src/UseTheForce/MnM_FF.cpp

/*
 * Copyright (c) 2007 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/MnM_FF.hpp"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/DarkSide/eam_interface.h"
#include "UseTheForce/DarkSide/suttonchen_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/StickyAtomTypesSectionParser.hpp"
#include "io/StickyPowerAtomTypesSectionParser.hpp"
#include "io/GayBerneAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"
#include "io/MetalNonMetalInteractionsSectionParser.hpp"
#include "io/EAMAtomTypesSectionParser.hpp"
#include "io/SCAtomTypesSectionParser.hpp"
#include "io/OptionSectionParser.hpp"
#include "UseTheForce/ForceFieldCreator.hpp"


namespace oopse {
   
  MnM_FF::MnM_FF() {    
    
    //set default force field filename
    setForceFieldFileName("MnM.frc");
    
    //The order of adding section parsers is important.
    //OptionSectionParser must come first to set options for other parsers
    //DirectionalAtomTypesSectionParser should be added before
    //AtomTypesSectionParser, and these two section parsers will actually
    //create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
    //DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
    //is a subclass of AtomType and 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 DirectionalAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_));
    spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
    spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
    
  }
  
  void MnM_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)) {
      at->makeFortranAtomType();
    }
    
    for (at = atomTypeCont_.beginType(i); at != NULL;
         at = atomTypeCont_.nextType(i)) {
      at->complete();
    }
    
    hasSCtypes_ = false;
    for (at = atomTypeCont_.beginType(i); at != NULL;
         at = atomTypeCont_.nextType(i)) {
      if (at->isSC())
        hasSCtypes_ = true;
    }
    
    hasEAMtypes_ = false;
    for (at = atomTypeCont_.beginType(i); at != NULL;
         at = atomTypeCont_.nextType(i)) {
      if (at->isEAM())
        hasEAMtypes_ = true;
    }
    
    if (hasEAMtypes_ && hasSCtypes_) {
      sprintf(painCave.errMsg,
              "MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n");
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    /* 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() || at->isSC()) {
        
        /* 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() && !at2->isSC()) {
          
            /* 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 MnM_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;
  }
     
  MnM_FF::~MnM_FF() {
    destroyLJTypes();
    destroyStickyTypes();
    if (hasEAMtypes_) destroyEAMTypes();
    if (hasSCtypes_)  destroySCTypes();
  }
} //end namespace oopse

