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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "UseTheForce/EADM_FF.hpp"
#include "UseTheForce/DarkSide/eam_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/MetalNonMetalInteractionsSectionParser.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 MultipoleAtomTypesSectionParser(forceFieldOptions_)); 
    spMan_.push_back(new MetalNonMetalInteractionsSectionParser(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;
    ForceField::AtomTypeContainer::MapTypeIterator j;
    AtomType* at2;
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
    NonBondedInteractionType* nbit;

    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();
    }

    hasEAMtypes_ = false;
    for (at = atomTypeCont_.beginType(i); at != NULL;
         at = atomTypeCont_.nextType(i)) {
      if (at->isEAM())
        hasEAMtypes_ = true;
    }
  
    /* to handle metal-nonmetal interactions, first we loop over
       all atom types: */
   
    for (at = atomTypeCont_.beginType(i); at != NULL;
         at = atomTypeCont_.nextType(i)) {
    
      /* if we find a metallic atom, we need to compare against
         all other atom types */
    
      if (at->isEAM()) {
    
        /* loop over all other atom types */
        for (at2 = atomTypeCont_.beginType(j); at2 != NULL;
             at2 = atomTypeCont_.nextType(j)) {
    
          /* if the other partner is not a metallic type, we need to
             look for explicit non-bonded interactions */
          if (!at2->isEAM()) {

            /* get the name and ident of the metallic atom type */
            std::string at1s = at->getName();
            int atid1 = at->getIdent();

            /* get the name and ident of the nonmetallic atom type */
            std::string at2s = at2->getName();
            int atid2 = at2->getIdent();
            
            
            /* look for a match in the non-bonded interactions parsed
               from the force field file */
            nbit = getNonBondedInteractionType(at1s, at2s);
    
            /* if we found a match (even a partial match), punt to the
               interaction to poke our info down to fortran. */
            if (nbit != NULL){ 
               nbit->tellFortran(atid1, atid2);
            }
          }
        }
      }
    }

    delete ffStream;
  }


  RealType EADM_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;    
  }

  EADM_FF::~EADM_FF(){
    //We need to clean up the fortran side so we don't have bad things happen if
    //we try to create a second EADM force field.
    destroyEAMTypes();
  }
} //end namespace OpenMD
Revision:	1605
Committed:	Mon Aug 8 18:56:28 2011 UTC (13 years, 9 months ago) by jmichalk
File size:	7206 byte(s)
Log Message:	Forgot to svn add the EADM_FF.cpp/hpp -JRM
#	User	Rev	Content
1	jmichalk	1605	/*
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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include "UseTheForce/EADM_FF.hpp"
43			#include "UseTheForce/DarkSide/eam_interface.h"
44			#include "UseTheForce/ForceFieldFactory.hpp"
45
46			#include "io/DirectionalAtomTypesSectionParser.hpp"
47			#include "io/BaseAtomTypesSectionParser.hpp"
48			#include "io/AtomTypesSectionParser.hpp"
49			#include "io/LennardJonesAtomTypesSectionParser.hpp"
50			#include "io/ChargeAtomTypesSectionParser.hpp"
51			#include "io/MultipoleAtomTypesSectionParser.hpp"
52			#include "io/MetalNonMetalInteractionsSectionParser.hpp"
53			#include "io/EAMAtomTypesSectionParser.hpp"
54			#include "io/OptionSectionParser.hpp"
55
56			#include "UseTheForce/ForceFieldCreator.hpp"
57			#include "utils/simError.h"
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			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
74			spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_));
75			spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
76
77			}
78
79			void EADM_FF::parse(const std::string& filename) {
80			ifstrstream* ffStream;
81			ffStream = openForceFieldFile(filename);
82
83			spMan_.parse(ffStream, this);
84
85			ForceField::AtomTypeContainer::MapTypeIterator i;
86			AtomType* at;
87			ForceField::AtomTypeContainer::MapTypeIterator j;
88			AtomType* at2;
89			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
90			NonBondedInteractionType* nbit;
91
92			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
93			// useBase sets the responsibilities, and these have to be done
94			// after the atomTypes and Base types have all been scanned:
95
96			std::vector<AtomType*> ayb = at->allYourBase();
97			if (ayb.size() > 1) {
98			for (int j = ayb.size()-1; j > 0; j--) {
99
100			ayb[j-1]->useBase(ayb[j]);
101
102			}
103			}
104			at->makeFortranAtomType();
105			}
106
107			for( at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
108			at->complete();
109			}
110
111			hasEAMtypes_ = false;
112			for (at = atomTypeCont_.beginType(i); at != NULL;
113			at = atomTypeCont_.nextType(i)) {
114			if (at->isEAM())
115			hasEAMtypes_ = true;
116			}
117
118			/* to handle metal-nonmetal interactions, first we loop over
119			all atom types: */
120
121			for (at = atomTypeCont_.beginType(i); at != NULL;
122			at = atomTypeCont_.nextType(i)) {
123
124			/* if we find a metallic atom, we need to compare against
125			all other atom types */
126
127			if (at->isEAM()) {
128
129			/* loop over all other atom types */
130			for (at2 = atomTypeCont_.beginType(j); at2 != NULL;
131			at2 = atomTypeCont_.nextType(j)) {
132
133			/* if the other partner is not a metallic type, we need to
134			look for explicit non-bonded interactions */
135			if (!at2->isEAM()) {
136
137			/* get the name and ident of the metallic atom type */
138			std::string at1s = at->getName();
139			int atid1 = at->getIdent();
140
141			/* get the name and ident of the nonmetallic atom type */
142			std::string at2s = at2->getName();
143			int atid2 = at2->getIdent();
144
145
146			/* look for a match in the non-bonded interactions parsed
147			from the force field file */
148			nbit = getNonBondedInteractionType(at1s, at2s);
149
150			/* if we found a match (even a partial match), punt to the
151			interaction to poke our info down to fortran. */
152			if (nbit != NULL){
153			nbit->tellFortran(atid1, atid2);
154			}
155			}
156			}
157			}
158			}
159
160			delete ffStream;
161			}
162
163
164			RealType EADM_FF::getRcutFromAtomType(AtomType* at){
165			RealType rcut = 0.0;
166			if (at->isEAM()) {
167			GenericData* data = at->getPropertyByName("EAM");
168			if (data != NULL) {
169			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
170
171			if (eamData != NULL) {
172
173			EAMParam& eamParam = eamData->getData();
174			rcut = eamParam.rcut;
175			} else {
176			sprintf( painCave.errMsg,
177			"Can not cast GenericData to EAMParam\n");
178			painCave.severity = OPENMD_ERROR;
179			painCave.isFatal = 1;
180			simError();
181			}
182			} else {
183			sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
184			painCave.severity = OPENMD_ERROR;
185			painCave.isFatal = 1;
186			simError();
187			}
188			} else {
189			rcut = ForceField::getRcutFromAtomType(at);
190			}
191
192			return rcut;
193			}
194
195			EADM_FF::~EADM_FF(){
196			//We need to clean up the fortran side so we don't have bad things happen if
197			//we try to create a second EADM force field.
198			destroyEAMTypes();
199			}
200			} //end namespace OpenMD