src/UseTheForce/EAM_FF.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 "UseTheForce/EAM_FF.hpp"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/MultipoleAtomTypesSectionParser.hpp"
#include "io/NonBondedInteractionsSectionParser.hpp"
#include "io/EAMAtomTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"
#include "utils/simError.h"
namespace OpenMD {
    
  EAM_FF::EAM_FF(){

    //set default force field filename
    setForceFieldFileName("EAM.frc");

    //the order of adding section parsers are important
    //OptionSectionParser must come first to set options for other parsers
    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
  }

  void EAM_FF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFieldFile(filename);

    spMan_.parse(*ffStream, *this);

    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
      // useBase sets the responsibilities, and these have to be done 
      // after the atomTypes and Base types have all been scanned:

      std::vector<AtomType*> ayb = at->allYourBase();      
      if (ayb.size() > 1) {
        for (int j = ayb.size()-1; j > 0; j--) {
          
          ayb[j-1]->useBase(ayb[j]);

        }
      }
    }

    delete ffStream;
  }


  RealType EAM_FF::getRcutFromAtomType(AtomType* at){
    RealType rcut = 0.0;    
    if (at->isEAM()) {
      GenericData* data = at->getPropertyByName("EAM");
      if (data != NULL) {
        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);

        if (eamData != NULL) {

          EAMParam& eamParam = eamData->getData();
          rcut =  eamParam.rcut;
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to EAMParam\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
      } else {
        sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }    else {
      rcut = ForceField::getRcutFromAtomType(at);
    }
   
    return rcut;    
  }

} //end namespace OpenMD
Revision:	1703
Committed:	Mon Apr 23 21:08:08 2012 UTC (13 years ago) by jmichalk
File size:	5170 byte(s)
Log Message:	JRM Added additional section parsers to EAM_FF.cpp
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	366	* 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	gezelter	366	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	366	* 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	gezelter	366	*/
42
43			#include "UseTheForce/EAM_FF.hpp"
44			#include "UseTheForce/ForceFieldFactory.hpp"
45	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
46	gezelter	366	#include "io/AtomTypesSectionParser.hpp"
47	jmichalk	1703	#include "io/LennardJonesAtomTypesSectionParser.hpp"
48			#include "io/BondTypesSectionParser.hpp"
49			#include "io/ChargeAtomTypesSectionParser.hpp"
50			#include "io/MultipoleAtomTypesSectionParser.hpp"
51			#include "io/NonBondedInteractionsSectionParser.hpp"
52	gezelter	366	#include "io/EAMAtomTypesSectionParser.hpp"
53	chuckv	801	#include "io/OptionSectionParser.hpp"
54	gezelter	366	#include "UseTheForce/ForceFieldCreator.hpp"
55			#include "utils/simError.h"
56	gezelter	1390	namespace OpenMD {
57	gezelter	366
58	gezelter	507	EAM_FF::EAM_FF(){
59	gezelter	366
60			//set default force field filename
61			setForceFieldFileName("EAM.frc");
62
63			//the order of adding section parsers are important
64	chuckv	802	//OptionSectionParser must come first to set options for other parsers
65	chuckv	801	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
66	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
67	gezelter	366	spMan_.push_back(new AtomTypesSectionParser());
68	jmichalk	1703	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
69			spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
70			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
71			spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
72			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
73	chuckv	802	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
74	gezelter	507	}
75	gezelter	366
76	gezelter	507	void EAM_FF::parse(const std::string& filename) {
77	gezelter	366	ifstrstream* ffStream;
78			ffStream = openForceFieldFile(filename);
79
80			spMan_.parse(ffStream, this);
81
82			ForceField::AtomTypeContainer::MapTypeIterator i;
83			AtomType* at;
84
85			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
86	gezelter	1280	// useBase sets the responsibilities, and these have to be done
87			// after the atomTypes and Base types have all been scanned:
88
89			std::vector<AtomType*> ayb = at->allYourBase();
90			if (ayb.size() > 1) {
91			for (int j = ayb.size()-1; j > 0; j--) {
92
93			ayb[j-1]->useBase(ayb[j]);
94
95			}
96			}
97	gezelter	366	}
98
99	tim	425	delete ffStream;
100	gezelter	507	}
101	gezelter	366
102
103	tim	963	RealType EAM_FF::getRcutFromAtomType(AtomType* at){
104			RealType rcut = 0.0;
105	gezelter	366	if (at->isEAM()) {
106	gezelter	507	GenericData* data = at->getPropertyByName("EAM");
107			if (data != NULL) {
108			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
109	gezelter	366
110	gezelter	507	if (eamData != NULL) {
111	gezelter	366
112	gezelter	507	EAMParam& eamParam = eamData->getData();
113			rcut = eamParam.rcut;
114			} else {
115			sprintf( painCave.errMsg,
116			"Can not cast GenericData to EAMParam\n");
117	gezelter	1390	painCave.severity = OPENMD_ERROR;
118	gezelter	507	painCave.isFatal = 1;
119			simError();
120			}
121			} else {
122			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
123	gezelter	1390	painCave.severity = OPENMD_ERROR;
124	gezelter	507	painCave.isFatal = 1;
125			simError();
126			}
127	gezelter	366	} else {
128	gezelter	507	rcut = ForceField::getRcutFromAtomType(at);
129	gezelter	366	}
130
131			return rcut;
132	gezelter	507	}
133	gezelter	366
134	gezelter	1390	} //end namespace OpenMD