezelter	944	RigidBody* rb = static_cast<RigidBody*>(sd_);
61			std::vector<Atom*>::iterator ai;
62			Atom* atom;
63			for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
64			if (!createSingleBead(atom, beads)) {
65			sprintf( painCave.errMsg,
66			"BeadModel::createBeads Error: GayBerne and other non-spheric atoms should use RoughShell model\n");
67	gezelter	1390	painCave.severity = OPENMD_ERROR;
68	gezelter	944	painCave.isFatal = 1;
69			simError();
70			return false;
71	tim	898	}
72	gezelter	944	}
73			}
74	tim	898	return true;
75	gezelter	944	}
76
77			bool BeadModel::createSingleBead(Atom* atom, std::vector<BeadParam>& beads) {
78	tim	898	AtomType* atomType = atom->getAtomType();
79	gezelter	1710	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
80	tim	898	if (atomType->isGayBerne()) {
81	gezelter	944	return false;
82	gezelter	1710	} else if (lja.isLennardJones()){
83			BeadParam currBead;
84			currBead.atomName = atom->getType();
85			currBead.pos = atom->getPos();
86			currBead.radius = lja.getSigma()/2.0;
87			beads.push_back(currBead);
88	gezelter	946	} else {
89			int obanum = etab.GetAtomicNum((atom->getType()).c_str());
90			if (obanum != 0) {
91			BeadParam currBead;
92			currBead.atomName = atom->getType();
93			currBead.pos = atom->getPos();
94			currBead.radius = etab.GetVdwRad(obanum);
95			std::cout << "using rvdw = " << currBead.radius << " for atomic number " << obanum << "\n";
96			beads.push_back(currBead);
97			} else {
98			sprintf( painCave.errMsg,
99			"Could not find atom type in default element.txt\n");
100	gezelter	1390	painCave.severity = OPENMD_ERROR;
101	gezelter	946	painCave.isFatal = 1;
102			simError();
103	gezelter	944	}
104	gezelter	946	}
105			return true;
106	gezelter	944	}
107	tim	898	}