src/UseTheForce/ForceField.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. 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.
 */
 
/**
 * @file ForceField.cpp
 * @author tlin
 * @date 11/04/2004
 * @time 22:51am
 * @version 1.0
 */
  
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
#include "UseTheForce/DarkSide/atype_interface.h"
#include "UseTheForce/DarkSide/fForceOptions_interface.h"
#include "UseTheForce/DarkSide/switcheroo_interface.h"
namespace oopse {

  ForceField::ForceField() { 
    char* tempPath; 
    tempPath = getenv("FORCE_PARAM_PATH");

    if (tempPath == NULL) {
      //convert a macro from compiler to a string in c++
      STR_DEFINE(ffPath_, FRC_PATH );
    } else {
      ffPath_ = tempPath;
    }
  }


  ForceField::~ForceField() {
    deleteAtypes();
    deleteSwitch();
  }

  AtomType* ForceField::getAtomType(const std::string &at) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.find(keys);
  }

  BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    

    //try exact match first
    BondType* bondType = bondTypeCont_.find(keys);
    if (bondType) {
      return bondType;
    } else {
      //if no exact match found, try wild card match
      return bondTypeCont_.find(keys, wildCardAtomTypeName_);
    }

  }

  BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
                                    const std::string &at3) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    

    //try exact match first
    BendType* bendType = bendTypeCont_.find(keys);
    if (bendType) {
      return bendType;
    } else {
      //if no exact match found, try wild card match
      return bendTypeCont_.find(keys, wildCardAtomTypeName_);
    }
  }

  TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
                                          const std::string &at3, const std::string &at4) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    

    TorsionType* torsionType = torsionTypeCont_.find(keys);
    if (torsionType) {
      return torsionType;
    } else {
      //if no exact match found, try wild card match
      return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
    }
    
    return torsionTypeCont_.find(keys, wildCardAtomTypeName_);

  }

  NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    

    //try exact match first
    NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
    if (nbiType) {
      return nbiType;
    } else {
      //if no exact match found, try wild card match
      return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
    }

  }

  BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.find(keys);
  }

  BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
                                         const std::string &at3){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.find(keys);
  }

  TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
                                               const std::string &at3, const std::string &at4){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);   
    return torsionTypeCont_.find(keys);
  }

  NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ 
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return nonBondedInteractionTypeCont_.find(keys);
  }


  bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
    std::vector<std::string> keys;
    keys.push_back(at);
    return atomTypeCont_.add(keys, atomType);
  }

  bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return bondTypeCont_.add(keys, bondType);

  }

  bool ForceField::addBendType(const std::string &at1, const std::string &at2,
                               const std::string &at3, BendType* bendType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    return bendTypeCont_.add(keys, bendType);
  }

  bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
                                  const std::string &at3, const std::string &at4, TorsionType* torsionType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    keys.push_back(at3);    
    keys.push_back(at4);    
    return torsionTypeCont_.add(keys, torsionType);
  }

  bool ForceField::addNonBondedInteractionType(const std::string &at1, const std::string &at2, NonBondedInteractionType* nbiType) {
    std::vector<std::string> keys;
    keys.push_back(at1);
    keys.push_back(at2);    
    return nonBondedInteractionTypeCont_.add(keys, nbiType);

  }

  RealType ForceField::getRcutFromAtomType(AtomType* at) {
    /**@todo */
    GenericData* data;
    RealType rcut = 0.0;

    if (at->isLennardJones()) {
      data = at->getPropertyByName("LennardJones");
      if (data != NULL) {
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);

        if (ljData != NULL) {
          LJParam ljParam = ljData->getData();

          //by default use 2.5*sigma as cutoff radius
          rcut = 2.5 * ljParam.sigma;
                
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to LJParam\n");
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();          
        }            
      } else {
        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
    }

    return rcut;    
  }


  ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
    std::string forceFieldFilename(filename);
    ifstrstream* ffStream = new ifstrstream();
    
    //try to open the force filed file in current directory first    
    ffStream->open(forceFieldFilename.c_str());
    if(!ffStream->is_open()){

      forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
      ffStream->open( forceFieldFilename.c_str() );

      //if current directory does not contain the force field file,
      //try to open it in the path        
      if(!ffStream->is_open()){

        sprintf( painCave.errMsg,
                 "Error opening the force field parameter file:\n"
                 "\t%s\n"
                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
                 "variable?\n",
                 forceFieldFilename.c_str() );
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    }  

    return ffStream;

