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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1790 by gezelter, Thu Aug 30 17:18:22 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	>	* @time 22:51am
48	>	* @version 1.0
49	>	*/
50	>
51	>	#include <algorithm>
52	>	#include "brains/ForceField.hpp"
53	>	#include "utils/simError.h"
54
55	<	AtomType* ForceField::getMatchingAtomType(const string &at) {
55	>	#include "io/OptionSectionParser.hpp"
56	>	#include "io/BaseAtomTypesSectionParser.hpp"
57	>	#include "io/DirectionalAtomTypesSectionParser.hpp"
58	>	#include "io/AtomTypesSectionParser.hpp"
59	>	#include "io/BendTypesSectionParser.hpp"
60	>	#include "io/BondTypesSectionParser.hpp"
61	>	#include "io/ChargeAtomTypesSectionParser.hpp"
62	>	#include "io/EAMAtomTypesSectionParser.hpp"
63	>	#include "io/FluctuatingChargeAtomTypesSectionParser.hpp"
64	>	#include "io/GayBerneAtomTypesSectionParser.hpp"
65	>	#include "io/InversionTypesSectionParser.hpp"
66	>	#include "io/LennardJonesAtomTypesSectionParser.hpp"
67	>	#include "io/MultipoleAtomTypesSectionParser.hpp"
68	>	#include "io/NonBondedInteractionsSectionParser.hpp"
69	>	#include "io/PolarizableAtomTypesSectionParser.hpp"
70	>	#include "io/SCAtomTypesSectionParser.hpp"
71	>	#include "io/ShapeAtomTypesSectionParser.hpp"
72	>	#include "io/StickyAtomTypesSectionParser.hpp"
73	>	#include "io/StickyPowerAtomTypesSectionParser.hpp"
74	>	#include "io/TorsionTypesSectionParser.hpp"
75
76	<	map<string, AtomType*>::iterator iter;
77	<
78	<	iter = atomTypeMap.find(at);
79	<	if (iter != atomTypeMap.end()) {
80	<	return iter->second;
10	<	} else {
11	<	return NULL;
12	<	}
13	<	}
76	>	#include "types/LennardJonesAdapter.hpp"
77	>	#include "types/EAMAdapter.hpp"
78	>	#include "types/SuttonChenAdapter.hpp"
79	>	#include "types/GayBerneAdapter.hpp"
80	>	#include "types/StickyAdapter.hpp"
81
82	<	BondType* ForceField::getMatchingBondType(const string &at1,
16	<	const string &at2) {
82	>	namespace OpenMD {
83
84	<	map<pair<string,string>, BondType*>::iterator iter;
19	<	vector<BondType*> foundTypes;
84	>	ForceField::ForceField(std::string ffName) {
85
86	<	iter = bondTypeMap.find(pair<at1, at2>);
87	<	if (iter != bondTypeMap.end()) {
88	<	// exact match, so just return it
89	<	return iter->second;
90	<	}
86	>	char* tempPath;
87	>	tempPath = getenv("FORCE_PARAM_PATH");
88	>
89	>	if (tempPath == NULL) {
90	>	//convert a macro from compiler to a string in c++
91	>	STR_DEFINE(ffPath_, FRC_PATH );
92	>	} else {
93	>	ffPath_ = tempPath;
94	>	}
95
96	<	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	<	}
96	>	setForceFieldFileName(ffName + ".frc");
97
98	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
99	<	if (iter != bondTypeMap.end()) {
100	<	foundTypes.push_back(iter->second);
98	>	/**
99	>	* The order of adding section parsers is important.
100	>	*
101	>	* OptionSectionParser must come first to set options for other
102	>	* parsers
103	>	*
104	>	* DirectionalAtomTypesSectionParser should be added before
105	>	* AtomTypesSectionParser, and these two section parsers will
106	>	* actually create "real" AtomTypes (AtomTypesSectionParser will
107	>	* create AtomType and DirectionalAtomTypesSectionParser will
108	>	* create DirectionalAtomType, which is a subclass of AtomType and
109	>	* should come first).
110	>	*
111	>	* Other AtomTypes Section Parsers will not create the "real"
112	>	* AtomType, they only add and set some attributes of the AtomType
113	>	* (via the Adapters). Thus ordering of these is not important.
114	>	* AtomTypesSectionParser should be added before other atom type
115	>	*
116	>	* The order of BondTypesSectionParser, BendTypesSectionParser and
117	>	* TorsionTypesSectionParser, etc. are not important.
