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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 1465 by chuckv, Fri Jul 9 23:08:25 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	+
61		char* tempPath;
62		tempPath = getenv("FORCE_PARAM_PATH");
63	<
63	>
64		if (tempPath == NULL) {
65		//convert a macro from compiler to a string in c++
66		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 133 | Line 134 | namespace oopse {
134		ii++;
135		}
136
136	–	// sort the foundBonds by the score:
137
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	<	std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";
144	<	BondType* bestType = bondTypeCont_.find(theKeys);
145	<	if (bestType)
146	<	return bestType;
147	<	else {
148	<	//if no exact match found, try wild card match
149	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
138	>	if (foundBonds.size() > 0) {
139	>	// sort the foundBonds by the score:
140	>	std::sort(foundBonds.begin(), foundBonds.end());
141	>
142	>	int bestScore = foundBonds[0].first;
143	>	std::vector<std::string> theKeys = foundBonds[0].second;
144	>
145	>	BondType* bestType = bondTypeCont_.find(theKeys);
146	>
147	>	return bestType;
148	>	} else {
149	>	//if no exact match found, try wild card match
150	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
151		}
152		}
153		}
#	Line 220 | Line 221 | namespace oopse {
221		jj++;
222		}
223
224	<	std::sort(foundBends.begin(), foundBends.end());
225	<
226	<	int jscore = foundBends[0].first;
227	<	int ikscore = foundBends[0].second;
228	<	std::vector<std::string> theKeys = foundBends[0].third;
229	<
230	<	std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";
231	<
232	<	BendType* bestType = bendTypeCont_.find(theKeys);
232	<	if (bestType)
233	<	return bestType;
234	<	else {
235	<
224	>	if (foundBends.size() > 0) {
225	>	std::sort(foundBends.begin(), foundBends.end());
226	>	int jscore = foundBends[0].first;
227	>	int ikscore = foundBends[0].second;
228	>	std::vector<std::string> theKeys = foundBends[0].third;
229	>
230	>	BendType* bestType = bendTypeCont_.find(theKeys);
231	>	return bestType;
232	>	} else {
233		//if no exact match found, try wild card match
234		return bendTypeCont_.find(keys, wildCardAtomTypeName_);
235		}
236		}
237		}
238
242	–
239		TorsionType* ForceField::getTorsionType(const std::string &at1,
240		const std::string &at2,
241		const std::string &at3,
#	Line 327 | Line 323 | namespace oopse {
323		jj++;
324		}
325
326	<	std::sort(foundTorsions.begin(), foundTorsions.end());
327	<
328	<	int jkscore = foundTorsions[0].first;
329	<	int ilscore = foundTorsions[0].second;
330	<	std::vector<std::string> theKeys = foundTorsions[0].third;
331	<
332	<	std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
333	<
338	<
339	<	TorsionType* bestType = torsionTypeCont_.find(theKeys);
340	<	if (bestType) {
341	<	return bestType;
326	>	if (foundTorsions.size() > 0) {
327	>	std::sort(foundTorsions.begin(), foundTorsions.end());
328	>	int jkscore = foundTorsions[0].first;
329	>	int ilscore = foundTorsions[0].second;
330	>	std::vector<std::string> theKeys = foundTorsions[0].third;
331	>
332	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
333	>	return bestType;
334		} else {
335		//if no exact match found, try wild card match
336		return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 357 | Line 349 | namespace oopse {
349		keys.push_back(at4);
350
351		//try exact match first
352	<	InversionType* inversionType = inversionTypeCont_.find(keys);
352	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
353		if (inversionType) {
354		return inversionType;
355		} else {
#	Line 419 | Line 411 | namespace oopse {
411		myKeys.push_back((*k)->getName());
412		myKeys.push_back((*l)->getName());
413
414	<	InversionType* inversionType = inversionTypeCont_.find(myKeys);
414	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
415		if (inversionType) {
416		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
417		}
#	Line 431 | Line 423 | namespace oopse {
423		}
424		jj++;
425		}
426	<
427	<	std::sort(foundInversions.begin(), foundInversions.end());
428	<
429	<	int iscore = foundInversions[0].first;
430	<	int jklscore = foundInversions[0].second;
431	<	std::vector<std::string> theKeys = foundInversions[0].third;
432	<
433	<	std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
434	<
443	<
444	<	InversionType* bestType = inversionTypeCont_.find(theKeys);
445	<	if (bestType) {
446	<	return bestType;
426	>
427	>	if (foundInversions.size() > 0) {
428	>	std::sort(foundInversions.begin(), foundInversions.end());
429	>	int iscore = foundInversions[0].first;
430	>	int jklscore = foundInversions[0].second;
431	>	std::vector<std::string> theKeys = foundInversions[0].third;
432	>
433	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
434	>	return bestType;
435		} else {
436		//if no exact match found, try wild card match
437		return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 522 | Line 510 | namespace oopse {
510		return atomTypeCont_.add(keys, atomType);
511		}
512
513	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
514	+	std::vector<std::string> keys;
515	+	keys.push_back(at);
516	+	return atomTypeCont_.replace(keys, atomType);
517	+	}
518	+
519		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
520		BondType* bondType) {
521		std::vector<std::string> keys;
#	Line 593 | Line 587 | namespace oopse {
587		} else {
588		sprintf( painCave.errMsg,
589		"Can not cast GenericData to LJParam\n");
590	<	painCave.severity = OOPSE_ERROR;
590	>	painCave.severity = OPENMD_ERROR;
591		painCave.isFatal = 1;
592		simError();
593		}
594		} else {
595		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
596	<	painCave.severity = OOPSE_ERROR;
596	>	painCave.severity = OPENMD_ERROR;
597		painCave.isFatal = 1;
598		simError();
599		}
#	Line 629 | Line 623 | namespace oopse {
623		"\tHave you tried setting the FORCE_PARAM_PATH environment "
624		"variable?\n",
625		forceFieldFilename.c_str() );
626	<	painCave.severity = OOPSE_ERROR;
626	>	painCave.severity = OPENMD_ERROR;
627		painCave.isFatal = 1;
628		simError();
629		}
#	Line 642 | Line 636 | namespace oopse {
636		forceFieldOptions_.makeFortranOptions(theseFortranOptions);
637		setfForceOptions(&theseFortranOptions);
638		}
639	<	} //end namespace oopse
639	>	} //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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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