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"
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();
  }

  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_);

  }

  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);
  }
  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);
  }

  double ForceField::getRcutFromAtomType(AtomType* at) {
    /**@todo */
    GenericData* data;
    double 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:	2520
Committed:	Wed Dec 28 21:42:43 2005 UTC (18 years, 6 months ago) by chuckv
File size:	8343 byte(s)
Log Message:	Force options passed to fortran.
#	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	1930	namespace oopse {
55	gezelter	1711
56	gezelter	2204	ForceField::ForceField() {
57	gezelter	1930	char* tempPath;
58			tempPath = getenv("FORCE_PARAM_PATH");
59	gezelter	1711
60	gezelter	1930	if (tempPath == NULL) {
61	gezelter	2204	//convert a macro from compiler to a string in c++
62			STR_DEFINE(ffPath_, FRC_PATH );
63	gezelter	1930	} else {
64	gezelter	2204	ffPath_ = tempPath;
65	gezelter	1930	}
66	gezelter	2204	}
67	gezelter	1711
68	tim	2172
69	gezelter	2204	ForceField::~ForceField() {
70	tim	2172	deleteAtypes();
71	gezelter	2204	}
72	tim	2172
73	gezelter	2204	AtomType* ForceField::getAtomType(const std::string &at) {
74	gezelter	1930	std::vector<std::string> keys;
75			keys.push_back(at);
76			return atomTypeCont_.find(keys);
77	gezelter	2204	}
78	gezelter	1711
79	gezelter	2204	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
80	gezelter	1930	std::vector<std::string> keys;
81			keys.push_back(at1);
82			keys.push_back(at2);
83	gezelter	1711
84	gezelter	1930	//try exact match first
85			BondType* bondType = bondTypeCont_.find(keys);
86			if (bondType) {
87	gezelter	2204	return bondType;
88	gezelter	1930	} else {
89	gezelter	2204	//if no exact match found, try wild card match
90			return bondTypeCont_.find(keys, wildCardAtomTypeName_);
91	gezelter	1930	}
92	gezelter	1711
93	gezelter	2204	}
94	gezelter	1711
95	gezelter	2204	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
96			const std::string &at3) {
97	gezelter	1930	std::vector<std::string> keys;
98			keys.push_back(at1);
99			keys.push_back(at2);
100			keys.push_back(at3);
101	gezelter	1711
102	gezelter	1930	//try exact match first
103			BendType* bendType = bendTypeCont_.find(keys);
104			if (bendType) {
105	gezelter	2204	return bendType;
106	gezelter	1930	} else {
107	gezelter	2204	//if no exact match found, try wild card match
108			return bendTypeCont_.find(keys, wildCardAtomTypeName_);
109	gezelter	1930	}
110	gezelter	2204	}
111	gezelter	1711
112	gezelter	2204	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
113			const std::string &at3, const std::string &at4) {
114	gezelter	1930	std::vector<std::string> keys;
115			keys.push_back(at1);
116			keys.push_back(at2);
117			keys.push_back(at3);
118			keys.push_back(at4);
119	gezelter	1711
120	gezelter	1930	TorsionType* torsionType = torsionTypeCont_.find(keys);
121			if (torsionType) {
122	gezelter	2204	return torsionType;
123	gezelter	1930	} else {
124	gezelter	2204	//if no exact match found, try wild card match
125			return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
126	gezelter	1930	}
127	gezelter	1711
128	gezelter	1930	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
129	gezelter	1711
130	gezelter	2204	}
131	gezelter	1711
132	gezelter	2204	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
133	gezelter	1930	std::vector<std::string> keys;
134			keys.push_back(at1);
135			keys.push_back(at2);
136			return bondTypeCont_.find(keys);
137	gezelter	2204	}
138	gezelter	1711
139	gezelter	2204	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
140			const std::string &at3){
141	gezelter	1930	std::vector<std::string> keys;
142			keys.push_back(at1);
143			keys.push_back(at2);
144			keys.push_back(at3);
145			return bendTypeCont_.find(keys);
146	gezelter	2204	}
147	gezelter	1711