118	>	*/
119	>
120	>	spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
121	>	spMan_.push_back(new BaseAtomTypesSectionParser());
122	>	spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_));
123	>	spMan_.push_back(new AtomTypesSectionParser());
124	>
125	>	spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
126	>	spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_));
127	>	spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_));
128	>	spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_));
129	>	spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_));
130	>	spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_));
131	>	spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_));
132	>	spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
133	>	spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_));
134	>	spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_));
135	>	spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_));
136	>
137	>	spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_));
138	>	spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_));
139	>	spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_));
140	>	spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_));
141	>
142	>	spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_));
143		}
144
145	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
146	<	if (iter != bondTypeMap.end()) {
147	<	foundTypes.push_back(iter->second);
145	>	void ForceField::parse(const std::string& filename) {
146	>	ifstrstream* ffStream;
147	>
148	>	ffStream = openForceFieldFile(filename);
149	>
150	>	spMan_.parse(*ffStream, *this);
151	>
152	>	ForceField::AtomTypeContainer::MapTypeIterator i;
153	>	AtomType* at;
154	>
155	>	for (at = atomTypeCont_.beginType(i); at != NULL;
156	>	at = atomTypeCont_.nextType(i)) {
157	>
158	>	// useBase sets the responsibilities, and these have to be done
159	>	// after the atomTypes and Base types have all been scanned:
160	>
161	>	std::vector<AtomType*> ayb = at->allYourBase();
162	>	if (ayb.size() > 1) {
163	>	for (int j = ayb.size()-1; j > 0; j--) {
164	>
165	>	ayb[j-1]->useBase(ayb[j]);
166	>
167	>	}
168	>	}
169	>	}
170	>
171	>	delete ffStream;
172		}
173
174	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
175	<	if (iter != bondTypeMap.end()) {
176	<	foundTypes.push_back(iter->second);
174	>	/**
175	>	* getAtomType by string
176	>	*
177	>	* finds the requested atom type in this force field using the string
178	>	* name of the atom type.
179	>	*/
180	>	AtomType* ForceField::getAtomType(const std::string &at) {
181	>	std::vector<std::string> keys;
182	>	keys.push_back(at);
183	>	return atomTypeCont_.find(keys);
184		}
185
186	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
187	<	if (iter != bondTypeMap.end()) {
188	<	foundTypes.push_back(iter->second);
186	>	/**
187	>	* getAtomType by ident
188	>	*
189	>	* finds the requested atom type in this force field using the
190	>	* integer ident instead of the string name of the atom type.
191	>	*/
192	>	AtomType* ForceField::getAtomType(int ident) {
193	>	std::string at = atypeIdentToName.find(ident)->second;
194	>	return getAtomType(at);
195		}
196	+
197	+	BondType* ForceField::getBondType(const std::string &at1,
198	+	const std::string &at2) {
199	+	std::vector<std::string> keys;
200	+	keys.push_back(at1);
201	+	keys.push_back(at2);
202	+
203	+	//try exact match first
204	+	BondType* bondType = bondTypeCont_.find(keys);
205	+	if (bondType) {
206	+	return bondType;
207	+	} else {
208	+	AtomType* atype1;
209	+	AtomType* atype2;
210	+	std::vector<std::string> at1key;
211	+	at1key.push_back(at1);
212	+	atype1 = atomTypeCont_.find(at1key);
213
214	<	if (foundTypes.empty()) {
215	<	return NULL;
216	<	} else {
56	<
214	>	std::vector<std::string> at2key;
215	>	at2key.push_back(at2);
216	>	atype2 = atomTypeCont_.find(at2key);
217
218	<
218	>	// query atom types for their chains of responsibility
219	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
220	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
221
222	+	std::vector<AtomType*>::iterator i;
223	+	std::vector<AtomType*>::iterator j;
224
225	+	int ii = 0;
226	+	int jj = 0;
227	+	int bondTypeScore;
228
229	+	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
230	+
231	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
232	+	jj = 0;
233	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
