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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1905 by gezelter, Wed Jul 17 20:39:58 2013 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, 234107 (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		/**
44		* @file ForceField.cpp
45		* @author tlin
46		* @date 11/04/2004
46	–	* @time 22:51am
47		* @version 1.0
48		*/
49
50		#include <algorithm>
51	<	#include "UseTheForce/ForceField.hpp"
51	>	#include "brains/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 {
53
54	<	ForceField::ForceField() {
54	>	#include "io/OptionSectionParser.hpp"
55	>	#include "io/BaseAtomTypesSectionParser.hpp"
56	>	#include "io/DirectionalAtomTypesSectionParser.hpp"
57	>	#include "io/AtomTypesSectionParser.hpp"
58	>	#include "io/BendTypesSectionParser.hpp"
59	>	#include "io/BondTypesSectionParser.hpp"
60	>	#include "io/ChargeAtomTypesSectionParser.hpp"
61	>	#include "io/EAMAtomTypesSectionParser.hpp"
62	>	#include "io/FluctuatingChargeAtomTypesSectionParser.hpp"
63	>	#include "io/GayBerneAtomTypesSectionParser.hpp"
64	>	#include "io/InversionTypesSectionParser.hpp"
65	>	#include "io/LennardJonesAtomTypesSectionParser.hpp"
66	>	#include "io/MultipoleAtomTypesSectionParser.hpp"
67	>	#include "io/NonBondedInteractionsSectionParser.hpp"
68	>	#include "io/PolarizableAtomTypesSectionParser.hpp"
69	>	#include "io/SCAtomTypesSectionParser.hpp"
70	>	#include "io/ShapeAtomTypesSectionParser.hpp"
71	>	#include "io/StickyAtomTypesSectionParser.hpp"
72	>	#include "io/StickyPowerAtomTypesSectionParser.hpp"
73	>	#include "io/TorsionTypesSectionParser.hpp"
74	>
75	>	#include "types/LennardJonesAdapter.hpp"
76	>	#include "types/EAMAdapter.hpp"
77	>	#include "types/SuttonChenAdapter.hpp"
78	>	#include "types/GayBerneAdapter.hpp"
79	>	#include "types/StickyAdapter.hpp"
80	>
81	>	namespace OpenMD {
82	>
83	>	ForceField::ForceField(std::string ffName): wildCardAtomTypeName_("X") {
84	>
85		char* tempPath;
86		tempPath = getenv("FORCE_PARAM_PATH");
87	<
87	>
88		if (tempPath == NULL) {
89		//convert a macro from compiler to a string in c++
90		STR_DEFINE(ffPath_, FRC_PATH );
91		} else {
92		ffPath_ = tempPath;
93		}
94	+
95	+	setForceFieldFileName(ffName + ".frc");
96	+
97	+	/**
98	+	* The order of adding section parsers is important.
99	+	*
100	+	* OptionSectionParser must come first to set options for other
101	+	* parsers
102	+	*
103	+	* DirectionalAtomTypesSectionParser should be added before
104	+	* AtomTypesSectionParser, and these two section parsers will
105	+	* actually create "real" AtomTypes (AtomTypesSectionParser will
106	+	* create AtomType and DirectionalAtomTypesSectionParser will
107	+	* create DirectionalAtomType, which is a subclass of AtomType and
108	+	* should come first).
109	+	*
110	+	* Other AtomTypes Section Parsers will not create the "real"
111	+	* AtomType, they only add and set some attributes of the AtomType
112	+	* (via the Adapters). Thus ordering of these is not important.
113	+	* AtomTypesSectionParser should be added before other atom type
114	+	*
115	+	* The order of BondTypesSectionParser, BendTypesSectionParser and
116	+	* TorsionTypesSectionParser, etc. are not important.
117	+	*/
118	+
119	+	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
120	+	spMan_.push_back(new BaseAtomTypesSectionParser());
121	+	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
122	+	spMan_.push_back(new AtomTypesSectionParser());
123	+
124	+	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
125	+	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
126	+	spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
127	+	spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_));
128	+	spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_));
129	+	spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
130	+	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
131	+	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
132	+	spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
133	+	spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
134	+	spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
135	+
136	+	spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
137	+	spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
138	+	spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
139	+	spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
140	+
141	+	spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
142		}
143
144	+	void ForceField::parse(const std::string& filename) {
145	+	ifstrstream* ffStream;
146
147	<	ForceField::~ForceField() {
148	<	deleteAtypes();
149	<	deleteSwitch();
147	>	ffStream = openForceFieldFile(filename);
148	>
149	>	spMan_.parse(*ffStream, *this);
150	>
151	>	ForceField::AtomTypeContainer::MapTypeIterator i;
152	>	AtomType* at;
153	>
154	>	for (at = atomTypeCont_.beginType(i); at != NULL;
155	>	at = atomTypeCont_.nextType(i)) {
156	>
157	>	// useBase sets the responsibilities, and these have to be done
158	>	// after the atomTypes and Base types have all been scanned:
159	>
160	>	std::vector<AtomType*> ayb = at->allYourBase();
161	>	if (ayb.size() > 1) {
162	>	for (int j = ayb.size()-1; j > 0; j--) {
163	>
164	>	ayb[j-1]->useBase(ayb[j]);
165	>
166	>	}
167	>	}
168	>	}
169	>
170	>	delete ffStream;
171		}
172
173	+	/**
174	+	* getAtomType by string
175	+	*
176	+	* finds the requested atom type in this force field using the string
177	+	* name of the atom type.
