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. 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/MnM_FF.hpp"
#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/BaseAtomTypesSectionParser.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 OpenMD {
   
  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 BaseAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
    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)) {
      // 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();
    }
    
    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 = OPENMD_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 = 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;
  }
     
  MnM_FF::~MnM_FF() {
    destroyStickyTypes();
    if (hasEAMtypes_) destroyEAMTypes();
    if (hasSCtypes_)  destroySCTypes();
  }
} //end namespace OpenMD

Revision:	1467
Committed:	Sat Jul 17 15:33:03 2010 UTC (14 years, 9 months ago) by gezelter
File size:	9650 byte(s)
Log Message:	well, it compiles, but still segfaults
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1152	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1152	* 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	chuckv	1152	*/
41
42
43			#include "UseTheForce/MnM_FF.hpp"
44			#include "UseTheForce/DarkSide/sticky_interface.h"
45			#include "UseTheForce/DarkSide/eam_interface.h"
46			#include "UseTheForce/DarkSide/suttonchen_interface.h"
47			#include "UseTheForce/ForceFieldFactory.hpp"
48			#include "io/DirectionalAtomTypesSectionParser.hpp"
49	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
50	chuckv	1152	#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	1390	namespace OpenMD {
68	gezelter	1238
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	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
89	gezelter	1282	spMan_.push_back(new AtomTypesSectionParser());
90	gezelter	1238	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
91			spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
92			spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
93			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
94			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
95			spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
96			spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
97			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
98			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
99			spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_));
100			spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
101			spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
102			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
103
104	chuckv	1162	}
105
106	gezelter	1238	void MnM_FF::parse(const std::string& filename) {
107			ifstrstream* ffStream;
108
109			ffStream = openForceFieldFile(filename);
110	chuckv	1152
111	gezelter	1238	spMan_.parse(ffStream, this);
112	chuckv	1162
113	gezelter	1238	ForceField::AtomTypeContainer::MapTypeIterator i;
114			AtomType* at;
115			ForceField::AtomTypeContainer::MapTypeIterator j;
116			AtomType* at2;
117			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
118			NonBondedInteractionType* nbit;
119
120			for (at = atomTypeCont_.beginType(i); at != NULL;
121			at = atomTypeCont_.nextType(i)) {
122	gezelter	1280	// useBase sets the responsibilities, and these have to be done
123			// after the atomTypes and Base types have all been scanned:
124
125			std::vector<AtomType*> ayb = at->allYourBase();
126			if (ayb.size() > 1) {
127			for (int j = ayb.size()-1; j > 0; j--) {
128
129			ayb[j-1]->useBase(ayb[j]);
130
131			}
132			}
133	gezelter	1238	at->makeFortranAtomType();
134			}
135
136			for (at = atomTypeCont_.beginType(i); at != NULL;
137			at = atomTypeCont_.nextType(i)) {
138			at->complete();
139			}
140
141			hasSCtypes_ = false;
142			for (at = atomTypeCont_.beginType(i); at != NULL;
143			at = atomTypeCont_.nextType(i)) {
144			if (at->isSC())
145			hasSCtypes_ = true;
146			}
147
148			hasEAMtypes_ = false;
149			for (at = atomTypeCont_.beginType(i); at != NULL;
150			at = atomTypeCont_.nextType(i)) {
151			if (at->isEAM())
152			hasEAMtypes_ = true;
153			}
154
155			if (hasEAMtypes_ && hasSCtypes_) {
156			sprintf(painCave.errMsg,
157			"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n");
158	gezelter	1390	painCave.severity = OPENMD_ERROR;
159	gezelter	1238	painCave.isFatal = 1;
160			simError();
161			}
162
163			/* to handle metal-nonmetal interactions, first we loop over
164			all atom types: */
165
166			for (at = atomTypeCont_.beginType(i); at != NULL;
167			at = atomTypeCont_.nextType(i)) {
168	chuckv	1162
169	gezelter	1238	/* if we find a metallic atom, we need to compare against
170			all other atom types */
171
172			if (at->isEAM() \|\| at->isSC()) {
173
174			/* loop over all other atom types */
175			for (at2 = atomTypeCont_.beginType(j); at2 != NULL;
176			at2 = atomTypeCont_.nextType(j)) {
177
178			/* if the other partner is not a metallic type, we need to
179			look for explicit non-bonded interactions */
180			if (!at2->isEAM() && !at2->isSC()) {
181	chuckv	1162
182	gezelter	1238	/* get the name and ident of the metallic atom type */
183			std::string at1s = at->getName();
184			int atid1 = at->getIdent();
185	chuckv	1162
186	gezelter	1238	/* get the name and ident of the nonmetallic atom type */
187			std::string at2s = at2->getName();
188			int atid2 = at2->getIdent();
189	chuckv	1162
190	gezelter	1238	/* look for a match in the non-bonded interactions parsed
191			from the force field file */
192			nbit = getNonBondedInteractionType(at1s, at2s);
193	chuckv	1252
194	gezelter	1238	/* if we found a match (even a partial match), punt to the
195			interaction to poke our info down to fortran. */
196			if (nbit != NULL) nbit->tellFortran(atid1, atid2);
197			}
198			}
199	chuckv	1162	}
200	chuckv	1152	}
201	gezelter	1238
202			delete ffStream;
203
204	chuckv	1152	}
205	chuckv	1162
206
207	gezelter	1238	RealType MnM_FF::getRcutFromAtomType(AtomType* at) {
208			RealType rcut = 0.0;
209			if (at->isEAM()) {
210			GenericData* data = at->getPropertyByName("EAM");
211			if (data != NULL) {
212			EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
213
214			if (eamData != NULL) {
215
216			EAMParam& eamParam = eamData->getData();
217			rcut = eamParam.rcut;
218			}
219			else {
220			sprintf(painCave.errMsg,
221			"Can not cast GenericData to EAMParam\n");
222	gezelter	1390	painCave.severity = OPENMD_ERROR;
223	gezelter	1238	painCave.isFatal = 1;
224			simError();
225			}
226			}
227			else {
228			sprintf(painCave.errMsg, "Can not find EAM Parameters\n");
229	gezelter	1390	painCave.severity = OPENMD_ERROR;
230	gezelter	1238	painCave.isFatal = 1;
231			simError();
232			}
233			}
234			else {
235			rcut = ForceField::getRcutFromAtomType(at);
236			}
237
238			return rcut;
239			}
240
241			MnM_FF::~MnM_FF() {
242			destroyStickyTypes();
243			if (hasEAMtypes_) destroyEAMTypes();
244			if (hasSCtypes_) destroySCTypes();
245			}
246	gezelter	1390	} //end namespace OpenMD
247	chuckv	1162