234	+
235	+	bondTypeScore = ii + jj;
236	+
237	+	std::vector<std::string> myKeys;
238	+	myKeys.push_back((*i)->getName());
239	+	myKeys.push_back((*j)->getName());
240	+
241	+	BondType* bondType = bondTypeCont_.find(myKeys);
242	+	if (bondType) {
243	+	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
244	+	}
245	+	jj++;
246	+	}
247	+	ii++;
248	+	}
249	+
250	+
251	+	if (foundBonds.size() > 0) {
252	+	// sort the foundBonds by the score:
253	+	std::sort(foundBonds.begin(), foundBonds.end());
254	+
255	+	int bestScore = foundBonds[0].first;
256	+	std::vector<std::string> theKeys = foundBonds[0].second;
257	+
258	+	BondType* bestType = bondTypeCont_.find(theKeys);
259	+
260	+	return bestType;
261	+	} else {
262	+	//if no exact match found, try wild card match
263	+	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
264	+	}
265	+	}
266	+	}
267
268	+	BendType* ForceField::getBendType(const std::string &at1,
269	+	const std::string &at2,
270	+	const std::string &at3) {
271	+	std::vector<std::string> keys;
272	+	keys.push_back(at1);
273	+	keys.push_back(at2);
274	+	keys.push_back(at3);
275
276	+	//try exact match first
277	+	BendType* bendType = bendTypeCont_.find(keys);
278	+	if (bendType) {
279	+	return bendType;
280	+	} else {
281
282	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
283	<	const string &at3);
284	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
285	<	const string &at3, const string &at4);
282	>	AtomType* atype1;
283	>	AtomType* atype2;
284	>	AtomType* atype3;
285	>	std::vector<std::string> at1key;
286	>	at1key.push_back(at1);
287	>	atype1 = atomTypeCont_.find(at1key);
288	>
289	>	std::vector<std::string> at2key;
290	>	at2key.push_back(at2);
291	>	atype2 = atomTypeCont_.find(at2key);
292
293	<	double ForceField::getRcutForAtomType(AtomType* at);
293	>	std::vector<std::string> at3key;
294	>	at3key.push_back(at3);
295	>	atype3 = atomTypeCont_.find(at3key);
296
297	+	// query atom types for their chains of responsibility
298	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
299	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
300	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
301
302	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
303	<
304	<	vector<vector<string> > results;
302	>	std::vector<AtomType*>::iterator i;
303	>	std::vector<AtomType*>::iterator j;
304	>	std::vector<AtomType*>::iterator k;
305
306	<
306	>	int ii = 0;
307	>	int jj = 0;
308	>	int kk = 0;
309	>	int IKscore;
310
311	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
312
313	<	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
314	<
315	<	int nStrings;
316	<	vector<string> oneResult;
317	<	vector<vector<string> > allResults;
313	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
314	>	ii = 0;
315	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
316	>	kk = 0;
317	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
318	>
319	>	IKscore = ii + kk;
320
321	<	nStrings = myAts.size();
321	>	std::vector<std::string> myKeys;
322	>	myKeys.push_back((*i)->getName());
323	>	myKeys.push_back((*j)->getName());
324	>	myKeys.push_back((*k)->getName());
325
326	<	if (nStrings == 1) {
327	<	oneResult.push_back(wildcardCharacter);
328	<	allResults.push_back(oneResult);
329	<	return allResults;
330	<	} else {
331	<
332	<	for (i=0; i < nStrings; i++) {
333	<	oneResult = myAts;
334	<	replace(oneResult.begin(), oneResult.end(),
326	>	BendType* bendType = bendTypeCont_.find(myKeys);
327	>	if (bendType) {
328	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
329	>	}
330	>	kk++;
331	>	}
332	>	ii++;
333	>	}
334	>	jj++;
335	>	}
336	>
337	>	if (foundBends.size() > 0) {
338	>	std::sort(foundBends.begin(), foundBends.end());
339	>	int jscore = foundBends[0].first;
340	>	int ikscore = foundBends[0].second;
341	>	std::vector<std::string> theKeys = foundBends[0].third;
342	>
343	>	BendType* bestType = bendTypeCont_.find(theKeys);
344	>	return bestType;
345	>	} else {
346	>	//if no exact match found, try wild card match
347	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
348	>	}
349	>	}
350	>	}
351	>
352	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
353	>	const std::string &at2,
354	>	const std::string &at3,
355	>	const std::string &at4) {
356	>	std::vector<std::string> keys;
357	>	keys.push_back(at1);
358	>	keys.push_back(at2);
359	>	keys.push_back(at3);
360	>	keys.push_back(at4);
361	>
362	>
