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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */


#include "UseTheForce/MnM_FF.hpp"
#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/NonBondedInteractionsSectionParser.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 NonBondedInteractionsSectionParser(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]);
        }
      }
    }
    
    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();
    }
    
    delete ffStream;
  
  }
  
  
  RealType MnM_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:	7796 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	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	1152	*/
42
43
44			#include "UseTheForce/MnM_FF.hpp"
45			#include "UseTheForce/ForceFieldFactory.hpp"
46			#include "io/DirectionalAtomTypesSectionParser.hpp"
47	gezelter	1280	#include "io/BaseAtomTypesSectionParser.hpp"
48	chuckv	1152	#include "io/AtomTypesSectionParser.hpp"
49			#include "io/LennardJonesAtomTypesSectionParser.hpp"
50			#include "io/ChargeAtomTypesSectionParser.hpp"
51			#include "io/MultipoleAtomTypesSectionParser.hpp"
52			#include "io/StickyAtomTypesSectionParser.hpp"
53			#include "io/StickyPowerAtomTypesSectionParser.hpp"
54			#include "io/GayBerneAtomTypesSectionParser.hpp"
55			#include "io/BondTypesSectionParser.hpp"
56			#include "io/BendTypesSectionParser.hpp"
57			#include "io/TorsionTypesSectionParser.hpp"
58	gezelter	1501	#include "io/NonBondedInteractionsSectionParser.hpp"
59	chuckv	1152	#include "io/EAMAtomTypesSectionParser.hpp"
60			#include "io/SCAtomTypesSectionParser.hpp"
61			#include "io/OptionSectionParser.hpp"
62			#include "UseTheForce/ForceFieldCreator.hpp"
63
64
65	gezelter	1390	namespace OpenMD {
66	gezelter	1238
67			MnM_FF::MnM_FF() {
68
69			//set default force field filename
70			setForceFieldFileName("MnM.frc");
71
72			//The order of adding section parsers is important.
73			//OptionSectionParser must come first to set options for other parsers
74			//DirectionalAtomTypesSectionParser should be added before
75			//AtomTypesSectionParser, and these two section parsers will actually
76			//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
77			//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
78			//is a subclass of AtomType and should come first). Other AtomTypes Section
79			//Parser will not create the "real" AtomType, they only add and set some
80			//attribute of the AtomType. Thus their order are not important.
81			//AtomTypesSectionParser should be added before other atom type section
82			//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
83			//and AtomTypesSectionParser. The order of BondTypesSectionParser,
84			//BendTypesSectionParser and TorsionTypesSectionParser are not important.
85			spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
86	gezelter	1280	spMan_.push_back(new BaseAtomTypesSectionParser());
87	gezelter	1282	spMan_.push_back(new AtomTypesSectionParser());
88	gezelter	1238	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
89			spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
90			spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
91			spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
92			spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
93			spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
94			spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
95			spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
96			spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
97	gezelter	1501	spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
98	gezelter	1238	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
99			spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
100			spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
101
102	chuckv	1162	}
103
104	gezelter	1238	void MnM_FF::parse(const std::string& filename) {
105			ifstrstream* ffStream;
106
107			ffStream = openForceFieldFile(filename);
108	chuckv	1152
109	gezelter	1238	spMan_.parse(ffStream, this);
110	chuckv	1162
111	gezelter	1238	ForceField::AtomTypeContainer::MapTypeIterator i;
112			AtomType* at;
113			ForceField::AtomTypeContainer::MapTypeIterator j;
114			AtomType* at2;
115			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
116			NonBondedInteractionType* nbit;
117
118			for (at = atomTypeCont_.beginType(i); at != NULL;
119			at = atomTypeCont_.nextType(i)) {
120	gezelter	1280	// useBase sets the responsibilities, and these have to be done
121			// after the atomTypes and Base types have all been scanned:
122
123			std::vector<AtomType*> ayb = at->allYourBase();
124			if (ayb.size() > 1) {
125			for (int j = ayb.size()-1; j > 0; j--) {
126			ayb[j-1]->useBase(ayb[j]);
127			}
128			}
129	gezelter	1238	}
130
131			hasSCtypes_ = false;
132			for (at = atomTypeCont_.beginType(i); at != NULL;
133			at = atomTypeCont_.nextType(i)) {
134			if (at->isSC())
135			hasSCtypes_ = true;
136			}
137
138			hasEAMtypes_ = false;
139			for (at = atomTypeCont_.beginType(i); at != NULL;
140			at = atomTypeCont_.nextType(i)) {
141			if (at->isEAM())
142			hasEAMtypes_ = true;
143			}
144
145			if (hasEAMtypes_ && hasSCtypes_) {
146			sprintf(painCave.errMsg,
147			"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n");
148	gezelter	1390	painCave.severity = OPENMD_ERROR;
149	gezelter	1238	painCave.isFatal = 1;
150			simError();
151			}
152
153			delete ffStream;
154
155	chuckv	1152	}
156	chuckv	1162
157
158	gezelter	1238	RealType MnM_FF::getRcutFromAtomType(AtomType* at) {
159			RealType rcut = 0.0;
160			if (at->isEAM()) {
161			GenericData* data = at->getPropertyByName("EAM");
162			if (data != NULL) {
163	gezelter	1710	EAMAtypeData* eamData = dynamic_cast<EAMAtypeData*>(data);
164	gezelter	1238
165			if (eamData != NULL) {
166
167	gezelter	1710	EAMAtypeParameters* eamParam = eamData->getData();
168			rcut = eamParam->rcut;
169	gezelter	1238	}
170			else {
171			sprintf(painCave.errMsg,
172			"Can not cast GenericData to EAMParam\n");
173	gezelter	1390	painCave.severity = OPENMD_ERROR;
174	gezelter	1238	painCave.isFatal = 1;
175			simError();
176			}
177			}
178			else {
179			sprintf(painCave.errMsg, "Can not find EAM Parameters\n");
180	gezelter	1390	painCave.severity = OPENMD_ERROR;
181	gezelter	1238	painCave.isFatal = 1;
182			simError();
183			}
184			}
185			else {
186			rcut = ForceField::getRcutFromAtomType(at);
187			}
188
189			return rcut;
190			}
191	gezelter	1390	} //end namespace OpenMD
192	chuckv	1162