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:	1195
Committed:	Thu Dec 6 20:04:02 2007 UTC (17 years, 4 months ago) by cpuglis
File size:	9648 byte(s)
Log Message:	Many fixes for Charmm-type torsions.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	507	/**
43			* @file ForceField.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 22:51am
47			* @version 1.0
48			*/
49	gezelter	246
50	gezelter	206	#include "UseTheForce/ForceField.hpp"
51	gezelter	246	#include "utils/simError.h"
52	tim	475	#include "UseTheForce/DarkSide/atype_interface.h"
53	chuckv	821	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	gezelter	939	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	gezelter	246	namespace oopse {
56	gezelter	206
57	gezelter	507	ForceField::ForceField() {
58	gezelter	246	char* tempPath;
59			tempPath = getenv("FORCE_PARAM_PATH");
60	gezelter	206
61	gezelter	246	if (tempPath == NULL) {
62	gezelter	507	//convert a macro from compiler to a string in c++
63			STR_DEFINE(ffPath_, FRC_PATH );
64	gezelter	246	} else {
65	gezelter	507	ffPath_ = tempPath;
66	gezelter	246	}
67	gezelter	507	}
68	gezelter	206
69	tim	475
70	gezelter	507	ForceField::~ForceField() {
71	tim	475	deleteAtypes();
72	gezelter	939	deleteSwitch();
73	gezelter	507	}
74	tim	475
75	gezelter	507	AtomType* ForceField::getAtomType(const std::string &at) {
76	gezelter	246	std::vector<std::string> keys;
77			keys.push_back(at);
78			return atomTypeCont_.find(keys);
79	gezelter	507	}
80	gezelter	206
81	cpuglis	1195	BondType* ForceField::getBondType(const std::string &at1,
82			const std::string &at2) {
83	gezelter	246	std::vector<std::string> keys;
84			keys.push_back(at1);
85			keys.push_back(at2);
86	gezelter	206
87	gezelter	246	//try exact match first
88			BondType* bondType = bondTypeCont_.find(keys);
89			if (bondType) {
90	gezelter	507	return bondType;
91	gezelter	246	} else {
92	gezelter	507	//if no exact match found, try wild card match
93			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
94	gezelter	246	}
95	gezelter	507	}
96	gezelter	206
97	cpuglis	1195	BendType* ForceField::getBendType(const std::string &at1,
98			const std::string &at2,
99	gezelter	507	const std::string &at3) {
100	gezelter	246	std::vector<std::string> keys;
101			keys.push_back(at1);
102			keys.push_back(at2);
103			keys.push_back(at3);
104	gezelter	206
105	gezelter	246	//try exact match first
106			BendType* bendType = bendTypeCont_.find(keys);
107			if (bendType) {
108	gezelter	507	return bendType;
109	gezelter	246	} else {
110	gezelter	507	//if no exact match found, try wild card match
111			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
112	gezelter	246	}
113	gezelter	507	}
114	gezelter	206
115	cpuglis	1195	TorsionType* ForceField::getTorsionType(const std::string &at1,
116			const std::string &at2,
117			const std::string &at3,
118			const std::string &at4) {
119	gezelter	246	std::vector<std::string> keys;
120			keys.push_back(at1);
121			keys.push_back(at2);
122			keys.push_back(at3);
123			keys.push_back(at4);
124	gezelter	206
125	gezelter	246	TorsionType* torsionType = torsionTypeCont_.find(keys);
126			if (torsionType) {
127	gezelter	507	return torsionType;
128	gezelter	246	} else {
129	gezelter	507	//if no exact match found, try wild card match
130			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
131	gezelter	246	}
132	gezelter	206
133	gezelter	246	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
134	gezelter	507	}
135	gezelter	206
136	chuckv	1151	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
137			std::vector<std::string> keys;
138			keys.push_back(at1);
139			keys.push_back(at2);
140	cpuglis	1195
141	chuckv	1151	//try exact match first
142			NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
143			if (nbiType) {
144			return nbiType;
145			} else {
146			//if no exact match found, try wild card match
147			return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
148	cpuglis	1195	}
149	chuckv	1151	}
150	cpuglis	1195
151			BondType* ForceField::getExactBondType(const std::string &at1,
152			const std::string &at2){
153	gezelter	246	std::vector<std::string> keys;
154			keys.push_back(at1);
155			keys.push_back(at2);
156			return bondTypeCont_.find(keys);
157	gezelter	507	}
158	cpuglis	1195
159			BendType* ForceField::getExactBendType(const std::string &at1,
160			const std::string &at2,
161	gezelter	507	const std::string &at3){
162	gezelter	246	std::vector<std::string> keys;
163			keys.push_back(at1);
164			keys.push_back(at2);
165			keys.push_back(at3);
166			return bendTypeCont_.find(keys);
167	gezelter	507	}
168	cpuglis	1195
