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root/OpenMD/trunk/src/brains/ForceField.cpp

Comparing:
trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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		/**
#	Line 52 | Line 52
52		#include "utils/simError.h"
53		#include "utils/Tuple.hpp"
54		#include "UseTheForce/DarkSide/atype_interface.h"
55	<	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	<	namespace oopse {
55	>	namespace OpenMD {
56
57		ForceField::ForceField() {
58	+
59		char* tempPath;
60		tempPath = getenv("FORCE_PARAM_PATH");
61	<
61	>
62		if (tempPath == NULL) {
63		//convert a macro from compiler to a string in c++
64		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 71 | Line 70 | namespace oopse {
70
71		ForceField::~ForceField() {
72		deleteAtypes();
74	–	deleteSwitch();
73		}
74
75		AtomType* ForceField::getAtomType(const std::string &at) {
#	Line 133 | Line 131 | namespace oopse {
131		ii++;
132		}
133
136	–	// sort the foundBonds by the score:
134
135	<	std::sort(foundBonds.begin(), foundBonds.end());
136	<
137	<	int bestScore = foundBonds[0].first;
138	<	std::vector<std::string> theKeys = foundBonds[0].second;
139	<
140	<	std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";
141	<	BondType* bestType = bondTypeCont_.find(theKeys);
142	<	if (bestType)
143	<	return bestType;
144	<	else {
145	<	//if no exact match found, try wild card match
146	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
135	>	if (foundBonds.size() > 0) {
136	>	// sort the foundBonds by the score:
137	>	std::sort(foundBonds.begin(), foundBonds.end());
138	>
139	>	int bestScore = foundBonds[0].first;
140	>	std::vector<std::string> theKeys = foundBonds[0].second;
141	>
142	>	BondType* bestType = bondTypeCont_.find(theKeys);
143	>
144	>	return bestType;
145	>	} else {
146	>	//if no exact match found, try wild card match
147	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
148		}
149		}
150		}
#	Line 220 | Line 218 | namespace oopse {
218		jj++;
219		}
220
221	<	std::sort(foundBends.begin(), foundBends.end());
222	<
223	<	int jscore = foundBends[0].first;
224	<	int ikscore = foundBends[0].second;
225	<	std::vector<std::string> theKeys = foundBends[0].third;
226	<
227	<	std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";
228	<
229	<	BendType* bestType = bendTypeCont_.find(theKeys);
232	<	if (bestType)
233	<	return bestType;
234	<	else {
235	<
221	>	if (foundBends.size() > 0) {
222	>	std::sort(foundBends.begin(), foundBends.end());
223	>	int jscore = foundBends[0].first;
224	>	int ikscore = foundBends[0].second;
225	>	std::vector<std::string> theKeys = foundBends[0].third;
226	>
227	>	BendType* bestType = bendTypeCont_.find(theKeys);
228	>	return bestType;
229	>	} else {
230		//if no exact match found, try wild card match
231		return bendTypeCont_.find(keys, wildCardAtomTypeName_);
232		}
233		}
234		}
235
242	–
236		TorsionType* ForceField::getTorsionType(const std::string &at1,
237		const std::string &at2,
238		const std::string &at3,
#	Line 327 | Line 320 | namespace oopse {
320		jj++;
321		}
322
323	<	std::sort(foundTorsions.begin(), foundTorsions.end());
324	<
325	<	int jkscore = foundTorsions[0].first;
326	<	int ilscore = foundTorsions[0].second;
327	<	std::vector<std::string> theKeys = foundTorsions[0].third;
328	<
329	<	std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
330	<
338	<
339	<	TorsionType* bestType = torsionTypeCont_.find(theKeys);
340	<	if (bestType) {
341	<	return bestType;
323	>	if (foundTorsions.size() > 0) {
324	>	std::sort(foundTorsions.begin(), foundTorsions.end());
325	>	int jkscore = foundTorsions[0].first;
326	>	int ilscore = foundTorsions[0].second;
327	>	std::vector<std::string> theKeys = foundTorsions[0].third;
328	>
329	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
330	>	return bestType;
331		} else {
332		//if no exact match found, try wild card match
333		return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 357 | Line 346 | namespace oopse {
346		keys.push_back(at4);
347
348		//try exact match first
349	<	InversionType* inversionType = inversionTypeCont_.find(keys);
349	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
350		if (inversionType) {
351		return inversionType;
352		} else {
#	Line 419 | Line 408 | namespace oopse {
408		myKeys.push_back((*k)->getName());
409		myKeys.push_back((*l)->getName());
410
411	<	InversionType* inversionType = inversionTypeCont_.find(myKeys);
411	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
412		if (inversionType) {
413		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
414		}
#	Line 431 | Line 420 | namespace oopse {
420		}
421		jj++;
422		}
423	<
424	<	std::sort(foundInversions.begin(), foundInversions.end());
425	<
426	<	int iscore = foundInversions[0].first;
427	<	int jklscore = foundInversions[0].second;
428	<	std::vector<std::string> theKeys = foundInversions[0].third;
429	<
430	<	std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
431	<
443	<
444	<	InversionType* bestType = inversionTypeCont_.find(theKeys);
445	<	if (bestType) {
446	<	return bestType;
423	>
424	>	if (foundInversions.size() > 0) {
425	>	std::sort(foundInversions.begin(), foundInversions.end());
426	>	int iscore = foundInversions[0].first;
427	>	int jklscore = foundInversions[0].second;
428	>	std::vector<std::string> theKeys = foundInversions[0].third;
429	>
430	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
431	>	return bestType;
432		} else {
433		//if no exact match found, try wild card match
434		return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 522 | Line 507 | namespace oopse {
507		return atomTypeCont_.add(keys, atomType);
508		}
509
510	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
511	+	std::vector<std::string> keys;
512	+	keys.push_back(at);
513	+	return atomTypeCont_.replace(keys, atomType);
514	+	}
515	+
516		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
517		BondType* bondType) {
518		std::vector<std::string> keys;
#	Line 593 | Line 584 | namespace oopse {
584		} else {
585		sprintf( painCave.errMsg,
586		"Can not cast GenericData to LJParam\n");
587	<	painCave.severity = OOPSE_ERROR;
587	>	painCave.severity = OPENMD_ERROR;
588		painCave.isFatal = 1;
589		simError();
590		}
591		} else {
592		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
593	<	painCave.severity = OOPSE_ERROR;
593	>	painCave.severity = OPENMD_ERROR;
594		painCave.isFatal = 1;
595		simError();
596		}
#	Line 629 | Line 620 | namespace oopse {
620		"\tHave you tried setting the FORCE_PARAM_PATH environment "
621		"variable?\n",
622		forceFieldFilename.c_str() );
623	<	painCave.severity = OOPSE_ERROR;
623	>	painCave.severity = OPENMD_ERROR;
624		painCave.isFatal = 1;
625		simError();
626		}
#	Line 637 | Line 628 | namespace oopse {
628		return ffStream;
629		}
630
631	<	void ForceField::setFortranForceOptions(){
641	<	ForceOptions theseFortranOptions;
642	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
643	<	setfForceOptions(&theseFortranOptions);
644	<	}
645	<	} //end namespace oopse
631	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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