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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 51 | Line 52
52		#include "UseTheForce/ForceField.hpp"
53		#include "utils/simError.h"
54		#include "utils/Tuple.hpp"
55	<	#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 68 | Line 67 | namespace oopse {
67		}
68		}
69
70	<
71	<	ForceField::~ForceField() {
72	<	deleteAtypes();
73	<	deleteSwitch();
74	<	}
75	<
70	>	/**
71	>	* getAtomType by string
72	>	*
73	>	* finds the requested atom type in this force field using the string
74	>	* name of the atom type.
75	>	*/
76		AtomType* ForceField::getAtomType(const std::string &at) {
77		std::vector<std::string> keys;
78		keys.push_back(at);
79		return atomTypeCont_.find(keys);
80		}
81
82	+	/**
83	+	* getAtomType by ident
84	+	*
85	+	* finds the requested atom type in this force field using the
86	+	* integer ident instead of the string name of the atom type.
87	+	*/
88	+	AtomType* ForceField::getAtomType(int ident) {
89	+	std::string at = atypeIdentToName.find(ident)->second;
90	+	return getAtomType(at);
91	+	}
92	+
93		BondType* ForceField::getBondType(const std::string &at1,
94		const std::string &at2) {
95		std::vector<std::string> keys;
#	Line 133 | Line 143 | namespace oopse {
143		ii++;
144		}
145
136	–	// sort the foundBonds by the score:
146
147	<	std::sort(foundBonds.begin(), foundBonds.end());
148	<
149	<	int bestScore = foundBonds[0].first;
150	<	std::vector<std::string> theKeys = foundBonds[0].second;
151	<
152	<	std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1]  << "\t(score = "<< bestScore << ")\n";
153	<	BondType* bestType = bondTypeCont_.find(theKeys);
154	<	if (bestType)
155	<	return bestType;
156	<	else {
157	<	//if no exact match found, try wild card match
158	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
147	>	if (foundBonds.size() > 0) {
148	>	// sort the foundBonds by the score:
149	>	std::sort(foundBonds.begin(), foundBonds.end());
150	>
151	>	int bestScore = foundBonds[0].first;
152	>	std::vector<std::string> theKeys = foundBonds[0].second;
153	>
154	>	BondType* bestType = bondTypeCont_.find(theKeys);
155	>
156	>	return bestType;
157	>	} else {
158	>	//if no exact match found, try wild card match
159	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
160		}
161		}
162		}
#	Line 220 | Line 230 | namespace oopse {
230		jj++;
231		}
232
233	<	std::sort(foundBends.begin(), foundBends.end());
234	<
235	<	int jscore = foundBends[0].first;
236	<	int ikscore = foundBends[0].second;
237	<	std::vector<std::string> theKeys = foundBends[0].third;
238	<
239	<	std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n";
240	<
241	<	BendType* bestType = bendTypeCont_.find(theKeys);
232	<	if (bestType)
233	<	return bestType;
234	<	else {
235	<
233	>	if (foundBends.size() > 0) {
234	>	std::sort(foundBends.begin(), foundBends.end());
235	>	int jscore = foundBends[0].first;
236	>	int ikscore = foundBends[0].second;
237	>	std::vector<std::string> theKeys = foundBends[0].third;
238	>
239	>	BendType* bestType = bendTypeCont_.find(theKeys);
240	>	return bestType;
241	>	} else {
242		//if no exact match found, try wild card match
243		return bendTypeCont_.find(keys, wildCardAtomTypeName_);
244		}
245		}
246		}
247
242	–
248		TorsionType* ForceField::getTorsionType(const std::string &at1,
249		const std::string &at2,
250		const std::string &at3,
#	Line 327 | Line 332 | namespace oopse {
332		jj++;
333		}
334
335	<	std::sort(foundTorsions.begin(), foundTorsions.end());
336	<
337	<	int jkscore = foundTorsions[0].first;
338	<	int ilscore = foundTorsions[0].second;
339	<	std::vector<std::string> theKeys = foundTorsions[0].third;
340	<
341	<	std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n";
342	<
338	<
339	<	TorsionType* bestType = torsionTypeCont_.find(theKeys);
340	<	if (bestType) {
341	<	return bestType;
335	>	if (foundTorsions.size() > 0) {
336	>	std::sort(foundTorsions.begin(), foundTorsions.end());
337	>	int jkscore = foundTorsions[0].first;
338	>	int ilscore = foundTorsions[0].second;
339	>	std::vector<std::string> theKeys = foundTorsions[0].third;
340	>
341	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
342	>	return bestType;
343		} else {
344		//if no exact match found, try wild card match
345		return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 357 | Line 358 | namespace oopse {
358		keys.push_back(at4);
359
360		//try exact match first
361	<	InversionType* inversionType = inversionTypeCont_.find(keys);
361	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
362		if (inversionType) {
363		return inversionType;
364		} else {
#	Line 419 | Line 420 | namespace oopse {
420		myKeys.push_back((*k)->getName());
421		myKeys.push_back((*l)->getName());
422
423	<	InversionType* inversionType = inversionTypeCont_.find(myKeys);
423	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
424		if (inversionType) {
425		foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
426		}