363	>	//try exact match first
364	>	TorsionType* torsionType = torsionTypeCont_.find(keys);
365	>	if (torsionType) {
366	>	return torsionType;
367	>	} else {
368	>
369	>	AtomType* atype1;
370	>	AtomType* atype2;
371	>	AtomType* atype3;
372	>	AtomType* atype4;
373	>	std::vector<std::string> at1key;
374	>	at1key.push_back(at1);
375	>	atype1 = atomTypeCont_.find(at1key);
376	>
377	>	std::vector<std::string> at2key;
378	>	at2key.push_back(at2);
379	>	atype2 = atomTypeCont_.find(at2key);
380	>
381	>	std::vector<std::string> at3key;
382	>	at3key.push_back(at3);
383	>	atype3 = atomTypeCont_.find(at3key);
384	>
385	>	std::vector<std::string> at4key;
386	>	at4key.push_back(at4);
387	>	atype4 = atomTypeCont_.find(at4key);
388	>
389	>	// query atom types for their chains of responsibility
390	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
391	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
392	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
393	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
394	>
395	>	std::vector<AtomType*>::iterator i;
396	>	std::vector<AtomType*>::iterator j;
397	>	std::vector<AtomType*>::iterator k;
398	>	std::vector<AtomType*>::iterator l;
399	>
400	>	int ii = 0;
401	>	int jj = 0;
402	>	int kk = 0;
403	>	int ll = 0;
404	>	int ILscore;
405	>	int JKscore;
406	>
407	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
408	>
409	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
410	>	kk = 0;
411	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
412	>	ii = 0;
413	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
414	>	ll = 0;
415	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
416	>
417	>	ILscore = ii + ll;
418	>	JKscore = jj + kk;
419	>
420	>	std::vector<std::string> myKeys;
421	>	myKeys.push_back((*i)->getName());
422	>	myKeys.push_back((*j)->getName());
423	>	myKeys.push_back((*k)->getName());
424	>	myKeys.push_back((*l)->getName());
425	>
426	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
427	>	if (torsionType) {
428	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
429	>	}
430	>	ll++;
431	>	}
432	>	ii++;
433	>	}
434	>	kk++;
435	>	}
436	>	jj++;
437	>	}
438	>
439	>	if (foundTorsions.size() > 0) {
440	>	std::sort(foundTorsions.begin(), foundTorsions.end());
441	>	int jkscore = foundTorsions[0].first;
442	>	int ilscore = foundTorsions[0].second;
443	>	std::vector<std::string> theKeys = foundTorsions[0].third;
444	>
445	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
446	>	return bestType;
447	>	} else {
448	>	//if no exact match found, try wild card match
449	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
450	>	}
451	>	}
452	>	}
453	>
454	>	InversionType* ForceField::getInversionType(const std::string &at1,
455	>	const std::string &at2,
456	>	const std::string &at3,
457	>	const std::string &at4) {
458	>	std::vector<std::string> keys;
459	>	keys.push_back(at1);
460	>	keys.push_back(at2);
461	>	keys.push_back(at3);
462	>	keys.push_back(at4);
463	>
464	>	//try exact match first
465	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
466	>	if (inversionType) {
467	>	return inversionType;
468	>	} else {
469	>
470	>	AtomType* atype1;
471	>	AtomType* atype2;
472	>	AtomType* atype3;
473	>	AtomType* atype4;
474	>	std::vector<std::string> at1key;
475	>	at1key.push_back(at1);
476	>	atype1 = atomTypeCont_.find(at1key);
477	>
478	>	std::vector<std::string> at2key;
479	>	at2key.push_back(at2);
480	>	atype2 = atomTypeCont_.find(at2key);
481	>
482	>	std::vector<std::string> at3key;
483	>	at3key.push_back(at3);
484	>	atype3 = atomTypeCont_.find(at3key);
485	>
486	>	std::vector<std::string> at4key;
487	>	at4key.push_back(at4);
488	>	atype4 = atomTypeCont_.find(at4key);
489	>
490	>	// query atom types for their chains of responsibility
491	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
492	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
493	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
494	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
495	>
496	>	std::vector<AtomType*>::iterator i;
497	>	std::vector<AtomType*>::iterator j;
498	>	std::vector<AtomType*>::iterator k;
499	>	std::vector<AtomType*>::iterator l;
500	>
501	>	int ii = 0;
502	>	int jj = 0;
503	>	int kk = 0;
504	>	int ll = 0;
505	>	int Iscore;
506	>	int JKLscore;
507	>
508	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
509	>
510	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
