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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 1629 by gezelter, Wed Sep 14 21:15:17 2011 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 51 | Line 51
51		#include "UseTheForce/ForceField.hpp"
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 {
54	>	namespace OpenMD {
55
56		ForceField::ForceField() {
57	+
58		char* tempPath;
59		tempPath = getenv("FORCE_PARAM_PATH");
60	<
60	>
61		if (tempPath == NULL) {
62		//convert a macro from compiler to a string in c++
63		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 68 | Line 66 | namespace oopse {
66		}
67		}
68
69	<
70	<	ForceField::~ForceField() {
71	<	deleteAtypes();
72	<	deleteSwitch();
73	<	}
74	<
69	>	/**
70	>	* getAtomType by string
71	>	*
72	>	* finds the requested atom type in this force field using the string
73	>	* name of the atom type.
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	+	/**
82	+	* getAtomType by ident
83	+	*
84	+	* finds the requested atom type in this force field using the
85	+	* integer ident instead of the string name of the atom type.
86	+	*/
87	+	AtomType* ForceField::getAtomType(int ident) {
88	+	std::string at = atypeIdentToName.find(ident)->second;
89	+	return getAtomType(at);
90	+	}
91	+
92		BondType* ForceField::getBondType(const std::string &at1,
93		const std::string &at2) {
94		std::vector<std::string> keys;
#	Line 133 | Line 142 | namespace oopse {
142		ii++;
143		}
144
136	–	// sort the foundBonds by the score:
145
146	<	std::sort(foundBonds.begin(), foundBonds.end());
147	<
148	<	int bestScore = foundBonds[0].first;
149	<	std::vector<std::string> theKeys = foundBonds[0].second;
150	<
151	<	std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";
152	<	BondType* bestType = bondTypeCont_.find(theKeys);
153	<	if (bestType)
154	<	return bestType;
155	<	else {
156	<	//if no exact match found, try wild card match
157	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
146	>	if (foundBonds.size() > 0) {
147	>	// sort the foundBonds by the score:
148	>	std::sort(foundBonds.begin(), foundBonds.end());
149	>
150	>	int bestScore = foundBonds[0].first;
151	>	std::vector<std::string> theKeys = foundBonds[0].second;
152	>
153	>	BondType* bestType = bondTypeCont_.find(theKeys);
154	>
155	>	return bestType;
156	>	} else {
157	>	//if no exact match found, try wild card match
158	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
159		}
160		}
161		}
#	Line 220 | Line 229 | namespace oopse {
229		jj++;
230		}
231
232	<	std::sort(foundBends.begin(), foundBends.end());
233	<
234	<	int jscore = foundBends[0].first;
235	<	int ikscore = foundBends[0].second;
236	<	std::vector<std::string> theKeys = foundBends[0].third;
237	<
238	<	std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";
239	<
240	<	BendType* bestType = bendTypeCont_.find(theKeys);
232	<	if (bestType)
233	<	return bestType;
234	<	else {
235	<
232	>	if (foundBends.size() > 0) {
233	>	std::sort(foundBends.begin(), foundBends.end());
234	>	int jscore = foundBends[0].first;
235	>	int ikscore = foundBends[0].second;
236	>	std::vector<std::string> theKeys = foundBends[0].third;
237	>
238	>	BendType* bestType = bendTypeCont_.find(theKeys);
239	>	return bestType;
240	>	} else {
241		//if no exact match found, try wild card match
242		return bendTypeCont_.find(keys, wildCardAtomTypeName_);
243		}
244		}
245		}
246
242	–
247		TorsionType* ForceField::getTorsionType(const std::string &at1,
248		const std::string &at2,
249		const std::string &at3,
#	Line 327 | Line 331 | namespace oopse {
331		jj++;
332		}
333
334	<	std::sort(foundTorsions.begin(), foundTorsions.end());
335	<
336	<	int jkscore = foundTorsions[0].first;
337	<	int ilscore = foundTorsions[0].second;
338	<	std::vector<std::string> theKeys = foundTorsions[0].third;
339	<
340	<	std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
341	<
338	<
339	<	TorsionType* bestType = torsionTypeCont_.find(theKeys);
340	<	if (bestType) {
341	<	return bestType;
334	>	if (foundTorsions.size() > 0) {
335	>	std::sort(foundTorsions.begin(), foundTorsions.end());
336	>	int jkscore = foundTorsions[0].first;
337	>	int ilscore = foundTorsions[0].second;
338	>	std::vector<std::string> theKeys = foundTorsions[0].third;
339	>
340	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
341	>	return bestType;
342		} else {
343		//if no exact match found, try wild card match
344		return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 357 | Line 357 | namespace oopse {
357		keys.push_back(at4);
358
359		//try exact match first
360	<	InversionType* inversionType = inversionTypeCont_.find(keys);
360	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
361		if (inversionType) {
362		return inversionType;
363		} else {
#	Line 419 | Line 419 | namespace oopse {
419		myKeys.push_back((*k)->getName());
420		myKeys.push_back((*l)->getName());
421
422	<	InversionType* inversionType = inversionTypeCont_.find(myKeys);
422	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
423		if (inversionType) {
