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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "UseTheForce/EAM_FF.hpp"
#include "UseTheForce/DarkSide/eam_interface.h"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/DirectionalAtomTypesSectionParser.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ChargeAtomTypesSectionParser.hpp"
#include "io/MultipoleAtomTypesSectionParser.hpp"
#include "io/EAMAtomTypesSectionParser.hpp"
#include "io/StickyAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"
#include "utils/simError.h"
namespace oopse {
    
  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
    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the 
    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
    //important. AtomTypesSectionParser should be added before other atom type section parsers.
    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. 
    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
    //not important.
    spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
    spMan_.push_back(new BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    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]);

        }
      }
      at->makeFortranAtomType();
    }

    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
      at->complete();
    }

    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 = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
      } else {
        sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }    else {
      rcut = ForceField::getRcutFromAtomType(at);
    }
   
    return rcut;    
  }

  EAM_FF::~EAM_FF(){
    // We need to clean up the fortran side so we don't have bad things happen if
    // we try to create a second EAM force field.
    destroyEAMTypes();
  }
} //end namespace oopse
Revision:	1280
Committed:	Wed Jul 16 02:07:09 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/UseTheForce/EAM_FF.cpp*
File size:	6108 byte(s)
Log Message:	All your base are belong to us!
#	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			* 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "UseTheForce/EAM_FF.hpp"
43	chuckv	472	#include "UseTheForce/DarkSide/eam_interface.h"
44	gezelter	366	#include "UseTheForce/DarkSide/lj_interface.h"
45			#include "UseTheForce/DarkSide/sticky_interface.h"
46			#include "UseTheForce/ForceFieldFactory.hpp"
47			#include "io/DirectionalAtomTypesSectionParser.hpp"
48	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
49	gezelter	366	#include "io/AtomTypesSectionParser.hpp"
50			#include "io/LennardJonesAtomTypesSectionParser.hpp"
51	tim	414	#include "io/ChargeAtomTypesSectionParser.hpp"
52			#include "io/MultipoleAtomTypesSectionParser.hpp"
53	gezelter	366	#include "io/EAMAtomTypesSectionParser.hpp"
54			#include "io/StickyAtomTypesSectionParser.hpp"
55			#include "io/BondTypesSectionParser.hpp"
56			#include "io/BendTypesSectionParser.hpp"
57			#include "io/TorsionTypesSectionParser.hpp"
58	chuckv	801	#include "io/OptionSectionParser.hpp"
59	gezelter	366	#include "UseTheForce/ForceFieldCreator.hpp"
60			#include "utils/simError.h"
61			namespace oopse {
62
63	gezelter	507	EAM_FF::EAM_FF(){
64	gezelter	366
65			//set default force field filename
66			setForceFieldFileName("EAM.frc");
67
68			//the order of adding section parsers are important
69	chuckv	802	//OptionSectionParser must come first to set options for other parsers
70	gezelter	366	//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
71			//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
72			//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
73			//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
74			//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
75			//important. AtomTypesSectionParser should be added before other atom type section parsers.
76			//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
77			//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
78			//not important.
79	chuckv	801	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
80	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
81	gezelter	366	spMan_.push_back(new AtomTypesSectionParser());
82	chuckv	802	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
83	chuckv	801
84	gezelter	366
85	gezelter	507	}
86	gezelter	366
87	gezelter	507	void EAM_FF::parse(const std::string& filename) {
88	gezelter	366	ifstrstream* ffStream;
89			ffStream = openForceFieldFile(filename);
90
91			spMan_.parse(ffStream, this);
92
93			ForceField::AtomTypeContainer::MapTypeIterator i;
94			AtomType* at;
95
96			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
97	gezelter	1280	// useBase sets the responsibilities, and these have to be done
98			// after the atomTypes and Base types have all been scanned:
99
100			std::vector<AtomType*> ayb = at->allYourBase();
101			if (ayb.size() > 1) {
102			for (int j = ayb.size()-1; j > 0; j--) {
103
104			ayb[j-1]->useBase(ayb[j]);
105
106			}
107			}
108	gezelter	507	at->makeFortranAtomType();
109	gezelter	366	}
110
111			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
112	gezelter	507	at->complete();
113	gezelter	366	}
114	tim	425
115			delete ffStream;
116	gezelter	507	}
117	gezelter	366
118
119	tim	963	RealType EAM_FF::getRcutFromAtomType(AtomType* at){
120			RealType rcut = 0.0;
121	gezelter	366	if (at->isEAM()) {
122	gezelter	507	GenericData* data = at->getPropertyByName("EAM");
123			if (data != NULL) {
124			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
125	gezelter	366
126	gezelter	507	if (eamData != NULL) {
127	gezelter	366
128	gezelter	507	EAMParam& eamParam = eamData->getData();
129			rcut = eamParam.rcut;
130			} else {
131			sprintf( painCave.errMsg,
132			"Can not cast GenericData to EAMParam\n");
133			painCave.severity = OOPSE_ERROR;
134			painCave.isFatal = 1;
135			simError();
136			}
137			} else {
138			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
139			painCave.severity = OOPSE_ERROR;
140			painCave.isFatal = 1;
141			simError();
142			}
143	gezelter	366	} else {
144	gezelter	507	rcut = ForceField::getRcutFromAtomType(at);
145	gezelter	366	}
146
147			return rcut;
148	gezelter	507	}
149	gezelter	366
150	chuckv	472	EAM_FF::~EAM_FF(){
151			// We need to clean up the fortran side so we don't have bad things happen if
152			// we try to create a second EAM force field.
153			destroyEAMTypes();
154			}
155	gezelter	366	} //end namespace oopse