178	+	*/
179		AtomType* ForceField::getAtomType(const std::string &at) {
180		std::vector<std::string> keys;
181		keys.push_back(at);
182		return atomTypeCont_.find(keys);
183		}
184
185	+	/**
186	+	* getAtomType by ident
187	+	*
188	+	* finds the requested atom type in this force field using the
189	+	* integer ident instead of the string name of the atom type.
190	+	*/
191	+	AtomType* ForceField::getAtomType(int ident) {
192	+	std::string at = atypeIdentToName.find(ident)->second;
193	+	return getAtomType(at);
194	+	}
195	+
196		BondType* ForceField::getBondType(const std::string &at1,
197		const std::string &at2) {
198		std::vector<std::string> keys;
#	Line 114 | Line 227 | namespace oopse {
227
228		std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
229
230	<	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
230	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
231		jj = 0;
232	<	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
232	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
233
234		bondTypeScore = ii + jj;
235
#	Line 134 | Line 247 | namespace oopse {
247		}
248
249
250	<	if (foundBonds.size() > 0) {
250	>	if (!foundBonds.empty()) {
251		// sort the foundBonds by the score:
252		std::sort(foundBonds.begin(), foundBonds.end());
253
141	–	int bestScore = foundBonds[0].first;
254		std::vector<std::string> theKeys = foundBonds[0].second;
255
256		BondType* bestType = bondTypeCont_.find(theKeys);
#	Line 196 | Line 308 | namespace oopse {
308
309		std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
310
311	<	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
311	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
312		ii = 0;
313	<	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
313	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
314		kk = 0;
315	<	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
315	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
316
317		IKscore = ii + kk;
318
#	Line 220 | Line 332 | namespace oopse {
332		jj++;
333		}
334
335	<	if (foundBends.size() > 0) {
335	>	if (!foundBends.empty()) {
336		std::sort(foundBends.begin(), foundBends.end());
225	–	int jscore = foundBends[0].first;
226	–	int ikscore = foundBends[0].second;
337		std::vector<std::string> theKeys = foundBends[0].third;
338
339		BendType* bestType = bendTypeCont_.find(theKeys);
#	Line 292 | Line 402 | namespace oopse {
402
403		std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
404
405	<	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
405	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
406		kk = 0;
407	<	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
407	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
408		ii = 0;
409	<	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
409	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
410		ll = 0;
411	<	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
411	>	for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
412
413		ILscore = ii + ll;
414		JKscore = jj + kk;
#	Line 322 | Line 432 | namespace oopse {
432		jj++;
433		}
434
435	<	if (foundTorsions.size() > 0) {
435	>	if (!foundTorsions.empty()) {
436		std::sort(foundTorsions.begin(), foundTorsions.end());
327	–	int jkscore = foundTorsions[0].first;
328	–	int ilscore = foundTorsions[0].second;
437		std::vector<std::string> theKeys = foundTorsions[0].third;
438
439		TorsionType* bestType = torsionTypeCont_.find(theKeys);
#	Line 393 | Line 501 | namespace oopse {
501
502		std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
503
504	<	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
504	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
505		kk = 0;
506	<	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
506	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
507		ii = 0;
508	<	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
508	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
509		ll = 0;
510	<	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
510	>	for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
511
512		Iscore = ii;
513		JKLscore = jj + kk + ll;
#	Line 423 | Line 531 | namespace oopse {
531		jj++;
532		}
533
534	<	if (foundInversions.size() > 0) {
534	>	if (!foundInversions.empty()) {
535		std::sort(foundInversions.begin(), foundInversions.end());
428	–	int iscore = foundInversions[0].first;
429	–	int jklscore = foundInversions[0].second;
536		std::vector<std::string> theKeys = foundInversions[0].third;
537
538		InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
#	Line 439 | Line 545 | namespace oopse {
545		}
546
547		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
548	+
549		std::vector<std::string> keys;
550		keys.push_back(at1);
551		keys.push_back(at2);
#	Line 448 | Line 555 | namespace oopse {
555		if (nbiType) {