  }

  void ForceField::setFortranForceOptions(){
    ForceOptions theseFortranOptions;
    forceFieldOptions_.makeFortranOptions(theseFortranOptions);
    setfForceOptions(&theseFortranOptions);
  }
} //end namespace oopse
Revision:	3153
Committed:	Fri Jul 6 18:15:03 2007 UTC (17 years ago) by chuckv
File size:	9497 byte(s)
Log Message:	Changes to allow for non-bonded interactions.
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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. 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	gezelter	2204	/**
43			* @file ForceField.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49	gezelter	1930
50	gezelter	1711	#include "UseTheForce/ForceField.hpp"
51	gezelter	1930	#include "utils/simError.h"
52	tim	2172	#include "UseTheForce/DarkSide/atype_interface.h"
53	chuckv	2520	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	gezelter	2722	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	gezelter	1930	namespace oopse {
56	gezelter	1711
57	gezelter	2204	ForceField::ForceField() {
58	gezelter	1930	char* tempPath;
59			tempPath = getenv("FORCE_PARAM_PATH");
60	gezelter	1711
61	gezelter	1930	if (tempPath == NULL) {
62	gezelter	2204	//convert a macro from compiler to a string in c++
63			STR_DEFINE(ffPath_, FRC_PATH );
64	gezelter	1930	} else {
65	gezelter	2204	ffPath_ = tempPath;
66	gezelter	1930	}
67	gezelter	2204	}
68	gezelter	1711
69	tim	2172
70	gezelter	2204	ForceField::~ForceField() {
71	tim	2172	deleteAtypes();
72	gezelter	2722	deleteSwitch();
73	gezelter	2204	}
74	tim	2172
75	gezelter	2204	AtomType* ForceField::getAtomType(const std::string &at) {
76	gezelter	1930	std::vector<std::string> keys;
77			keys.push_back(at);
78			return atomTypeCont_.find(keys);
79	gezelter	2204	}
80	gezelter	1711
81	gezelter	2204	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
82	gezelter	1930	std::vector<std::string> keys;
83			keys.push_back(at1);
84			keys.push_back(at2);
85	gezelter	1711
86	gezelter	1930	//try exact match first
87			BondType* bondType = bondTypeCont_.find(keys);
88			if (bondType) {
89	gezelter	2204	return bondType;
90	gezelter	1930	} else {
91	gezelter	2204	//if no exact match found, try wild card match
92			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
93	gezelter	1930	}
94	gezelter	1711
95	gezelter	2204	}
96	gezelter	1711
97	gezelter	2204	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
98			const std::string &at3) {
99	gezelter	1930	std::vector<std::string> keys;
100			keys.push_back(at1);
101			keys.push_back(at2);
102			keys.push_back(at3);
103	gezelter	1711
104	gezelter	1930	//try exact match first
105			BendType* bendType = bendTypeCont_.find(keys);
106			if (bendType) {
107	gezelter	2204	return bendType;
108	gezelter	1930	} else {
109	gezelter	2204	//if no exact match found, try wild card match
110			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
111	gezelter	1930	}
112	gezelter	2204	}
113	gezelter	1711
114	gezelter	2204	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
115			const std::string &at3, const std::string &at4) {
116	gezelter	1930	std::vector<std::string> keys;
117			keys.push_back(at1);
118			keys.push_back(at2);
119			keys.push_back(at3);
120			keys.push_back(at4);
121	gezelter	1711
122	gezelter	1930	TorsionType* torsionType = torsionTypeCont_.find(keys);
123			if (torsionType) {
124	gezelter	2204	return torsionType;
125	gezelter	1930	} else {
126	gezelter	2204	//if no exact match found, try wild card match
127			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
128	gezelter	1930	}
129	gezelter	1711
130	gezelter	1930	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
131	gezelter	1711
132	gezelter	2204	}
133	gezelter	1711
134	chuckv	3153	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
135			std::vector<std::string> keys;
136			keys.push_back(at1);
137			keys.push_back(at2);
138
139			//try exact match first
140			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
141			if (nbiType) {
142			return nbiType;
143			} else {
144			//if no exact match found, try wild card match
145			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
146			}
147
148			}
149
150	gezelter	2204	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
151	gezelter	1930	std::vector<std::string> keys;
152			keys.push_back(at1);
153			keys.push_back(at2);
154			return bondTypeCont_.find(keys);
155	gezelter	2204	}
156	gezelter	1711
157	gezelter	2204	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
158			const std::string &at3){
159	gezelter	1930	std::vector<std::string> keys;
160			keys.push_back(at1);
161			keys.push_back(at2);
162			keys.push_back(at3);