511	>	kk = 0;
512	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
513	>	ii = 0;
514	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
515	>	ll = 0;
516	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
517	>
518	>	Iscore = ii;
519	>	JKLscore = jj + kk + ll;
520	>
521	>	std::vector<std::string> myKeys;
522	>	myKeys.push_back((*i)->getName());
523	>	myKeys.push_back((*j)->getName());
524	>	myKeys.push_back((*k)->getName());
525	>	myKeys.push_back((*l)->getName());
526	>
527	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
528	>	if (inversionType) {
529	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
530	>	}
531	>	ll++;
532	>	}
533	>	ii++;
534	>	}
535	>	kk++;
536	>	}
537	>	jj++;
538	>	}
539	>
540	>	if (foundInversions.size() > 0) {
541	>	std::sort(foundInversions.begin(), foundInversions.end());
542	>	int iscore = foundInversions[0].first;
543	>	int jklscore = foundInversions[0].second;
544	>	std::vector<std::string> theKeys = foundInversions[0].third;
545	>
546	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
547	>	return bestType;
548	>	} else {
549	>	//if no exact match found, try wild card match
550	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
551	>	}
552	>	}
553	>	}
554	>
555	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
556	>
557	>	std::vector<std::string> keys;
558	>	keys.push_back(at1);
559	>	keys.push_back(at2);
560	>
561	>	//try exact match first
562	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
563	>	if (nbiType) {
564	>	return nbiType;
565	>	} else {
566	>	AtomType* atype1;
567	>	AtomType* atype2;
568	>	std::vector<std::string> at1key;
569	>	at1key.push_back(at1);
570	>	atype1 = atomTypeCont_.find(at1key);
571	>
572	>	std::vector<std::string> at2key;
573	>	at2key.push_back(at2);
574	>	atype2 = atomTypeCont_.find(at2key);
575	>
576	>	// query atom types for their chains of responsibility
577	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
578	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
579	>
580	>	std::vector<AtomType*>::iterator i;
581	>	std::vector<AtomType*>::iterator j;
582	>
583	>	int ii = 0;
584	>	int jj = 0;
585	>	int nbiTypeScore;
586	>
587	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
588	>
589	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
590	>	jj = 0;
591	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
592	>
593	>	nbiTypeScore = ii + jj;
594	>
595	>	std::vector<std::string> myKeys;
596	>	myKeys.push_back((*i)->getName());
597	>	myKeys.push_back((*j)->getName());
598	>
599	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
600	>	if (nbiType) {
601	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
602	>	}
603	>	jj++;
604	>	}
605	>	ii++;
606	>	}
607	>
608	>
609	>	if (foundNBI.size() > 0) {
610	>	// sort the foundNBI by the score:
611	>	std::sort(foundNBI.begin(), foundNBI.end());
612	>
613	>	int bestScore = foundNBI[0].first;
614	>	std::vector<std::string> theKeys = foundNBI[0].second;
615	>
616	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
617	>	return bestType;
618	>	} else {
619	>	//if no exact match found, try wild card match
620	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
621	>	}
622	>	}
623	>	}
624	>
625	>	BondType* ForceField::getExactBondType(const std::string &at1,
626	>	const std::string &at2){
627	>	std::vector<std::string> keys;
628	>	keys.push_back(at1);
629	>	keys.push_back(at2);
630	>	return bondTypeCont_.find(keys);
631	>	}
632	>
633	>	BendType* ForceField::getExactBendType(const std::string &at1,
634	>	const std::string &at2,
635	>	const std::string &at3){
636	>	std::vector<std::string> keys;
637	>	keys.push_back(at1);
638	>	keys.push_back(at2);
639	>	keys.push_back(at3);
640	>	return bendTypeCont_.find(keys);
641	>	}
642	>
643	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
644	>	const std::string &at2,
645	>	const std::string &at3,
646	>	const std::string &at4){
647	>	std::vector<std::string> keys;
648	>	keys.push_back(at1);
649	>	keys.push_back(at2);
650	>	keys.push_back(at3);
651	>	keys.push_back(at4);
652	>	return torsionTypeCont_.find(keys);
653	>	}
654	>
655	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
656	>	const std::string &at2,
657	>	const std::string &at3,
658	>	const std::string &at4){
659	>	std::vector<std::string> keys;
660	>	keys.push_back(at1);
661	>	keys.push_back(at2);
662	>	keys.push_back(at3);
663	>	keys.push_back(at4);
664	>	return inversionTypeCont_.find(keys);
