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root/OpenMD/branches/development/src/brains/ForceField.cpp

Comparing:
trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
branches/development/src/brains/ForceField.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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	<	/**
44	<	* @file ForceField.cpp
45	<	* @author tlin
46	<	* @date 11/04/2004
47	<	* @time 22:51am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file ForceField.cpp
45	>	* @author tlin
46	>	* @date 11/04/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include "UseTheForce/ForceField.hpp"
50	>	#include <algorithm>
51	>	#include "brains/ForceField.hpp"
52		#include "utils/simError.h"
52	–	#include "UseTheForce/DarkSide/atype_interface.h"
53	–	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) {
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 );
89	>	//convert a macro from compiler to a string in c++
90	>	STR_DEFINE(ffPath_, FRC_PATH );
91		} else {
92	<	ffPath_ = tempPath;
92	>	ffPath_ = tempPath;
93		}
65	–	}
94
95	+	setForceFieldFileName(ffName + ".frc");
96
97	<	ForceField::~ForceField() {
98	<	deleteAtypes();
99	<	}
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	<	AtomType* ForceField::getAtomType(const std::string &at) {
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	>	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	<	}
183	>	}
184
185	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
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;
199		keys.push_back(at1);
200		keys.push_back(at2);
#	Line 83 | Line 202 | BondType* ForceField::getBondType(const std::string &a
202		//try exact match first
203		BondType* bondType = bondTypeCont_.find(keys);
204		if (bondType) {
205	<	return bondType;
205	>	return bondType;
206		} else {
207	<	//if no exact match found, try wild card match
208	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
209	<	}
207	>	AtomType* atype1;
208	>	AtomType* atype2;
209	>	std::vector<std::string> at1key;
210	>	at1key.push_back(at1);
211	>	atype1 = atomTypeCont_.find(at1key);
212	>
213	>	std::vector<std::string> at2key;
214	>	at2key.push_back(at2);
215	>	atype2 = atomTypeCont_.find(at2key);
216
217	<	}
217	>	// query atom types for their chains of responsibility
218	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
219	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
220
221	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
222	<	const std::string &at3) {
221	>	std::vector<AtomType*>::iterator i;
222	>	std::vector<AtomType*>::iterator j;
223	>
224	>	int ii = 0;
225	>	int jj = 0;
226	>	int bondTypeScore;
227	>
228	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
229	>
230	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
231	>	jj = 0;
232	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
233	>
234	>	bondTypeScore = ii + jj;
235	>
236	>	std::vector<std::string> myKeys;
237	>	myKeys.push_back((*i)->getName());
238	>	myKeys.push_back((*j)->getName());
239	>
240	>	BondType* bondType = bondTypeCont_.find(myKeys);
241	>	if (bondType) {
242	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
243	>	}
244	>	jj++;
245	>	}
246	>	ii++;
247	>	}
248	>
249	>
250	>	if (foundBonds.size() > 0) {
251	>	// sort the foundBonds by the score:
252	>	std::sort(foundBonds.begin(), foundBonds.end());
253	>
254	>	int bestScore = foundBonds[0].first;
255	>	std::vector<std::string> theKeys = foundBonds[0].second;
256	>
257	>	BondType* bestType = bondTypeCont_.find(theKeys);
258	>
259	>	return bestType;
260	>	} else {
261	>	//if no exact match found, try wild card match
262	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
263	>	}
264	>	}
265	>	}
266	>
267	>	BendType* ForceField::getBendType(const std::string &at1,
268	>	const std::string &at2,
269	>	const std::string &at3) {
270		std::vector<std::string> keys;
271		keys.push_back(at1);
272		keys.push_back(at2);
#	Line 101 | Line 275 | BendType* ForceField::getBendType(const std::string &a
275		//try exact match first
276		BendType* bendType = bendTypeCont_.find(keys);
277		if (bendType) {
278	<	return bendType;
278	>	return bendType;
279		} else {
280	<	//if no exact match found, try wild card match
281	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
280	>
281	>	AtomType* atype1;
282	>	AtomType* atype2;
283	>	AtomType* atype3;
284	>	std::vector<std::string> at1key;
285	>	at1key.push_back(at1);
286	>	atype1 = atomTypeCont_.find(at1key);