424		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
425		}
#	Line 431 | Line 431 | namespace oopse {
431		}
432		jj++;
433		}
434	<
435	<	std::sort(foundInversions.begin(), foundInversions.end());
436	<
437	<	int iscore = foundInversions[0].first;
438	<	int jklscore = foundInversions[0].second;
439	<	std::vector<std::string> theKeys = foundInversions[0].third;
440	<
441	<	std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
442	<
443	<
444	<	InversionType* bestType = inversionTypeCont_.find(theKeys);
445	<	if (bestType) {
446	<	return bestType;
434	>
435	>	if (foundInversions.size() > 0) {
436	>	std::sort(foundInversions.begin(), foundInversions.end());
437	>	int iscore = foundInversions[0].first;
438	>	int jklscore = foundInversions[0].second;
439	>	std::vector<std::string> theKeys = foundInversions[0].third;
440	>
441	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
442	>	return bestType;
443		} else {
444		//if no exact match found, try wild card match
445		return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 452 | Line 448 | namespace oopse {
448		}
449
450		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
451	+
452		std::vector<std::string> keys;
453		keys.push_back(at1);
454		keys.push_back(at2);
#	Line 461 | Line 458 | namespace oopse {
458		if (nbiType) {
459		return nbiType;
460		} else {
461	<	//if no exact match found, try wild card match
462	<	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
463	<	}
461	>	AtomType* atype1;
462	>	AtomType* atype2;
463	>	std::vector<std::string> at1key;
464	>	at1key.push_back(at1);
465	>	atype1 = atomTypeCont_.find(at1key);
466	>
467	>	std::vector<std::string> at2key;
468	>	at2key.push_back(at2);
469	>	atype2 = atomTypeCont_.find(at2key);
470	>
471	>	// query atom types for their chains of responsibility
472	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
473	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
474	>
475	>	std::vector<AtomType*>::iterator i;
476	>	std::vector<AtomType*>::iterator j;
477	>
478	>	int ii = 0;
479	>	int jj = 0;
480	>	int nbiTypeScore;
481	>
482	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
483	>
484	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
485	>	jj = 0;
486	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
487	>
488	>	nbiTypeScore = ii + jj;
489	>
490	>	std::vector<std::string> myKeys;
491	>	myKeys.push_back((*i)->getName());
492	>	myKeys.push_back((*j)->getName());
493	>
494	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
495	>	if (nbiType) {
496	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
497	>	}
498	>	jj++;
499	>	}
500	>	ii++;
501	>	}
502	>
503	>
504	>	if (foundNBI.size() > 0) {
505	>	// sort the foundNBI by the score:
506	>	std::sort(foundNBI.begin(), foundNBI.end());
507	>
508	>	int bestScore = foundNBI[0].first;
509	>	std::vector<std::string> theKeys = foundNBI[0].second;
510	>
511	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
512	>	return bestType;
513	>	} else {
514	>	//if no exact match found, try wild card match
515	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
516	>	}
517	>	}
518		}
519
520		BondType* ForceField::getExactBondType(const std::string &at1,
#	Line 519 | Line 570 | namespace oopse {
570		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
571		std::vector<std::string> keys;
572		keys.push_back(at);
573	+	atypeIdentToName[atomType->getIdent()] = at;
574		return atomTypeCont_.add(keys, atomType);
575		}
576
577	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
578	+	std::vector<std::string> keys;
579	+	keys.push_back(at);
580	+	atypeIdentToName[atomType->getIdent()] = at;
581	+	return atomTypeCont_.replace(keys, atomType);
582	+	}
583	+
584		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
585		BondType* bondType) {
586		std::vector<std::string> keys;
#	Line 593 | Line 652 | namespace oopse {
652		} else {
653		sprintf( painCave.errMsg,
654		"Can not cast GenericData to LJParam\n");
655	<	painCave.severity = OOPSE_ERROR;
655	>	painCave.severity = OPENMD_ERROR;
656		painCave.isFatal = 1;
657		simError();
658		}
659		} else {
660		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
661	<	painCave.severity = OOPSE_ERROR;
661	>	painCave.severity = OPENMD_ERROR;
662		painCave.isFatal = 1;
663		simError();
664		}
#	Line 629 | Line 688 | namespace oopse {
688		"\tHave you tried setting the FORCE_PARAM_PATH environment "
689		"variable?\n",
690		forceFieldFilename.c_str() );
691	<	painCave.severity = OOPSE_ERROR;
691	>	painCave.severity = OPENMD_ERROR;
692		painCave.isFatal = 1;
693		simError();
694		}
#	Line 637 | Line 696 | namespace oopse {
696		return ffStream;
697		}
698
699	<	void ForceField::setFortranForceOptions(){
641	<	ForceOptions theseFortranOptions;
642	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
643	<	setfForceOptions(&theseFortranOptions);
644	<	}
645	<	} //end namespace oopse
699	>	} //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 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

#	Line 0 | Line 1
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