163			return bendTypeCont_.find(keys);
164	gezelter	2204	}
165	gezelter	1711
166	gezelter	2204	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
167			const std::string &at3, const std::string &at4){
168	gezelter	1930	std::vector<std::string> keys;
169			keys.push_back(at1);
170			keys.push_back(at2);
171			keys.push_back(at3);
172			keys.push_back(at4);
173			return torsionTypeCont_.find(keys);
174	gezelter	2204	}
175	chuckv	3153
176			NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
177			std::vector<std::string> keys;
178			keys.push_back(at1);
179			keys.push_back(at2);
180			return nonBondedInteractionTypeCont_.find(keys);
181			}
182
183
184	gezelter	2204	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
185	gezelter	1930	std::vector<std::string> keys;
186			keys.push_back(at);
187			return atomTypeCont_.add(keys, atomType);
188	gezelter	2204	}
189	gezelter	1711
190	gezelter	2204	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
191	gezelter	1930	std::vector<std::string> keys;
192			keys.push_back(at1);
193			keys.push_back(at2);
194			return bondTypeCont_.add(keys, bondType);
195	gezelter	1711
196	gezelter	2204	}
197	gezelter	1711
198	gezelter	2204	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
199			const std::string &at3, BendType* bendType) {
200	gezelter	1930	std::vector<std::string> keys;
201			keys.push_back(at1);
202			keys.push_back(at2);
203			keys.push_back(at3);
204			return bendTypeCont_.add(keys, bendType);
205	gezelter	2204	}
206	gezelter	1711
207	gezelter	2204	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
208			const std::string &at3, const std::string &at4, TorsionType* torsionType) {
209	gezelter	1930	std::vector<std::string> keys;
210			keys.push_back(at1);
211			keys.push_back(at2);
212			keys.push_back(at3);
213			keys.push_back(at4);
214			return torsionTypeCont_.add(keys, torsionType);
215	gezelter	2204	}
216	gezelter	1711
217	chuckv	3153	bool ForceField::addNonBondedInteractionType(const std::string &at1, const std::string &at2, NonBondedInteractionType* nbiType) {
218			std::vector<std::string> keys;
219			keys.push_back(at1);
220			keys.push_back(at2);
221			return nonBondedInteractionTypeCont_.add(keys, nbiType);
222
223			}
224
225	tim	2759	RealType ForceField::getRcutFromAtomType(AtomType* at) {
226	gezelter	1930	/*@todo /
227			GenericData* data;
228	tim	2759	RealType rcut = 0.0;
229	gezelter	1711
230	gezelter	1930	if (at->isLennardJones()) {
231	gezelter	2204	data = at->getPropertyByName("LennardJones");
232			if (data != NULL) {
233			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
234	gezelter	1711
235	gezelter	2204	if (ljData != NULL) {
236			LJParam ljParam = ljData->getData();
237	gezelter	1711
238	gezelter	2204	//by default use 2.5*sigma as cutoff radius
239			rcut = 2.5 * ljParam.sigma;
240	gezelter	1930
241	gezelter	2204	} else {
242			sprintf( painCave.errMsg,
243			"Can not cast GenericData to LJParam\n");
244			painCave.severity = OOPSE_ERROR;
245			painCave.isFatal = 1;
246			simError();
247			}
248			} else {
249			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
250			painCave.severity = OOPSE_ERROR;
251			painCave.isFatal = 1;
252			simError();
253			}
254	gezelter	1930	}
255	gezelter	1711
256	gezelter	1930	return rcut;
257	gezelter	2204	}
258	gezelter	1711
259	gezelter	1930
260	gezelter	2204	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
261	gezelter	1930	std::string forceFieldFilename(filename);
262			ifstrstream* ffStream = new ifstrstream();
263
264			//try to open the force filed file in current directory first
265			ffStream->open(forceFieldFilename.c_str());
266			if(!ffStream->is_open()){
267
268	gezelter	2204	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
269			ffStream->open( forceFieldFilename.c_str() );
270	gezelter	1930
271	gezelter	2204	//if current directory does not contain the force field file,
272			//try to open it in the path
273			if(!ffStream->is_open()){
274	gezelter	1930
275	gezelter	2204	sprintf( painCave.errMsg,
276			"Error opening the force field parameter file:\n"
277			"\t%s\n"
278			"\tHave you tried setting the FORCE_PARAM_PATH environment "
279			"variable?\n",
280			forceFieldFilename.c_str() );
281			painCave.severity = OOPSE_ERROR;
282			painCave.isFatal = 1;
283			simError();
284			}
285	gezelter	1930	}
286
287			return ffStream;
288
289	gezelter	2204	}
290	gezelter	1930
291	chuckv	2520	void ForceField::setFortranForceOptions(){
292			ForceOptions theseFortranOptions;
293			forceFieldOptions_.makeFortranOptions(theseFortranOptions);
294			setfForceOptions(&theseFortranOptions);
295			}
296	gezelter	1930	} //end namespace oopse