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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "UseTheForce/EAM_FF.hpp"
#include "UseTheForce/DarkSide/eam_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/BaseAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.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 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 = 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;    
  }

  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 OpenMD
Revision:	1467
Committed:	Sat Jul 17 15:33:03 2010 UTC (14 years, 9 months ago) by gezelter
File size:	4900 byte(s)
Log Message:	well, it compiles, but still segfaults
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	366	*/
41
42			#include "UseTheForce/EAM_FF.hpp"
43	chuckv	472	#include "UseTheForce/DarkSide/eam_interface.h"
44	gezelter	366	#include "UseTheForce/DarkSide/sticky_interface.h"
45			#include "UseTheForce/ForceFieldFactory.hpp"
46	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
47	gezelter	366	#include "io/AtomTypesSectionParser.hpp"
48			#include "io/EAMAtomTypesSectionParser.hpp"
49	chuckv	801	#include "io/OptionSectionParser.hpp"
50	gezelter	366	#include "UseTheForce/ForceFieldCreator.hpp"
51			#include "utils/simError.h"
52	gezelter	1390	namespace OpenMD {
53	gezelter	366
54	gezelter	507	EAM_FF::EAM_FF(){
55	gezelter	366
56			//set default force field filename
57			setForceFieldFileName("EAM.frc");
58
59			//the order of adding section parsers are important
60	chuckv	802	//OptionSectionParser must come first to set options for other parsers
61	chuckv	801	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
62	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
63	gezelter	366	spMan_.push_back(new AtomTypesSectionParser());
64	chuckv	802	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
65	gezelter	507	}
66	gezelter	366
67	gezelter	507	void EAM_FF::parse(const std::string& filename) {
68	gezelter	366	ifstrstream* ffStream;
69			ffStream = openForceFieldFile(filename);
70
71			spMan_.parse(ffStream, this);
72
73			ForceField::AtomTypeContainer::MapTypeIterator i;
74			AtomType* at;
75
76			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
77	gezelter	1280	// useBase sets the responsibilities, and these have to be done
78			// after the atomTypes and Base types have all been scanned:
79
80			std::vector<AtomType*> ayb = at->allYourBase();
81			if (ayb.size() > 1) {
82			for (int j = ayb.size()-1; j > 0; j--) {
83
84			ayb[j-1]->useBase(ayb[j]);
85
86			}
87			}
88	gezelter	507	at->makeFortranAtomType();
89	gezelter	366	}
90
91			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
92	gezelter	507	at->complete();
93	gezelter	366	}
94	tim	425
95			delete ffStream;
96	gezelter	507	}
97	gezelter	366
98
99	tim	963	RealType EAM_FF::getRcutFromAtomType(AtomType* at){
100			RealType rcut = 0.0;
101	gezelter	366	if (at->isEAM()) {
102	gezelter	507	GenericData* data = at->getPropertyByName("EAM");
103			if (data != NULL) {
104			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
105	gezelter	366
106	gezelter	507	if (eamData != NULL) {
107	gezelter	366
108	gezelter	507	EAMParam& eamParam = eamData->getData();
109			rcut = eamParam.rcut;
110			} else {
111			sprintf( painCave.errMsg,
112			"Can not cast GenericData to EAMParam\n");
113	gezelter	1390	painCave.severity = OPENMD_ERROR;
114	gezelter	507	painCave.isFatal = 1;
115			simError();
116			}
117			} else {
118			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
119	gezelter	1390	painCave.severity = OPENMD_ERROR;
120	gezelter	507	painCave.isFatal = 1;
121			simError();
122			}
123	gezelter	366	} else {
124	gezelter	507	rcut = ForceField::getRcutFromAtomType(at);
125	gezelter	366	}
126
127			return rcut;
128	gezelter	507	}
129	gezelter	366
130	chuckv	472	EAM_FF::~EAM_FF(){
131			// We need to clean up the fortran side so we don't have bad things happen if
132			// we try to create a second EAM force field.
133			destroyEAMTypes();
134			}
135	gezelter	1390	} //end namespace OpenMD