169			TorsionType* ForceField::getExactTorsionType(const std::string &at1,
170			const std::string &at2,
171			const std::string &at3,
172			const std::string &at4){
173	gezelter	246	std::vector<std::string> keys;
174			keys.push_back(at1);
175			keys.push_back(at2);
176			keys.push_back(at3);
177			keys.push_back(at4);
178			return torsionTypeCont_.find(keys);
179	gezelter	507	}
180	chuckv	1151
181			NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
182			std::vector<std::string> keys;
183			keys.push_back(at1);
184			keys.push_back(at2);
185			return nonBondedInteractionTypeCont_.find(keys);
186			}
187
188
189	gezelter	507	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
190	gezelter	246	std::vector<std::string> keys;
191			keys.push_back(at);
192			return atomTypeCont_.add(keys, atomType);
193	gezelter	507	}
194	gezelter	206
195	cpuglis	1195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
196			BondType* bondType) {
197	gezelter	246	std::vector<std::string> keys;
198			keys.push_back(at1);
199			keys.push_back(at2);
200	cpuglis	1195	return bondTypeCont_.add(keys, bondType);
201	gezelter	507	}
202	cpuglis	1195
203	gezelter	507	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
204			const std::string &at3, BendType* bendType) {
205	gezelter	246	std::vector<std::string> keys;
206			keys.push_back(at1);
207			keys.push_back(at2);
208			keys.push_back(at3);
209			return bendTypeCont_.add(keys, bendType);
210	gezelter	507	}
211	cpuglis	1195
212			bool ForceField::addTorsionType(const std::string &at1,
213			const std::string &at2,
214			const std::string &at3,
215			const std::string &at4,
216			TorsionType* torsionType) {
217	gezelter	246	std::vector<std::string> keys;
218			keys.push_back(at1);
219			keys.push_back(at2);
220			keys.push_back(at3);
221			keys.push_back(at4);
222			return torsionTypeCont_.add(keys, torsionType);
223	gezelter	507	}
224	gezelter	206
225	cpuglis	1195	bool ForceField::addNonBondedInteractionType(const std::string &at1,
226			const std::string &at2,
227			NonBondedInteractionType* nbiType) {
228	chuckv	1151	std::vector<std::string> keys;
229			keys.push_back(at1);
230			keys.push_back(at2);
231			return nonBondedInteractionTypeCont_.add(keys, nbiType);
232			}
233	cpuglis	1195
234	tim	963	RealType ForceField::getRcutFromAtomType(AtomType* at) {
235	gezelter	246	/*@todo /
236			GenericData* data;
237	tim	963	RealType rcut = 0.0;
238	cpuglis	1195
239	gezelter	246	if (at->isLennardJones()) {
240	gezelter	507	data = at->getPropertyByName("LennardJones");
241			if (data != NULL) {
242			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
243	cpuglis	1195
244	gezelter	507	if (ljData != NULL) {
245			LJParam ljParam = ljData->getData();
246	cpuglis	1195
247	gezelter	507	//by default use 2.5*sigma as cutoff radius
248			rcut = 2.5 * ljParam.sigma;
249	cpuglis	1195
250	gezelter	507	} else {
251			sprintf( painCave.errMsg,
252			"Can not cast GenericData to LJParam\n");
253			painCave.severity = OOPSE_ERROR;
254			painCave.isFatal = 1;
255			simError();
256			}
257			} else {
258			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
259			painCave.severity = OOPSE_ERROR;
260			painCave.isFatal = 1;
261			simError();
262			}
263	gezelter	246	}
264			return rcut;
265	gezelter	507	}
266	cpuglis	1195
267	gezelter	206
268	gezelter	507	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
269	gezelter	246	std::string forceFieldFilename(filename);
270			ifstrstream* ffStream = new ifstrstream();
271
272			//try to open the force filed file in current directory first
273			ffStream->open(forceFieldFilename.c_str());
274			if(!ffStream->is_open()){
275
276	gezelter	507	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
277			ffStream->open( forceFieldFilename.c_str() );
278	gezelter	246
279	gezelter	507	//if current directory does not contain the force field file,
280			//try to open it in the path
281			if(!ffStream->is_open()){
282	gezelter	246
283	gezelter	507	sprintf( painCave.errMsg,
284			"Error opening the force field parameter file:\n"
285			"\t%s\n"
286			"\tHave you tried setting the FORCE_PARAM_PATH environment "
287			"variable?\n",
288			forceFieldFilename.c_str() );
289			painCave.severity = OOPSE_ERROR;
290			painCave.isFatal = 1;
291			simError();
292			}
293	gezelter	246	}
294			return ffStream;
295	gezelter	507	}
296	gezelter	246
297	chuckv	821	void ForceField::setFortranForceOptions(){
298			ForceOptions theseFortranOptions;
299			forceFieldOptions_.makeFortranOptions(theseFortranOptions);
300			setfForceOptions(&theseFortranOptions);
301			}
302	gezelter	246	} //end namespace oopse