Revision:	1252
Committed:	Thu Jun 5 15:53:59 2008 UTC (17 years, 4 months ago) by chuckv
File size:	9229 byte(s)
Log Message:	Fixed typo in LJinteraction types. LJ-metal appears to work now.
#	User	Rev	Content
1	chuckv	1152	/*
2			* Copyright (c) 2007 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
43			#include "UseTheForce/MnM_FF.hpp"
44			#include "UseTheForce/DarkSide/lj_interface.h"
45			#include "UseTheForce/DarkSide/sticky_interface.h"
46			#include "UseTheForce/DarkSide/eam_interface.h"
47			#include "UseTheForce/DarkSide/suttonchen_interface.h"
48			#include "UseTheForce/ForceFieldFactory.hpp"
49			#include "io/DirectionalAtomTypesSectionParser.hpp"
50			#include "io/AtomTypesSectionParser.hpp"
51			#include "io/LennardJonesAtomTypesSectionParser.hpp"
52			#include "io/ChargeAtomTypesSectionParser.hpp"
53			#include "io/MultipoleAtomTypesSectionParser.hpp"
54			#include "io/StickyAtomTypesSectionParser.hpp"
55			#include "io/StickyPowerAtomTypesSectionParser.hpp"
56			#include "io/GayBerneAtomTypesSectionParser.hpp"
57			#include "io/BondTypesSectionParser.hpp"
58			#include "io/BendTypesSectionParser.hpp"
59			#include "io/TorsionTypesSectionParser.hpp"
60			#include "io/MetalNonMetalInteractionsSectionParser.hpp"
61			#include "io/EAMAtomTypesSectionParser.hpp"
62			#include "io/SCAtomTypesSectionParser.hpp"
63			#include "io/OptionSectionParser.hpp"
64			#include "UseTheForce/ForceFieldCreator.hpp"
65
66
67	gezelter	1238	namespace oopse {
68
69			MnM_FF::MnM_FF() {
70
71			//set default force field filename
72			setForceFieldFileName("MnM.frc");
73
74			//The order of adding section parsers is important.
75			//OptionSectionParser must come first to set options for other parsers
76			//DirectionalAtomTypesSectionParser should be added before
77			//AtomTypesSectionParser, and these two section parsers will actually
78			//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
79			//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
80			//is a subclass of AtomType and should come first). Other AtomTypes Section
81			//Parser will not create the "real" AtomType, they only add and set some
82			//attribute of the AtomType. Thus their order are not important.
83			//AtomTypesSectionParser should be added before other atom type section
84			//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
85			//and AtomTypesSectionParser. The order of BondTypesSectionParser,
86			//BendTypesSectionParser and TorsionTypesSectionParser are not important.
87			spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
88			spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
89			spMan_.push_back(new AtomTypesSectionParser());
90			spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
91			spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
92			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
93			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
94			spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
95			spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
96			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
97			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
98			spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_));
99			spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
100			spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
101			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
102
103	chuckv	1162	}
104
105	gezelter	1238	void MnM_FF::parse(const std::string& filename) {
106			ifstrstream* ffStream;
107
108			ffStream = openForceFieldFile(filename);
109	chuckv	1152
110	gezelter	1238	spMan_.parse(ffStream, this);
111	chuckv	1162
112	gezelter	1238	ForceField::AtomTypeContainer::MapTypeIterator i;
113			AtomType* at;
114			ForceField::AtomTypeContainer::MapTypeIterator j;
115			AtomType* at2;
116			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
117			NonBondedInteractionType* nbit;
118
119			for (at = atomTypeCont_.beginType(i); at != NULL;
120			at = atomTypeCont_.nextType(i)) {
121			at->makeFortranAtomType();
122			}
123
124			for (at = atomTypeCont_.beginType(i); at != NULL;
125			at = atomTypeCont_.nextType(i)) {
126			at->complete();
127			}
128
129			hasSCtypes_ = false;
130			for (at = atomTypeCont_.beginType(i); at != NULL;
131			at = atomTypeCont_.nextType(i)) {
132			if (at->isSC())
133			hasSCtypes_ = true;
134			}
135
136			hasEAMtypes_ = false;
137			for (at = atomTypeCont_.beginType(i); at != NULL;
138			at = atomTypeCont_.nextType(i)) {
139			if (at->isEAM())
140			hasEAMtypes_ = true;
141			}
142
143			if (hasEAMtypes_ && hasSCtypes_) {
144			sprintf(painCave.errMsg,
145			"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n");
146			painCave.severity = OOPSE_ERROR;
147			painCave.isFatal = 1;
148			simError();
149			}
150
151			/* to handle metal-nonmetal interactions, first we loop over
152			all atom types: */
153
154			for (at = atomTypeCont_.beginType(i); at != NULL;
155			at = atomTypeCont_.nextType(i)) {
156	chuckv	1162
157	gezelter	1238	/* if we find a metallic atom, we need to compare against
158			all other atom types */
159
160			if (at->isEAM() \|\| at->isSC()) {
161
162			/* loop over all other atom types */
163			for (at2 = atomTypeCont_.beginType(j); at2 != NULL;
164			at2 = atomTypeCont_.nextType(j)) {
165
166			/* if the other partner is not a metallic type, we need to
167			look for explicit non-bonded interactions */
168			if (!at2->isEAM() && !at2->isSC()) {
169	chuckv	1162
170	gezelter	1238	/* get the name and ident of the metallic atom type */
171			std::string at1s = at->getName();
172			int atid1 = at->getIdent();
173	chuckv	1162
174	gezelter	1238	/* get the name and ident of the nonmetallic atom type */
175			std::string at2s = at2->getName();
176			int atid2 = at2->getIdent();
177	chuckv	1162
178	gezelter	1238	/* look for a match in the non-bonded interactions parsed
179			from the force field file */
180			nbit = getNonBondedInteractionType(at1s, at2s);
181	chuckv	1252
182	gezelter	1238	/* if we found a match (even a partial match), punt to the
183			interaction to poke our info down to fortran. */
184			if (nbit != NULL) nbit->tellFortran(atid1, atid2);
185			}
186			}
187	chuckv	1162	}
188	chuckv	1152	}
189	gezelter	1238
190			delete ffStream;
191
192	chuckv	1152	}
193	chuckv	1162
194
195	gezelter	1238	RealType MnM_FF::getRcutFromAtomType(AtomType* at) {
196			RealType rcut = 0.0;
197			if (at->isEAM()) {
198			GenericData* data = at->getPropertyByName("EAM");
199			if (data != NULL) {
200			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
201
202			if (eamData != NULL) {
203
204			EAMParam& eamParam = eamData->getData();
205			rcut = eamParam.rcut;
206			}
207			else {
208			sprintf(painCave.errMsg,
209			"Can not cast GenericData to EAMParam\n");
210			painCave.severity = OOPSE_ERROR;
211			painCave.isFatal = 1;
212			simError();
213			}
214			}
215			else {
216			sprintf(painCave.errMsg, "Can not find EAM Parameters\n");
217			painCave.severity = OOPSE_ERROR;
218			painCave.isFatal = 1;
219			simError();
220			}
221			}
222			else {
223			rcut = ForceField::getRcutFromAtomType(at);
224			}
225
226			return rcut;
227			}
228
229			MnM_FF::~MnM_FF() {
230			destroyLJTypes();
231			destroyStickyTypes();
232			if (hasEAMtypes_) destroyEAMTypes();
233			if (hasSCtypes_) destroySCTypes();
234			}
235	chuckv	1152	} //end namespace oopse
236	chuckv	1162