665	>	}
666	>
667	>	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
668	>	std::vector<std::string> keys;
669	>	keys.push_back(at1);
670	>	keys.push_back(at2);
671	>	return nonBondedInteractionTypeCont_.find(keys);
672	>	}
673	>
674	>
675	>	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
676	>	std::vector<std::string> keys;
677	>	keys.push_back(at);
678	>	atypeIdentToName[atomType->getIdent()] = at;
679	>	return atomTypeCont_.add(keys, atomType);
680	>	}
681	>
682	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
683	>	std::vector<std::string> keys;
684	>	keys.push_back(at);
685	>	atypeIdentToName[atomType->getIdent()] = at;
686	>	return atomTypeCont_.replace(keys, atomType);
687	>	}
688	>
689	>	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
690	>	BondType* bondType) {
691	>	std::vector<std::string> keys;
692	>	keys.push_back(at1);
693	>	keys.push_back(at2);
694	>	return bondTypeCont_.add(keys, bondType);
695	>	}
696	>
697	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
698	>	const std::string &at3, BendType* bendType) {
699	>	std::vector<std::string> keys;
700	>	keys.push_back(at1);
701	>	keys.push_back(at2);
702	>	keys.push_back(at3);
703	>	return bendTypeCont_.add(keys, bendType);
704	>	}
705	>
706	>	bool ForceField::addTorsionType(const std::string &at1,
707	>	const std::string &at2,
708	>	const std::string &at3,
709	>	const std::string &at4,
710	>	TorsionType* torsionType) {
711	>	std::vector<std::string> keys;
712	>	keys.push_back(at1);
713	>	keys.push_back(at2);
714	>	keys.push_back(at3);
715	>	keys.push_back(at4);
716	>	return torsionTypeCont_.add(keys, torsionType);
717	>	}
718	>
719	>	bool ForceField::addInversionType(const std::string &at1,
720	>	const std::string &at2,
721	>	const std::string &at3,
722	>	const std::string &at4,
723	>	InversionType* inversionType) {
724	>	std::vector<std::string> keys;
725	>	keys.push_back(at1);
726	>	keys.push_back(at2);
727	>	keys.push_back(at3);
728	>	keys.push_back(at4);
729	>	return inversionTypeCont_.add(keys, inversionType);
730	>	}
731	>
732	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
733	>	const std::string &at2,
734	>	NonBondedInteractionType* nbiType) {
735	>	std::vector<std::string> keys;
736	>	keys.push_back(at1);
737	>	keys.push_back(at2);
738	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
739	>	}
740	>
741	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
742	>	RealType rcut(0.0);
743	>
744	>	LennardJonesAdapter lja = LennardJonesAdapter(at);
745	>	if (lja.isLennardJones()) {
746	>	rcut = 2.5 * lja.getSigma();
747	>	}
748	>	EAMAdapter ea = EAMAdapter(at);
749	>	if (ea.isEAM()) {
750	>	rcut = max(rcut, ea.getRcut());
751	>	}
752	>	SuttonChenAdapter sca = SuttonChenAdapter(at);
753	>	if (sca.isSuttonChen()) {
754	>	rcut = max(rcut, 2.0 * sca.getAlpha());
755	>	}
756	>	GayBerneAdapter gba = GayBerneAdapter(at);
757	>	if (gba.isGayBerne()) {
758	>	rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL()));
759	>	}
760	>	StickyAdapter sa = StickyAdapter(at);
761	>	if (sa.isSticky()) {
762	>	rcut = max(rcut, max(sa.getRu(), sa.getRup()));
763	>	}
764	>
765	>	return rcut;
766	>	}
767	>
768	>
769	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
770	>	std::string forceFieldFilename(filename);
771	>	ifstrstream* ffStream = new ifstrstream();
772	>
773	>	//try to open the force filed file in current directory first
774	>	ffStream->open(forceFieldFilename.c_str(), ifstream::in | ifstream::binary);
775	>
776	>	if(!ffStream->is_open()){
777	>
778	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
779	>	ffStream->open( forceFieldFilename.c_str(),
780	>	ifstream::in | ifstream::binary );
781	>
782	>	//if current directory does not contain the force field file,
783	>	//try to open it in the path
784	>	if(!ffStream->is_open()){
785	>
786	>	sprintf( painCave.errMsg,
787	>	"Error opening the force field parameter file:\n"
788	>	"\t%s\n"
789	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
790	>	"variable?\n",
791	>	forceFieldFilename.c_str() );
792	>	painCave.severity = OPENMD_ERROR;
793	>	painCave.isFatal = 1;
794	>	simError();
795	>	}
796	>	}
797	>	return ffStream;
798	>	}
799	>
800	>	} //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.
trunk/src/brains/ForceField.cpp (property svn:keywords), Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

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