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

Comparing:
trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 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	<	#include "UseTheForce/ForceField.hpp"
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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	>	* @version 1.0
48	>	*/
49	>
50	>	#include <algorithm>
51	>	#include "brains/ForceField.hpp"
52	>	#include "utils/simError.h"
53
54	<	AtomType* ForceField::getMatchingAtomType(const string &at) {
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	<	map<string, AtomType*>::iterator iter;
76	<
77	<	iter = atomTypeMap.find(at);
78	<	if (iter != atomTypeMap.end()) {
79	<	return iter->second;
10	<	} else {
11	<	return NULL;
12	<	}
13	<	}
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	<	BondType* ForceField::getMatchingBondType(const string &at1,
16	<	const string &at2) {
81	>	namespace OpenMD {
82
83	<	map<pair<string,string>, BondType*>::iterator iter;
19	<	vector<BondType*> foundTypes;
83	>	ForceField::ForceField(std::string ffName) {
84
85	<	iter = bondTypeMap.find(pair<at1, at2>);
86	<	if (iter != bondTypeMap.end()) {
87	<	// exact match, so just return it
88	<	return iter->second;
89	<	}
85	>	char* tempPath;
86	>	tempPath = getenv("FORCE_PARAM_PATH");
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	<	iter = bondTypeMap.find(pair<at2, at1>);
28	<	if (iter != bondTypeMap.end()) {
29	<	// exact match in reverse order, so just return it
30	<	return iter->second;
31	<	}
95	>	setForceFieldFileName(ffName + ".frc");
96
97	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
98	<	if (iter != bondTypeMap.end()) {
99	<	foundTypes.push_back(iter->second);
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	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
145	<	if (iter != bondTypeMap.end()) {
146	<	foundTypes.push_back(iter->second);
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	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
174	<	if (iter != bondTypeMap.end()) {
175	<	foundTypes.push_back(iter->second);
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	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
186	<	if (iter != bondTypeMap.end()) {
187	<	foundTypes.push_back(iter->second);
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);
201	+
202	+	//try exact match first
203	+	BondType* bondType = bondTypeCont_.find(keys);
204	+	if (bondType) {
205	+	return bondType;
206	+	} else {
207	+	AtomType* atype1;
208	+	AtomType* atype2;
209	+	std::vector<std::string> at1key;
210	+	at1key.push_back(at1);
211	+	atype1 = atomTypeCont_.find(at1key);
212
213	<	if (foundTypes.empty()) {
214	<	return NULL;
215	<	} else {
56	<
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	+	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);
273	+	keys.push_back(at3);
274
275	+	//try exact match first
276	+	BendType* bendType = bendTypeCont_.find(keys);
277	+	if (bendType) {
278	+	return bendType;
279	+	} else {
280
281	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
282	<	const string &at3);
283	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
284	<	const string &at3, const string &at4);
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	<	double ForceField::getRcutForAtomType(AtomType* at);
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	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
302	<
303	<	vector<vector<string> > results;
301	>	std::vector<AtomType*>::iterator i;
302	>	std::vector<AtomType*>::iterator j;
303	>	std::vector<AtomType*>::iterator k;
304
305	<
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	<	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
313	<
314	<	int nStrings;
315	<	vector<string> oneResult;
316	<	vector<vector<string> > allResults;
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	<	nStrings = myAts.size();
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	<	if (nStrings == 1) {
326	<	oneResult.push_back(wildcardCharacter);
327	<	allResults.push_back(oneResult);
328	<	return allResults;
329	<	} else {
330	<
331	<	for (i=0; i < nStrings; i++) {
332	<	oneResult = myAts;
333	<	replace(oneResult.begin(), oneResult.end(),
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	>	}
350	>
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;
366	>	} else {
367	>
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	>	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	>	keys.push_back(at3);
461	>	keys.push_back(at4);
462	>
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,
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	>
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	>	}
680	>
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	>	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,
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	>	}
717	>
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	>	}
766	>
767	>
768	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
769	>	std::string forceFieldFilename(filename);
770	>	ifstrstream* ffStream = new ifstrstream();
771	>
772	>	//try to open the force filed file in current directory first
773	>	ffStream->open(forceFieldFilename.c_str());
774	>	if(!ffStream->is_open()){
775	>
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()){
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 = OPENMD_ERROR;
790	>	painCave.isFatal = 1;
791	>	simError();
792	>	}
793	>	}
794	>	return ffStream;
795	>	}
796	>
797	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 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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