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/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/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() {
    destroyLJTypes();
    destroyStickyTypes();
    if (hasEAMtypes_) destroyEAMTypes();
    if (hasSCtypes_)  destroySCTypes();
  }
} //end namespace OpenMD

Revision:	1555
Committed:	Tue May 10 20:54:47 2011 UTC (13 years, 11 months ago) by gezelter
File size:	9717 byte(s)
Log Message:	Bug fix to traverse the base chains for NON-bonded interactions as well as bonded. This allows one to specify Metal - non-Metal interactions based on base types instead of exact matches.
#	Content
1	/*
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. 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
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/BaseAtomTypesSectionParser.hpp"
51	#include "io/AtomTypesSectionParser.hpp"
52	#include "io/LennardJonesAtomTypesSectionParser.hpp"
53	#include "io/ChargeAtomTypesSectionParser.hpp"
54	#include "io/MultipoleAtomTypesSectionParser.hpp"
55	#include "io/StickyAtomTypesSectionParser.hpp"
56	#include "io/StickyPowerAtomTypesSectionParser.hpp"
57	#include "io/GayBerneAtomTypesSectionParser.hpp"
58	#include "io/BondTypesSectionParser.hpp"
59	#include "io/BendTypesSectionParser.hpp"
60	#include "io/TorsionTypesSectionParser.hpp"
61	#include "io/MetalNonMetalInteractionsSectionParser.hpp"
62	#include "io/EAMAtomTypesSectionParser.hpp"
63	#include "io/SCAtomTypesSectionParser.hpp"
64	#include "io/OptionSectionParser.hpp"
65	#include "UseTheForce/ForceFieldCreator.hpp"
66
67
68	namespace OpenMD {
69
70	MnM_FF::MnM_FF() {
71
72	//set default force field filename
73	setForceFieldFileName("MnM.frc");
74
75	//The order of adding section parsers is important.
76	//OptionSectionParser must come first to set options for other parsers
77	//DirectionalAtomTypesSectionParser should be added before
78	//AtomTypesSectionParser, and these two section parsers will actually
79	//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and
80	//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which
81	//is a subclass of AtomType and should come first). Other AtomTypes Section
82	//Parser will not create the "real" AtomType, they only add and set some
83	//attribute of the AtomType. Thus their order are not important.
84	//AtomTypesSectionParser should be added before other atom type section
85	//parsers. Make sure they are added after DirectionalAtomTypesSectionParser
86	//and AtomTypesSectionParser. The order of BondTypesSectionParser,
87	//BendTypesSectionParser and TorsionTypesSectionParser are not important.
88	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
89	spMan_.push_back(new BaseAtomTypesSectionParser());
90	spMan_.push_back(new AtomTypesSectionParser());
91	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
92	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
93	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
94	spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
95	spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
96	spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
97	spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
98	spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
99	spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
100	spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_));
101	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
102	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
103	spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
104
105	}
106
107	void MnM_FF::parse(const std::string& filename) {
108	ifstrstream* ffStream;
109
110	ffStream = openForceFieldFile(filename);
111
112	spMan_.parse(ffStream, this);
113
114	ForceField::AtomTypeContainer::MapTypeIterator i;
115	AtomType* at;
116	ForceField::AtomTypeContainer::MapTypeIterator j;
117	AtomType* at2;
118	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k;
119	NonBondedInteractionType* nbit;
120
121	for (at = atomTypeCont_.beginType(i); at != NULL;
122	at = atomTypeCont_.nextType(i)) {
123	// useBase sets the responsibilities, and these have to be done
124	// after the atomTypes and Base types have all been scanned:
125
126	std::vector<AtomType*> ayb = at->allYourBase();
127	if (ayb.size() > 1) {
128	for (int j = ayb.size()-1; j > 0; j--) {
129	ayb[j-1]->useBase(ayb[j]);
130	}
131	}
132	at->makeFortranAtomType();
133	}
134
135	for (at = atomTypeCont_.beginType(i); at != NULL;
136	at = atomTypeCont_.nextType(i)) {
137	at->complete();
138	}
139
140	hasSCtypes_ = false;
141	for (at = atomTypeCont_.beginType(i); at != NULL;
142	at = atomTypeCont_.nextType(i)) {
143	if (at->isSC())
144	hasSCtypes_ = true;
145	}
146
147	hasEAMtypes_ = false;
148	for (at = atomTypeCont_.beginType(i); at != NULL;
149	at = atomTypeCont_.nextType(i)) {
150	if (at->isEAM())
151	hasEAMtypes_ = true;
152	}
153
154	if (hasEAMtypes_ && hasSCtypes_) {
155	sprintf(painCave.errMsg,
156	"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n");
157	painCave.severity = OPENMD_ERROR;
158	painCave.isFatal = 1;
159	simError();
160	}
161
162	/* to handle metal-nonmetal interactions, first we loop over
163	all atom types: */
164
165	for (at = atomTypeCont_.beginType(i); at != NULL;
166	at = atomTypeCont_.nextType(i)) {
167
168	/* if we find a metallic atom, we need to compare against
169	all other atom types */
170
171	if (at->isEAM() \|\| at->isSC()) {
172
173	/* loop over all other atom types */
174	for (at2 = atomTypeCont_.beginType(j); at2 != NULL;
175	at2 = atomTypeCont_.nextType(j)) {
176
177	/* if the other partner is not a metallic type, we need to
178	look for explicit non-bonded interactions */
179	if (!at2->isEAM() && !at2->isSC()) {
180
181	/* get the name and ident of the metallic atom type */
182	std::string at1s = at->getName();
183	int atid1 = at->getIdent();
184
185	/* get the name and ident of the nonmetallic atom type */
186	std::string at2s = at2->getName();
187	int atid2 = at2->getIdent();
188
189	/* look for a match in the non-bonded interactions parsed
190	from the force field file */
191	nbit = getNonBondedInteractionType(at1s, at2s);
192
193	/* if we found a match (even a partial match), punt to the
194	interaction to poke our info down to fortran. */
195	if (nbit != NULL) nbit->tellFortran(atid1, atid2);
196	}
197	}
198	}
199	}
200
201	delete ffStream;
202
203	}
204
205
206	RealType MnM_FF::getRcutFromAtomType(AtomType* at) {
207	RealType rcut = 0.0;
208	if (at->isEAM()) {
209	GenericData* data = at->getPropertyByName("EAM");
210	if (data != NULL) {
211	EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
212
213	if (eamData != NULL) {
214
215	EAMParam& eamParam = eamData->getData();
216	rcut = eamParam.rcut;
217	}
218	else {
219	sprintf(painCave.errMsg,
220	"Can not cast GenericData to EAMParam\n");
221	painCave.severity = OPENMD_ERROR;
222	painCave.isFatal = 1;
223	simError();
224	}
225	}
226	else {
227	sprintf(painCave.errMsg, "Can not find EAM Parameters\n");
228	painCave.severity = OPENMD_ERROR;
229	painCave.isFatal = 1;
230	simError();
231	}
232	}
233	else {
234	rcut = ForceField::getRcutFromAtomType(at);
235	}
236
237	return rcut;
238	}
239
240	MnM_FF::~MnM_FF() {
241	destroyLJTypes();
242	destroyStickyTypes();
243	if (hasEAMtypes_) destroyEAMTypes();
244	if (hasSCtypes_) destroySCTypes();
245	}
246	} //end namespace OpenMD
247