#	Line 431 | Line 432 | namespace oopse {
432		}
433		jj++;
434		}
435	<
436	<	std::sort(foundInversions.begin(), foundInversions.end());
437	<
438	<	int iscore = foundInversions[0].first;
439	<	int jklscore = foundInversions[0].second;
440	<	std::vector<std::string> theKeys = foundInversions[0].third;
441	<
442	<	std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1]  << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n";
443	<
443	<
444	<	InversionType* bestType = inversionTypeCont_.find(theKeys);
445	<	if (bestType) {
446	<	return bestType;
435	>
436	>	if (foundInversions.size() > 0) {
437	>	std::sort(foundInversions.begin(), foundInversions.end());
438	>	int iscore = foundInversions[0].first;
439	>	int jklscore = foundInversions[0].second;
440	>	std::vector<std::string> theKeys = foundInversions[0].third;
441	>
442	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
443	>	return bestType;
444		} else {
445		//if no exact match found, try wild card match
446		return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
#	Line 452 | Line 449 | namespace oopse {
449		}
450
451		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
452	+
453		std::vector<std::string> keys;
454		keys.push_back(at1);
455		keys.push_back(at2);
#	Line 461 | Line 459 | namespace oopse {
459		if (nbiType) {
460		return nbiType;
461		} else {
462	<	//if no exact match found, try wild card match
463	<	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
464	<	}
462	>	AtomType* atype1;
463	>	AtomType* atype2;
464	>	std::vector<std::string> at1key;
465	>	at1key.push_back(at1);
466	>	atype1 = atomTypeCont_.find(at1key);
467	>
468	>	std::vector<std::string> at2key;
469	>	at2key.push_back(at2);
470	>	atype2 = atomTypeCont_.find(at2key);
471	>
472	>	// query atom types for their chains of responsibility
473	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
474	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
475	>
476	>	std::vector<AtomType*>::iterator i;
477	>	std::vector<AtomType*>::iterator j;
478	>
479	>	int ii = 0;
480	>	int jj = 0;
481	>	int nbiTypeScore;
482	>
483	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
484	>
485	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
486	>	jj = 0;
487	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
488	>
489	>	nbiTypeScore = ii + jj;
490	>
491	>	std::vector<std::string> myKeys;
492	>	myKeys.push_back((*i)->getName());
493	>	myKeys.push_back((*j)->getName());
494	>
495	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
496	>	if (nbiType) {
497	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
498	>	}
499	>	jj++;
500	>	}
501	>	ii++;
502	>	}
503	>
504	>
505	>	if (foundNBI.size() > 0) {
506	>	// sort the foundNBI by the score:
507	>	std::sort(foundNBI.begin(), foundNBI.end());
508	>
509	>	int bestScore = foundNBI[0].first;
510	>	std::vector<std::string> theKeys = foundNBI[0].second;
511	>
512	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
513	>	return bestType;
514	>	} else {
515	>	//if no exact match found, try wild card match
516	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
517	>	}
518	>	}
519		}
520
521		BondType* ForceField::getExactBondType(const std::string &at1,
#	Line 519 | Line 571 | namespace oopse {
571		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
572		std::vector<std::string> keys;
573		keys.push_back(at);
574	+	atypeIdentToName[atomType->getIdent()] = at;
575		return atomTypeCont_.add(keys, atomType);
576		}
577
578	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
579	+	std::vector<std::string> keys;
580	+	keys.push_back(at);
581	+	atypeIdentToName[atomType->getIdent()] = at;
582	+	return atomTypeCont_.replace(keys, atomType);
583	+	}
584	+
585		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
586		BondType* bondType) {
587		std::vector<std::string> keys;
#	Line 593 | Line 653 | namespace oopse {
653		} else {
654		sprintf( painCave.errMsg,
655		"Can not cast GenericData to LJParam\n");
656	<	painCave.severity = OOPSE_ERROR;
656	>	painCave.severity = OPENMD_ERROR;
657		painCave.isFatal = 1;
658		simError();
659		}
660		} else {
661		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662	<	painCave.severity = OOPSE_ERROR;
662	>	painCave.severity = OPENMD_ERROR;
663		painCave.isFatal = 1;
664		simError();
665		}
#	Line 629 | Line 689 | namespace oopse {
689		"\tHave you tried setting the FORCE_PARAM_PATH environment "
690		"variable?\n",
691		forceFieldFilename.c_str() );
692	<	painCave.severity = OOPSE_ERROR;
692	>	painCave.severity = OPENMD_ERROR;
693		painCave.isFatal = 1;
694		simError();
695		}
#	Line 637 | Line 697 | namespace oopse {
697		return ffStream;
698		}
699
700	<	void ForceField::setFortranForceOptions(){
641	<	ForceOptions theseFortranOptions;
642	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
643	<	setfForceOptions(&theseFortranOptions);
644	<	}
645	<	} //end namespace oopse
700	>	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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