src/brains/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, 10 months ago) by cpuglis
Original Path:	*trunk/src/UseTheForce/ForceField.cpp*
File size:	9648 byte(s)
Log Message:	Many fixes for Charmm-type torsions.
#	Content
1	/*
2	* 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	/**
43	* @file ForceField.cpp
44	* @author tlin
45	* @date 11/04/2004
46	* @time 22:51am
47	* @version 1.0
48	*/
49
50	#include "UseTheForce/ForceField.hpp"
51	#include "utils/simError.h"
52	#include "UseTheForce/DarkSide/atype_interface.h"
53	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	namespace oopse {
56
57	ForceField::ForceField() {
58	char* tempPath;
59	tempPath = getenv("FORCE_PARAM_PATH");
60
61	if (tempPath == NULL) {
62	//convert a macro from compiler to a string in c++
63	STR_DEFINE(ffPath_, FRC_PATH );
64	} else {
65	ffPath_ = tempPath;
66	}
67	}
68
69
70	ForceField::~ForceField() {
71	deleteAtypes();
72	deleteSwitch();
73	}
74
75	AtomType* ForceField::getAtomType(const std::string &at) {
76	std::vector<std::string> keys;
77	keys.push_back(at);
78	return atomTypeCont_.find(keys);
79	}
80
81	BondType* ForceField::getBondType(const std::string &at1,
82	const std::string &at2) {
83	std::vector<std::string> keys;
84	keys.push_back(at1);
85	keys.push_back(at2);
86
87	//try exact match first
88	BondType* bondType = bondTypeCont_.find(keys);
89	if (bondType) {
90	return bondType;
91	} else {
92	//if no exact match found, try wild card match
93	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
94	}
95	}
96
97	BendType* ForceField::getBendType(const std::string &at1,
98	const std::string &at2,
99	const std::string &at3) {
100	std::vector<std::string> keys;
101	keys.push_back(at1);
102	keys.push_back(at2);
103	keys.push_back(at3);
104
105	//try exact match first
106	BendType* bendType = bendTypeCont_.find(keys);
107	if (bendType) {
108	return bendType;
109	} else {
110	//if no exact match found, try wild card match
111	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
112	}
113	}
114
115	TorsionType* ForceField::getTorsionType(const std::string &at1,
116	const std::string &at2,
117	const std::string &at3,
118	const std::string &at4) {
119	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
125	TorsionType* torsionType = torsionTypeCont_.find(keys);
126	if (torsionType) {
127	return torsionType;
128	} else {
129	//if no exact match found, try wild card match
130	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
131	}
132
133	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
134	}
135
136	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
141	//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	}
149	}
150
151	BondType* ForceField::getExactBondType(const std::string &at1,
152	const std::string &at2){
153	std::vector<std::string> keys;
154	keys.push_back(at1);
155	keys.push_back(at2);
156	return bondTypeCont_.find(keys);
157	}
158
159	BendType* ForceField::getExactBendType(const std::string &at1,
160	const std::string &at2,
161	const std::string &at3){
162	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	}
168
169	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
170	const std::string &at2,
171	const std::string &at3,
172	const std::string &at4){
173	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	}
180
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	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
190	std::vector<std::string> keys;
191	keys.push_back(at);
192	return atomTypeCont_.add(keys, atomType);
193	}
194
195	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
196	BondType* bondType) {
197	std::vector<std::string> keys;
198	keys.push_back(at1);
199	keys.push_back(at2);
200	return bondTypeCont_.add(keys, bondType);
201	}
202
203	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
204	const std::string &at3, BendType* bendType) {
205	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	}
211
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	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	}
224
225	bool ForceField::addNonBondedInteractionType(const std::string &at1,
226	const std::string &at2,
227	NonBondedInteractionType* nbiType) {
228	std::vector<std::string> keys;
229	keys.push_back(at1);
230	keys.push_back(at2);
231	return nonBondedInteractionTypeCont_.add(keys, nbiType);
232	}
233
234	RealType ForceField::getRcutFromAtomType(AtomType* at) {
235	/*@todo /
236	GenericData* data;
237	RealType rcut = 0.0;
238
239	if (at->isLennardJones()) {
240	data = at->getPropertyByName("LennardJones");
241	if (data != NULL) {
242	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
243
244	if (ljData != NULL) {
245	LJParam ljParam = ljData->getData();
246
247	//by default use 2.5*sigma as cutoff radius
248	rcut = 2.5 * ljParam.sigma;
249
250	} 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	}
264	return rcut;
265	}
266
267
268	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
269	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	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
277	ffStream->open( forceFieldFilename.c_str() );
278
279	//if current directory does not contain the force field file,
280	//try to open it in the path
281	if(!ffStream->is_open()){
282
283	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	}
294	return ffStream;
295	}
296
297	void ForceField::setFortranForceOptions(){
298	ForceOptions theseFortranOptions;
299	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
300	setfForceOptions(&theseFortranOptions);
301	}
302	} //end namespace oopse