148	gezelter	2204	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
149			const std::string &at3, const std::string &at4){
150	gezelter	1930	std::vector<std::string> keys;
151			keys.push_back(at1);
152			keys.push_back(at2);
153			keys.push_back(at3);
154			keys.push_back(at4);
155			return torsionTypeCont_.find(keys);
156	gezelter	2204	}
157			bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
158	gezelter	1930	std::vector<std::string> keys;
159			keys.push_back(at);
160			return atomTypeCont_.add(keys, atomType);
161	gezelter	2204	}
162	gezelter	1711
163	gezelter	2204	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
164	gezelter	1930	std::vector<std::string> keys;
165			keys.push_back(at1);
166			keys.push_back(at2);
167			return bondTypeCont_.add(keys, bondType);
168	gezelter	1711
169	gezelter	2204	}
170	gezelter	1711
171	gezelter	2204	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
172			const std::string &at3, BendType* bendType) {
173	gezelter	1930	std::vector<std::string> keys;
174			keys.push_back(at1);
175			keys.push_back(at2);
176			keys.push_back(at3);
177			return bendTypeCont_.add(keys, bendType);
178	gezelter	2204	}
179	gezelter	1711
180	gezelter	2204	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
181			const std::string &at3, const std::string &at4, TorsionType* torsionType) {
182	gezelter	1930	std::vector<std::string> keys;
183			keys.push_back(at1);
184			keys.push_back(at2);
185			keys.push_back(at3);
186			keys.push_back(at4);
187			return torsionTypeCont_.add(keys, torsionType);
188	gezelter	2204	}
189	gezelter	1711
190	gezelter	2204	double ForceField::getRcutFromAtomType(AtomType* at) {
191	gezelter	1930	/*@todo /
192			GenericData* data;
193			double rcut = 0.0;
194	gezelter	1711
195	gezelter	1930	if (at->isLennardJones()) {
196	gezelter	2204	data = at->getPropertyByName("LennardJones");
197			if (data != NULL) {
198			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
199	gezelter	1711
200	gezelter	2204	if (ljData != NULL) {
201			LJParam ljParam = ljData->getData();
202	gezelter	1711
203	gezelter	2204	//by default use 2.5*sigma as cutoff radius
204			rcut = 2.5 * ljParam.sigma;
205	gezelter	1930
206	gezelter	2204	} else {
207			sprintf( painCave.errMsg,
208			"Can not cast GenericData to LJParam\n");
209			painCave.severity = OOPSE_ERROR;
210			painCave.isFatal = 1;
211			simError();
212			}
213			} else {
214			sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
215			painCave.severity = OOPSE_ERROR;
216			painCave.isFatal = 1;
217			simError();
218			}
219	gezelter	1930	}
220	gezelter	1711
221	gezelter	1930	return rcut;
222	gezelter	2204	}
223	gezelter	1711
224	gezelter	1930
225	gezelter	2204	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
226	gezelter	1930	std::string forceFieldFilename(filename);
227			ifstrstream* ffStream = new ifstrstream();
228
229			//try to open the force filed file in current directory first
230			ffStream->open(forceFieldFilename.c_str());
231			if(!ffStream->is_open()){
232
233	gezelter	2204	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
234			ffStream->open( forceFieldFilename.c_str() );
235	gezelter	1930
236	gezelter	2204	//if current directory does not contain the force field file,
237			//try to open it in the path
238			if(!ffStream->is_open()){
239	gezelter	1930
240	gezelter	2204	sprintf( painCave.errMsg,
241			"Error opening the force field parameter file:\n"
242			"\t%s\n"
243			"\tHave you tried setting the FORCE_PARAM_PATH environment "
244			"variable?\n",
245			forceFieldFilename.c_str() );
246			painCave.severity = OOPSE_ERROR;
247			painCave.isFatal = 1;
248			simError();
249			}
250	gezelter	1930	}
251
252			return ffStream;
253
254	gezelter	2204	}
255	gezelter	1930
256	chuckv	2520	void ForceField::setFortranForceOptions(){
257			ForceOptions theseFortranOptions;
258			forceFieldOptions_.makeFortranOptions(theseFortranOptions);
259			setfForceOptions(&theseFortranOptions);
260			}
261	gezelter	1930	} //end namespace oopse