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:	3435
Committed:	Wed Jul 16 02:07:09 2008 UTC (15 years, 11 months ago) by gezelter
File size:	6108 byte(s)
Log Message:	All your base are belong to us!
#	Content
1	/*
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	#include "UseTheForce/DarkSide/eam_interface.h"
44	#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/BaseAtomTypesSectionParser.hpp"
49	#include "io/AtomTypesSectionParser.hpp"
50	#include "io/LennardJonesAtomTypesSectionParser.hpp"
51	#include "io/ChargeAtomTypesSectionParser.hpp"
52	#include "io/MultipoleAtomTypesSectionParser.hpp"
53	#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	#include "io/OptionSectionParser.hpp"
59	#include "UseTheForce/ForceFieldCreator.hpp"
60	#include "utils/simError.h"
61	namespace oopse {
62
63	EAM_FF::EAM_FF(){
64
65	//set default force field filename
66	setForceFieldFileName("EAM.frc");
67
68	//the order of adding section parsers are important
69	//OptionSectionParser must come first to set options for other parsers
70	//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	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
80	spMan_.push_back(new BaseAtomTypesSectionParser());
81	spMan_.push_back(new AtomTypesSectionParser());
82	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
83
84
85	}
86
87	void EAM_FF::parse(const std::string& filename) {
88	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	// 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	at->makeFortranAtomType();
109	}
110
111	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
112	at->complete();
113	}
114
115	delete ffStream;
116	}
117
118
119	RealType EAM_FF::getRcutFromAtomType(AtomType* at){
120	RealType rcut = 0.0;
121	if (at->isEAM()) {
122	GenericData* data = at->getPropertyByName("EAM");
123	if (data != NULL) {
124	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
125
126	if (eamData != NULL) {
127
128	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	} else {
144	rcut = ForceField::getRcutFromAtomType(at);
145	}
146
147	return rcut;
148	}
149
150	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	} //end namespace oopse