287	>
288	>	std::vector<std::string> at2key;
289	>	at2key.push_back(at2);
290	>	atype2 = atomTypeCont_.find(at2key);
291	>
292	>	std::vector<std::string> at3key;
293	>	at3key.push_back(at3);
294	>	atype3 = atomTypeCont_.find(at3key);
295	>
296	>	// query atom types for their chains of responsibility
297	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
298	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
299	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
300	>
301	>	std::vector<AtomType*>::iterator i;
302	>	std::vector<AtomType*>::iterator j;
303	>	std::vector<AtomType*>::iterator k;
304	>
305	>	int ii = 0;
306	>	int jj = 0;
307	>	int kk = 0;
308	>	int IKscore;
309	>
310	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
311	>
312	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
313	>	ii = 0;
314	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
315	>	kk = 0;
316	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
317	>
318	>	IKscore = ii + kk;
319	>
320	>	std::vector<std::string> myKeys;
321	>	myKeys.push_back((*i)->getName());
322	>	myKeys.push_back((*j)->getName());
323	>	myKeys.push_back((*k)->getName());
324	>
325	>	BendType* bendType = bendTypeCont_.find(myKeys);
326	>	if (bendType) {
327	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
328	>	}
329	>	kk++;
330	>	}
331	>	ii++;
332	>	}
333	>	jj++;
334	>	}
335	>
336	>	if (foundBends.size() > 0) {
337	>	std::sort(foundBends.begin(), foundBends.end());
338	>	int jscore = foundBends[0].first;
339	>	int ikscore = foundBends[0].second;
340	>	std::vector<std::string> theKeys = foundBends[0].third;
341	>
342	>	BendType* bestType = bendTypeCont_.find(theKeys);
343	>	return bestType;
344	>	} else {
345	>	//if no exact match found, try wild card match
346	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
347	>	}
348		}
349	<	}
349	>	}
350
351	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
352	<	const std::string &at3, const std::string &at4) {
351	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
352	>	const std::string &at2,
353	>	const std::string &at3,
354	>	const std::string &at4) {
355		std::vector<std::string> keys;
356		keys.push_back(at1);
357		keys.push_back(at2);
358		keys.push_back(at3);
359		keys.push_back(at4);
360
361	+
362	+	//try exact match first
363		TorsionType* torsionType = torsionTypeCont_.find(keys);
364		if (torsionType) {
365	<	return torsionType;
365	>	return torsionType;
366		} else {
123	–	//if no exact match found, try wild card match
124	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
125	–	}
126	–
127	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
367
368	<	}
368	>	AtomType* atype1;
369	>	AtomType* atype2;
370	>	AtomType* atype3;
371	>	AtomType* atype4;
372	>	std::vector<std::string> at1key;
373	>	at1key.push_back(at1);
374	>	atype1 = atomTypeCont_.find(at1key);
375	>
376	>	std::vector<std::string> at2key;
377	>	at2key.push_back(at2);
378	>	atype2 = atomTypeCont_.find(at2key);
379
380	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
380	>	std::vector<std::string> at3key;
381	>	at3key.push_back(at3);
382	>	atype3 = atomTypeCont_.find(at3key);
383	>
384	>	std::vector<std::string> at4key;
385	>	at4key.push_back(at4);
386	>	atype4 = atomTypeCont_.find(at4key);
387	>
388	>	// query atom types for their chains of responsibility
389	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
390	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
391	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
392	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
393	>
394	>	std::vector<AtomType*>::iterator i;
395	>	std::vector<AtomType*>::iterator j;
396	>	std::vector<AtomType*>::iterator k;
397	>	std::vector<AtomType*>::iterator l;
398	>
399	>	int ii = 0;
400	>	int jj = 0;
401	>	int kk = 0;
402	>	int ll = 0;
403	>	int ILscore;
404	>	int JKscore;
405	>
406	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
407	>
408	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
409	>	kk = 0;
410	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
411	>	ii = 0;
412	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
413	>	ll = 0;
414	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
415	>
416	>	ILscore = ii + ll;
417	>	JKscore = jj + kk;
418	>
419	>	std::vector<std::string> myKeys;
420	>	myKeys.push_back((*i)->getName());
421	>	myKeys.push_back((*j)->getName());
422	>	myKeys.push_back((*k)->getName());
