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Comparing trunk/src/UseTheForce/ForceField.cpp (file contents):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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 54 | Line 54
54		#include "UseTheForce/DarkSide/atype_interface.h"
55		#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56		#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	<	namespace oopse {
57	>	namespace OpenMD {
58
59		ForceField::ForceField() {
60		char* tempPath;
61		tempPath = getenv("FORCE_PARAM_PATH");
62
63		if (tempPath == NULL) {
64	<	//convert a macro from compiler to a string in c++
65	<	STR_DEFINE(ffPath_, FRC_PATH );
64	>	ffPath_ = "ORNULL(FRC_PATH)";
65		} else {
66		ffPath_ = tempPath;
67		}
#	Line 133 | Line 132 | namespace oopse {
132		ii++;
133		}
134
136	–	// sort the foundBonds by the score:
135
136	<	std::sort(foundBonds.begin(), foundBonds.end());
137	<
138	<	int bestScore = foundBonds[0].first;
139	<	std::vector<std::string> theKeys = foundBonds[0].second;
140	<
141	<	std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";
142	<	BondType* bestType = bondTypeCont_.find(theKeys);
143	<	if (bestType)
144	<	return bestType;
145	<	else {
146	<	//if no exact match found, try wild card match
147	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
136	>	if (foundBonds.size() > 0) {
137	>	// sort the foundBonds by the score:
138	>	std::sort(foundBonds.begin(), foundBonds.end());
139	>
140	>	int bestScore = foundBonds[0].first;
141	>	std::vector<std::string> theKeys = foundBonds[0].second;
142	>
143	>	BondType* bestType = bondTypeCont_.find(theKeys);
144	>
145	>	return bestType;
146	>	} else {
147	>	//if no exact match found, try wild card match
148	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
149		}
150		}
151		}
#	Line 220 | Line 219 | namespace oopse {
219		jj++;
220		}
221
222	<	std::sort(foundBends.begin(), foundBends.end());
223	<
224	<	int jscore = foundBends[0].first;
225	<	int ikscore = foundBends[0].second;
226	<	std::vector<std::string> theKeys = foundBends[0].third;
227	<
228	<	std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";
229	<
230	<	BendType* bestType = bendTypeCont_.find(theKeys);
232	<	if (bestType)
233	<	return bestType;
234	<	else {
235	<
222	>	if (foundBends.size() > 0) {
223	>	std::sort(foundBends.begin(), foundBends.end());
224	>	int jscore = foundBends[0].first;
225	>	int ikscore = foundBends[0].second;
226	>	std::vector<std::string> theKeys = foundBends[0].third;
227	>
228	>	BendType* bestType = bendTypeCont_.find(theKeys);
229	>	return bestType;
230	>	} else {
231		//if no exact match found, try wild card match
232		return bendTypeCont_.find(keys, wildCardAtomTypeName_);
233		}
234		}
235		}
236
242	–
237		TorsionType* ForceField::getTorsionType(const std::string &at1,
238		const std::string &at2,
239		const std::string &at3,
#	Line 327 | Line 321 | namespace oopse {
321		jj++;
322		}
323
324	<	std::sort(foundTorsions.begin(), foundTorsions.end());
325	<
326	<	int jkscore = foundTorsions[0].first;
327	<	int ilscore = foundTorsions[0].second;
328	<	std::vector<std::string> theKeys = foundTorsions[0].third;
329	<
330	<	std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
331	<
338	<
339	<	TorsionType* bestType = torsionTypeCont_.find(theKeys);
340	<	if (bestType) {
341	<	return bestType;
324	>	if (foundTorsions.size() > 0) {
325	>	std::sort(foundTorsions.begin(), foundTorsions.end());
326	>	int jkscore = foundTorsions[0].first;
327	>	int ilscore = foundTorsions[0].second;
328	>	std::vector<std::string> theKeys = foundTorsions[0].third;
329	>
330	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
331	>	return bestType;
332		} else {
333		//if no exact match found, try wild card match
334		return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 357 | Line 347 | namespace oopse {
347		keys.push_back(at4);
348
349		//try exact match first
350	<	InversionType* inversionType = inversionTypeCont_.find(keys);
350	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
351		if (inversionType) {
352		return inversionType;
353		} else {
#	Line 419 | Line 409 | namespace oopse {
409		myKeys.push_back((*k)->getName());
410		myKeys.push_back((*l)->getName());
411
412	<	InversionType* inversionType = inversionTypeCont_.find(myKeys);
412	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
413		if (inversionType) {
414		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
415		}
#	Line 431 | Line 421 | namespace oopse {
421		}
422		jj++;
423		}
424	<
425	<	std::sort(foundInversions.begin(), foundInversions.end());
426	<
427	<	int iscore = foundInversions[0].first;
428	<	int jklscore = foundInversions[0].second;
429	<	std::vector<std::string> theKeys = foundInversions[0].third;
430	<
431	<	std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
432	<
443	<
444	<	InversionType* bestType = inversionTypeCont_.find(theKeys);
445	<	if (bestType) {
446	<	return bestType;
424	>
425	>	if (foundInversions.size() > 0) {
426	>	std::sort(foundInversions.begin(), foundInversions.end());
427	>	int iscore = foundInversions[0].first;
428	>	int jklscore = foundInversions[0].second;
429	>	std::vector<std::string> theKeys = foundInversions[0].third;
430	>
431	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
432	>	return bestType;
433		} else {
434		//if no exact match found, try wild card match
435		return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 522 | Line 508 | namespace oopse {
508		return atomTypeCont_.add(keys, atomType);
509		}
510
511	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
512	+	std::vector<std::string> keys;
513	+	keys.push_back(at);
514	+	return atomTypeCont_.replace(keys, atomType);
515	+	}
516	+
517		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
518		BondType* bondType) {
519		std::vector<std::string> keys;
#	Line 593 | Line 585 | namespace oopse {
585		} else {
586		sprintf( painCave.errMsg,
587		"Can not cast GenericData to LJParam\n");
588	<	painCave.severity = OOPSE_ERROR;
588	>	painCave.severity = OPENMD_ERROR;
589		painCave.isFatal = 1;
590		simError();
591		}
592		} else {
593		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
594	<	painCave.severity = OOPSE_ERROR;
594	>	painCave.severity = OPENMD_ERROR;
595		painCave.isFatal = 1;
596		simError();
597		}
#	Line 629 | Line 621 | namespace oopse {
621		"\tHave you tried setting the FORCE_PARAM_PATH environment "
622		"variable?\n",
623		forceFieldFilename.c_str() );
624	<	painCave.severity = OOPSE_ERROR;
624	>	painCave.severity = OPENMD_ERROR;
625		painCave.isFatal = 1;
626		simError();
627		}
#	Line 642 | Line 634 | namespace oopse {
634		forceFieldOptions_.makeFortranOptions(theseFortranOptions);
635		setfForceOptions(&theseFortranOptions);
636		}
637	<	} //end namespace oopse
637	>	} //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.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
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