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/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 "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
    //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 DirectionalAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
    spMan_.push_back(new ChargeAtomTypesSectionParser());
    spMan_.push_back(new MultipoleAtomTypesSectionParser());
    spMan_.push_back(new EAMAtomTypesSectionParser());
    spMan_.push_back(new StickyAtomTypesSectionParser());
    spMan_.push_back(new BondTypesSectionParser());
    spMan_.push_back(new BendTypesSectionParser());
    spMan_.push_back(new TorsionTypesSectionParser());
    
}

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)) {
        at->makeFortranAtomType();
    }

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

    delete ffStream;
}


double EAM_FF::getRcutFromAtomType(AtomType* at){
    double 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:	2169
Committed:	Tue Apr 12 17:12:27 2005 UTC (19 years, 3 months ago) by chuckv
File size:	6131 byte(s)
Log Message:	Updates to deallocate object in fortran.
#	User	Rev	Content
1	gezelter	2050	/*
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			* 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	2169	#include "UseTheForce/DarkSide/eam_interface.h"
44	gezelter	2050	#include "UseTheForce/DarkSide/lj_interface.h"
45			#include "UseTheForce/DarkSide/sticky_interface.h"
46			#include "UseTheForce/ForceFieldFactory.hpp"
47			#include "io/DirectionalAtomTypesSectionParser.hpp"
48			#include "io/AtomTypesSectionParser.hpp"
49			#include "io/LennardJonesAtomTypesSectionParser.hpp"
50	tim	2098	#include "io/ChargeAtomTypesSectionParser.hpp"
51			#include "io/MultipoleAtomTypesSectionParser.hpp"
52	gezelter	2050	#include "io/EAMAtomTypesSectionParser.hpp"
53			#include "io/StickyAtomTypesSectionParser.hpp"
54			#include "io/BondTypesSectionParser.hpp"
55			#include "io/BendTypesSectionParser.hpp"
56			#include "io/TorsionTypesSectionParser.hpp"
57			#include "UseTheForce/ForceFieldCreator.hpp"
58			#include "utils/simError.h"
59			namespace oopse {
60
61			EAM_FF::EAM_FF(){
62
63			//set default force field filename
64			setForceFieldFileName("EAM.frc");
65
66			//the order of adding section parsers are important
67			//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
68			//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
69			//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
70			//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
71			//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
72			//important. AtomTypesSectionParser should be added before other atom type section parsers.
73			//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
74			//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
75			//not important.
76			spMan_.push_back(new DirectionalAtomTypesSectionParser());
77			spMan_.push_back(new AtomTypesSectionParser());
78			spMan_.push_back(new LennardJonesAtomTypesSectionParser());
79	tim	2098	spMan_.push_back(new ChargeAtomTypesSectionParser());
80			spMan_.push_back(new MultipoleAtomTypesSectionParser());
81	gezelter	2050	spMan_.push_back(new EAMAtomTypesSectionParser());
82			spMan_.push_back(new StickyAtomTypesSectionParser());
83			spMan_.push_back(new BondTypesSectionParser());
84			spMan_.push_back(new BendTypesSectionParser());
85			spMan_.push_back(new TorsionTypesSectionParser());
86
87			}
88
89			void EAM_FF::parse(const std::string& filename) {
90			ifstrstream* ffStream;
91			ffStream = openForceFieldFile(filename);
92
93			spMan_.parse(ffStream, this);
94
95			ForceField::AtomTypeContainer::MapTypeIterator i;
96			AtomType* at;
97
98			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
99			at->makeFortranAtomType();
100			}
101
102			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
103			at->complete();
104			}
105	tim	2109
106			delete ffStream;
107	gezelter	2050	}
108
109
110			double EAM_FF::getRcutFromAtomType(AtomType* at){
111			double rcut = 0.0;
112			if (at->isEAM()) {
113			GenericData* data = at->getPropertyByName("EAM");
114			if (data != NULL) {
115			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
116
117			if (eamData != NULL) {
118
119			EAMParam& eamParam = eamData->getData();
120			rcut = eamParam.rcut;
121			} else {
122			sprintf( painCave.errMsg,
123			"Can not cast GenericData to EAMParam\n");
124			painCave.severity = OOPSE_ERROR;
125			painCave.isFatal = 1;
126			simError();
127			}
128			} else {
129			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
130			painCave.severity = OOPSE_ERROR;
131			painCave.isFatal = 1;
132			simError();
133			}
134			} else {
135			rcut = ForceField::getRcutFromAtomType(at);
136			}
137
138			return rcut;
139			}
140
141	chuckv	2169	EAM_FF::~EAM_FF(){
142			// We need to clean up the fortran side so we don't have bad things happen if
143			// we try to create a second EAM force field.
144			destroyEAMTypes();
145			}
146	gezelter	2050	} //end namespace oopse