423	>	myKeys.push_back((*l)->getName());
424	>
425	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
426	>	if (torsionType) {
427	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
428	>	}
429	>	ll++;
430	>	}
431	>	ii++;
432	>	}
433	>	kk++;
434	>	}
435	>	jj++;
436	>	}
437	>
438	>	if (foundTorsions.size() > 0) {
439	>	std::sort(foundTorsions.begin(), foundTorsions.end());
440	>	int jkscore = foundTorsions[0].first;
441	>	int ilscore = foundTorsions[0].second;
442	>	std::vector<std::string> theKeys = foundTorsions[0].third;
443	>
444	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
445	>	return bestType;
446	>	} else {
447	>	//if no exact match found, try wild card match
448	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
449	>	}
450	>	}
451	>	}
452	>
453	>	InversionType* ForceField::getInversionType(const std::string &at1,
454	>	const std::string &at2,
455	>	const std::string &at3,
456	>	const std::string &at4) {
457		std::vector<std::string> keys;
458		keys.push_back(at1);
459		keys.push_back(at2);
460	<	return bondTypeCont_.find(keys);
461	<	}
460	>	keys.push_back(at3);
461	>	keys.push_back(at4);
462
463	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
464	<	const std::string &at3){
463	>	//try exact match first
464	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
465	>	if (inversionType) {
466	>	return inversionType;
467	>	} else {
468	>
469	>	AtomType* atype1;
470	>	AtomType* atype2;
471	>	AtomType* atype3;
472	>	AtomType* atype4;
473	>	std::vector<std::string> at1key;
474	>	at1key.push_back(at1);
475	>	atype1 = atomTypeCont_.find(at1key);
476	>
477	>	std::vector<std::string> at2key;
478	>	at2key.push_back(at2);
479	>	atype2 = atomTypeCont_.find(at2key);
480	>
481	>	std::vector<std::string> at3key;
482	>	at3key.push_back(at3);
483	>	atype3 = atomTypeCont_.find(at3key);
484	>
485	>	std::vector<std::string> at4key;
486	>	at4key.push_back(at4);
487	>	atype4 = atomTypeCont_.find(at4key);
488	>
489	>	// query atom types for their chains of responsibility
490	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
491	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
492	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
493	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
494	>
495	>	std::vector<AtomType*>::iterator i;
496	>	std::vector<AtomType*>::iterator j;
497	>	std::vector<AtomType*>::iterator k;
498	>	std::vector<AtomType*>::iterator l;
499	>
500	>	int ii = 0;
501	>	int jj = 0;
502	>	int kk = 0;
503	>	int ll = 0;
504	>	int Iscore;
505	>	int JKLscore;
506	>
507	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
508	>
509	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
510	>	kk = 0;
511	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
512	>	ii = 0;
513	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
514	>	ll = 0;
515	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
516	>
517	>	Iscore = ii;
518	>	JKLscore = jj + kk + ll;
519	>
520	>	std::vector<std::string> myKeys;
521	>	myKeys.push_back((*i)->getName());
522	>	myKeys.push_back((*j)->getName());
523	>	myKeys.push_back((*k)->getName());
524	>	myKeys.push_back((*l)->getName());
525	>
526	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
527	>	if (inversionType) {
528	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
529	>	}
530	>	ll++;
531	>	}
532	>	ii++;
533	>	}
534	>	kk++;
535	>	}
536	>	jj++;
537	>	}
538	>
539	>	if (foundInversions.size() > 0) {
540	>	std::sort(foundInversions.begin(), foundInversions.end());
541	>	int iscore = foundInversions[0].first;
542	>	int jklscore = foundInversions[0].second;
543	>	std::vector<std::string> theKeys = foundInversions[0].third;
544	>
545	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
546	>	return bestType;
547	>	} else {
548	>	//if no exact match found, try wild card match
549	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
550	>	}
551	>	}
552	>	}
553	>
554	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
555	>
556		std::vector<std::string> keys;
557		keys.push_back(at1);
558		keys.push_back(at2);
559	+
560	+	//try exact match first
561	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
562	+	if (nbiType) {
563	+	return nbiType;
564	+	} else {
565	+	AtomType* atype1;
566	+	AtomType* atype2;
567	+	std::vector<std::string> at1key;
568	+	at1key.push_back(at1);
569	+	atype1 = atomTypeCont_.find(at1key);
570	+
571	+	std::vector<std::string> at2key;
572	+	at2key.push_back(at2);
573	+	atype2 = atomTypeCont_.find(at2key);
