src/UseTheForce/EADM_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/EADM_FF.hpp"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/DirectionalAtomTypesSectionParser.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 {
    
  EADM_FF::EADM_FF(){

    //set default force field filename
    setForceFieldFileName("EADM.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 DirectionalAtomTypesSectionParser(forceFieldOptions_));
    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 EADM_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 EADM_FF::getRcutFromAtomType(AtomType* at){
    RealType rcut = 0.0;    
    if (at->isEAM()) {
      GenericData* data = at->getPropertyByName("EAM");
      if (data != NULL) {
        EAMAtypeData* eamData = dynamic_cast<EAMAtypeData*>(data);
        
        if (eamData != NULL) {
          
          EAMAtypeParameters* 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:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5325 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	User	Rev	Content
1	gezelter	1629	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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	1629	*/
42
43			#include "UseTheForce/EADM_FF.hpp"
44			#include "UseTheForce/ForceFieldFactory.hpp"
45			#include "io/DirectionalAtomTypesSectionParser.hpp"
46			#include "io/BaseAtomTypesSectionParser.hpp"
47			#include "io/AtomTypesSectionParser.hpp"
48			#include "io/LennardJonesAtomTypesSectionParser.hpp"
49	jmichalk	1656	#include "io/BondTypesSectionParser.hpp"
50	gezelter	1629	#include "io/ChargeAtomTypesSectionParser.hpp"
51			#include "io/MultipoleAtomTypesSectionParser.hpp"
52			#include "io/NonBondedInteractionsSectionParser.hpp"
53			#include "io/EAMAtomTypesSectionParser.hpp"
54			#include "io/OptionSectionParser.hpp"
55			#include "UseTheForce/ForceFieldCreator.hpp"
56			#include "utils/simError.h"
57
58			namespace OpenMD {
59
60			EADM_FF::EADM_FF(){
61
62			//set default force field filename
63			setForceFieldFileName("EADM.frc");
64
65			//the order of adding section parsers are important
66			//OptionSectionParser must come first to set options for other parsers
67
68			spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
69			spMan_.push_back(new BaseAtomTypesSectionParser());
70			spMan_.push_back(new AtomTypesSectionParser());
71			spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
72			spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
73	jmichalk	1656	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
74	gezelter	1629	spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
75			spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
76	jmichalk	1656	spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
77	gezelter	1629	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
78
79			}
80
81			void EADM_FF::parse(const std::string& filename) {
82			ifstrstream* ffStream;
83			ffStream = openForceFieldFile(filename);
84
85			spMan_.parse(ffStream, this);
86
87			ForceField::AtomTypeContainer::MapTypeIterator i;
88			AtomType* at;
89
90			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
91			// useBase sets the responsibilities, and these have to be done
92			// after the atomTypes and Base types have all been scanned:
93
94			std::vector<AtomType*> ayb = at->allYourBase();
95			if (ayb.size() > 1) {
96			for (int j = ayb.size()-1; j > 0; j--) {
97			ayb[j-1]->useBase(ayb[j]);
98			}
99			}
100			}
101			delete ffStream;
102			}
103
104
105			RealType EADM_FF::getRcutFromAtomType(AtomType* at){
106			RealType rcut = 0.0;
107			if (at->isEAM()) {
108			GenericData* data = at->getPropertyByName("EAM");
109			if (data != NULL) {
110	gezelter	1710	EAMAtypeData* eamData = dynamic_cast<EAMAtypeData*>(data);
111	gezelter	1629
112			if (eamData != NULL) {
113
114	gezelter	1710	EAMAtypeParameters* eamParam = eamData->getData();
115			rcut = eamParam->rcut;
116	gezelter	1629	} else {
117			sprintf( painCave.errMsg,
118			"Can not cast GenericData to EAMParam\n");
119			painCave.severity = OPENMD_ERROR;
120			painCave.isFatal = 1;
121			simError();
122			}
123			} else {
124			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
125			painCave.severity = OPENMD_ERROR;
126			painCave.isFatal = 1;
127			simError();
128			}
129			} else {
130			rcut = ForceField::getRcutFromAtomType(at);
131			}
132
133			return rcut;
134			}
135
136			} //end namespace OpenMD