556		return nbiType;
557		} else {
558	<	//if no exact match found, try wild card match
559	<	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
560	<	}
558	>	AtomType* atype1;
559	>	AtomType* atype2;
560	>	std::vector<std::string> at1key;
561	>	at1key.push_back(at1);
562	>	atype1 = atomTypeCont_.find(at1key);
563	>
564	>	std::vector<std::string> at2key;
565	>	at2key.push_back(at2);
566	>	atype2 = atomTypeCont_.find(at2key);
567	>
568	>	// query atom types for their chains of responsibility
569	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
570	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
571	>
572	>	std::vector<AtomType*>::iterator i;
573	>	std::vector<AtomType*>::iterator j;
574	>
575	>	int ii = 0;
576	>	int jj = 0;
577	>	int nbiTypeScore;
578	>
579	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
580	>
581	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
582	>	jj = 0;
583	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
584	>
585	>	nbiTypeScore = ii + jj;
586	>
587	>	std::vector<std::string> myKeys;
588	>	myKeys.push_back((*i)->getName());
589	>	myKeys.push_back((*j)->getName());
590	>
591	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
592	>	if (nbiType) {
593	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
594	>	}
595	>	jj++;
596	>	}
597	>	ii++;
598	>	}
599	>
600	>
601	>	if (!foundNBI.empty()) {
602	>	// sort the foundNBI by the score:
603	>	std::sort(foundNBI.begin(), foundNBI.end());
604	>	std::vector<std::string> theKeys = foundNBI[0].second;
605	>
606	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
607	>	return bestType;
608	>	} else {
609	>	//if no exact match found, try wild card match
610	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
611	>	}
612	>	}
613		}
614
615		BondType* ForceField::getExactBondType(const std::string &at1,
#	Line 506 | Line 665 | namespace oopse {
665		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
666		std::vector<std::string> keys;
667		keys.push_back(at);
668	+	atypeIdentToName[atomType->getIdent()] = at;
669		return atomTypeCont_.add(keys, atomType);
670		}
671
672		bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
673		std::vector<std::string> keys;
674		keys.push_back(at);
675	+	atypeIdentToName[atomType->getIdent()] = at;
676		return atomTypeCont_.replace(keys, atomType);
677		}
678
#	Line 568 | Line 729 | namespace oopse {
729		}
730
731		RealType ForceField::getRcutFromAtomType(AtomType* at) {
732	<	/**@todo */
572	<	GenericData* data;
573	<	RealType rcut = 0.0;
732	>	RealType rcut(0.0);
733
734	<	if (at->isLennardJones()) {
735	<	data = at->getPropertyByName("LennardJones");
736	<	if (data != NULL) {
578	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
579	<
580	<	if (ljData != NULL) {
581	<	LJParam ljParam = ljData->getData();
582	<
583	<	//by default use 2.5*sigma as cutoff radius
584	<	rcut = 2.5 * ljParam.sigma;
585	<
586	<	} else {
587	<	sprintf( painCave.errMsg,
588	<	"Can not cast GenericData to LJParam\n");
589	<	painCave.severity = OOPSE_ERROR;
590	<	painCave.isFatal = 1;
591	<	simError();
592	<	}
593	<	} else {
594	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
595	<	painCave.severity = OOPSE_ERROR;
596	<	painCave.isFatal = 1;
597	<	simError();
598	<	}
734	>	LennardJonesAdapter lja = LennardJonesAdapter(at);
735	>	if (lja.isLennardJones()) {
736	>	rcut = 2.5 * lja.getSigma();
737		}
738	+	EAMAdapter ea = EAMAdapter(at);
739	+	if (ea.isEAM()) {
740	+	rcut = max(rcut, ea.getRcut());
741	+	}
742	+	SuttonChenAdapter sca = SuttonChenAdapter(at);
743	+	if (sca.isSuttonChen()) {
744	+	rcut = max(rcut, 2.0 * sca.getAlpha());
745	+	}
746	+	GayBerneAdapter gba = GayBerneAdapter(at);
747	+	if (gba.isGayBerne()) {
748	+	rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
749	+	}
750	+	StickyAdapter sa = StickyAdapter(at);
751	+	if (sa.isSticky()) {
752	+	rcut = max(rcut, max(sa.getRu(), sa.getRup()));
753	+	}
754	+
755		return rcut;
756		}
757
#	Line 622 | Line 777 | namespace oopse {
777		"\tHave you tried setting the FORCE_PARAM_PATH environment "
778		"variable?\n",
779		forceFieldFilename.c_str() );
780	<	painCave.severity = OOPSE_ERROR;
780	>	painCave.severity = OPENMD_ERROR;
781		painCave.isFatal = 1;
782		simError();
783		}
#	Line 630 | Line 785 | namespace oopse {
785		return ffStream;
786		}
787
788	<	void ForceField::setFortranForceOptions(){
634	<	ForceOptions theseFortranOptions;
635	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
636	<	setfForceOptions(&theseFortranOptions);
637	<	}
638	<	} //end namespace oopse
788	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1303 by cli2, Mon Oct 13 21:35:22 2008 UTC vs.
trunk/src/brains/ForceField.cpp (property svn:keywords), Revision 1905 by gezelter, Wed Jul 17 20:39:58 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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