574	+
575	+	// query atom types for their chains of responsibility
576	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
577	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
578	+
579	+	std::vector<AtomType*>::iterator i;
580	+	std::vector<AtomType*>::iterator j;
581	+
582	+	int ii = 0;
583	+	int jj = 0;
584	+	int nbiTypeScore;
585	+
586	+	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
587	+
588	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
589	+	jj = 0;
590	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
591	+
592	+	nbiTypeScore = ii + jj;
593	+
594	+	std::vector<std::string> myKeys;
595	+	myKeys.push_back((*i)->getName());
596	+	myKeys.push_back((*j)->getName());
597	+
598	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
599	+	if (nbiType) {
600	+	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
601	+	}
602	+	jj++;
603	+	}
604	+	ii++;
605	+	}
606	+
607	+
608	+	if (foundNBI.size() > 0) {
609	+	// sort the foundNBI by the score:
610	+	std::sort(foundNBI.begin(), foundNBI.end());
611	+
612	+	int bestScore = foundNBI[0].first;
613	+	std::vector<std::string> theKeys = foundNBI[0].second;
614	+
615	+	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
616	+	return bestType;
617	+	} else {
618	+	//if no exact match found, try wild card match
619	+	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
620	+	}
621	+	}
622	+	}
623	+
624	+	BondType* ForceField::getExactBondType(const std::string &at1,
625	+	const std::string &at2){
626	+	std::vector<std::string> keys;
627	+	keys.push_back(at1);
628	+	keys.push_back(at2);
629	+	return bondTypeCont_.find(keys);
630	+	}
631	+
632	+	BendType* ForceField::getExactBendType(const std::string &at1,
633	+	const std::string &at2,
634	+	const std::string &at3){
635	+	std::vector<std::string> keys;
636	+	keys.push_back(at1);
637	+	keys.push_back(at2);
638		keys.push_back(at3);
639		return bendTypeCont_.find(keys);
640	<	}
641	<
642	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
643	<	const std::string &at3, const std::string &at4){
640	>	}
641	>
642	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
643	>	const std::string &at2,
644	>	const std::string &at3,
645	>	const std::string &at4){
646		std::vector<std::string> keys;
647		keys.push_back(at1);
648		keys.push_back(at2);
649		keys.push_back(at3);
650		keys.push_back(at4);
651		return torsionTypeCont_.find(keys);
652	<	}
653	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
652	>	}
653	>
654	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
655	>	const std::string &at2,
656	>	const std::string &at3,
657	>	const std::string &at4){
658		std::vector<std::string> keys;
659	+	keys.push_back(at1);
660	+	keys.push_back(at2);
661	+	keys.push_back(at3);
662	+	keys.push_back(at4);
663	+	return inversionTypeCont_.find(keys);
664	+	}
665	+
666	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
667	+	std::vector<std::string> keys;
668	+	keys.push_back(at1);
669	+	keys.push_back(at2);
670	+	return nonBondedInteractionTypeCont_.find(keys);
671	+	}
672	+
673	+
674	+	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
675	+	std::vector<std::string> keys;
676		keys.push_back(at);
677	+	atypeIdentToName[atomType->getIdent()] = at;
678		return atomTypeCont_.add(keys, atomType);
679	<	}
679	>	}
680
681	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
681	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
682		std::vector<std::string> keys;
683	+	keys.push_back(at);
684	+	atypeIdentToName[atomType->getIdent()] = at;
685	+	return atomTypeCont_.replace(keys, atomType);
686	+	}
687	+
688	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
689	+	BondType* bondType) {
690	+	std::vector<std::string> keys;
691		keys.push_back(at1);
692		keys.push_back(at2);
693	<	return bondTypeCont_.add(keys, bondType);
694	<
695	<	}
696	<
697	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
693	>	return bondTypeCont_.add(keys, bondType);
694	>	}
695	>
696	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
697	>	const std::string &at3, BendType* bendType) {
698		std::vector<std::string> keys;
699		keys.push_back(at1);
700		keys.push_back(at2);
701		keys.push_back(at3);
702		return bendTypeCont_.add(keys, bendType);
703	<	}
704	<
705	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
706	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
703	>	}
704	>
705	>	bool ForceField::addTorsionType(const std::string &at1,
706	>	const std::string &at2,
707	>	const std::string &at3,
708	>	const std::string &at4,
709	>	TorsionType* torsionType) {
710		std::vector<std::string> keys;
711		keys.push_back(at1);
712		keys.push_back(at2);
713		keys.push_back(at3);
714		keys.push_back(at4);
715		return torsionTypeCont_.add(keys, torsionType);
716	<	}
716	>	}
717
718	<	double ForceField::getRcutFromAtomType(AtomType* at) {
719	<	/**@todo */
720	<	GenericData* data;
721	<	double rcut = 0.0;
722	<
723	<	if (at->isLennardJones()) {
724	<	data = at->getPropertyByName("LennardJones");
725	<	if (data != NULL) {
726	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
727	<
728	<	if (ljData != NULL) {
729	<	LJParam ljParam = ljData->getData();
730	<
731	<	//by default use 2.5*sigma as cutoff radius
732	<	rcut = 2.5 * ljParam.sigma;
733	<
734	<	} else {
735	<	sprintf( painCave.errMsg,
736	<	"Can not cast GenericData to LJParam\n");
737	<	painCave.severity = OOPSE_ERROR;
738	<	painCave.isFatal = 1;
739	<	simError();
740	<	}
741	<	} else {
742	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
743	<	painCave.severity = OOPSE_ERROR;
744	<	painCave.isFatal = 1;
745	<	simError();
217	<	}
718	>	bool ForceField::addInversionType(const std::string &at1,
719	>	const std::string &at2,
720	>	const std::string &at3,
721	>	const std::string &at4,
722	>	InversionType* inversionType) {
723	>	std::vector<std::string> keys;
724	>	keys.push_back(at1);
725	>	keys.push_back(at2);
726	>	keys.push_back(at3);
727	>	keys.push_back(at4);
728	>	return inversionTypeCont_.add(keys, inversionType);
729	>	}
730	>
731	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
732	>	const std::string &at2,
733	>	NonBondedInteractionType* nbiType) {
734	>	std::vector<std::string> keys;
735	>	keys.push_back(at1);
736	>	keys.push_back(at2);
737	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
738	>	}
739	>
740	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
741	>	RealType rcut(0.0);
742	>
743	>	LennardJonesAdapter lja = LennardJonesAdapter(at);
744	>	if (lja.isLennardJones()) {
745	>	rcut = 2.5 * lja.getSigma();
746		}
747	+	EAMAdapter ea = EAMAdapter(at);
748	+	if (ea.isEAM()) {
749	+	rcut = max(rcut, ea.getRcut());
750	+	}
751	+	SuttonChenAdapter sca = SuttonChenAdapter(at);
752	+	if (sca.isSuttonChen()) {
753	+	rcut = max(rcut, 2.0 * sca.getAlpha());
754	+	}
755	+	GayBerneAdapter gba = GayBerneAdapter(at);
756	+	if (gba.isGayBerne()) {
757	+	rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
758	+	}
759	+	StickyAdapter sa = StickyAdapter(at);
760	+	if (sa.isSticky()) {
761	+	rcut = max(rcut, max(sa.getRu(), sa.getRup()));
762	+	}
763
764		return rcut;
765	<	}
765	>	}
766	>
767
768	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
768	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
769		std::string forceFieldFilename(filename);
770		ifstrstream* ffStream = new ifstrstream();
771
#	Line 229 | Line 773 | ifstrstream* ForceField::openForceFieldFile(const std:
773		ffStream->open(forceFieldFilename.c_str());
774		if(!ffStream->is_open()){
775
776	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
777	<	ffStream->open( forceFieldFilename.c_str() );
776	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
777	>	ffStream->open( forceFieldFilename.c_str() );
778
779	<	//if current directory does not contain the force field file,
780	<	//try to open it in the path
781	<	if(!ffStream->is_open()){
779	>	//if current directory does not contain the force field file,
780	>	//try to open it in the path
781	>	if(!ffStream->is_open()){
782
783	<	sprintf( painCave.errMsg,
784	<	"Error opening the force field parameter file:\n"
785	<	"\t%s\n"
786	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
787	<	"variable?\n",
788	<	forceFieldFilename.c_str() );
789	<	painCave.severity = OOPSE_ERROR;
790	<	painCave.isFatal = 1;
791	<	simError();
792	<	}
783	>	sprintf( painCave.errMsg,
784	>	"Error opening the force field parameter file:\n"
785	>	"\t%s\n"
786	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
787	>	"variable?\n",
788	>	forceFieldFilename.c_str() );
789	>	painCave.severity = OPENMD_ERROR;
790	>	painCave.isFatal = 1;
791	>	simError();
792	>	}
793		}
250	–
794		return ffStream;
795	+	}
796
797	<	}
254	<
255	<	} //end namespace oopse
797	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
branches/development/src/brains/ForceField.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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