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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 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, 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
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.empty()) {
251	>	// sort the foundBonds by the score:
252	>	std::sort(foundBonds.begin(), foundBonds.end());
253	>
254	>	std::vector<std::string> theKeys = foundBonds[0].second;
255	>
256	>	BondType* bestType = bondTypeCont_.find(theKeys);
257	>
258	>	return bestType;
259	>	} else {
260	>	//if no exact match found, try wild card match
261	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
262	>	}
263	>	}
264	>	}
265	>
266	>	BendType* ForceField::getBendType(const std::string &at1,
267	>	const std::string &at2,
268	>	const std::string &at3) {
269		std::vector<std::string> keys;
270		keys.push_back(at1);
271		keys.push_back(at2);
#	Line 101 | Line 274 | BendType* ForceField::getBendType(const std::string &a
274		//try exact match first
275		BendType* bendType = bendTypeCont_.find(keys);
276		if (bendType) {
277	<	return bendType;
277	>	return bendType;
278		} else {
279	<	//if no exact match found, try wild card match
280	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
279	>
280	>	AtomType* atype1;
281	>	AtomType* atype2;
282	>	AtomType* atype3;
283	>	std::vector<std::string> at1key;
284	>	at1key.push_back(at1);
285	>	atype1 = atomTypeCont_.find(at1key);
286	>
287	>	std::vector<std::string> at2key;
288	>	at2key.push_back(at2);
289	>	atype2 = atomTypeCont_.find(at2key);
290	>
291	>	std::vector<std::string> at3key;
292	>	at3key.push_back(at3);
293	>	atype3 = atomTypeCont_.find(at3key);
294	>
295	>	// query atom types for their chains of responsibility
296	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
297	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
298	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
299	>
300	>	std::vector<AtomType*>::iterator i;
301	>	std::vector<AtomType*>::iterator j;
302	>	std::vector<AtomType*>::iterator k;
303	>
304	>	int ii = 0;
305	>	int jj = 0;
306	>	int kk = 0;
307	>	int IKscore;
308	>
309	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
310	>
311	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
312	>	ii = 0;
313	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
314	>	kk = 0;
315	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
316	>
317	>	IKscore = ii + kk;
318	>
319	>	std::vector<std::string> myKeys;
320	>	myKeys.push_back((*i)->getName());
321	>	myKeys.push_back((*j)->getName());
322	>	myKeys.push_back((*k)->getName());
323	>
324	>	BendType* bendType = bendTypeCont_.find(myKeys);
325	>	if (bendType) {
326	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
327	>	}
328	>	kk++;
329	>	}
330	>	ii++;
331	>	}
332	>	jj++;
333	>	}
334	>
335	>	if (!foundBends.empty()) {
336	>	std::sort(foundBends.begin(), foundBends.end());
337	>	std::vector<std::string> theKeys = foundBends[0].third;
338	>
339	>	BendType* bestType = bendTypeCont_.find(theKeys);
340	>	return bestType;
341	>	} else {
342	>	//if no exact match found, try wild card match
343	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
344	>	}
345		}
346	<	}
346	>	}
347
348	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
349	<	const std::string &at3, const std::string &at4) {
348	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
349	>	const std::string &at2,
350	>	const std::string &at3,
351	>	const std::string &at4) {
352		std::vector<std::string> keys;
353		keys.push_back(at1);
354		keys.push_back(at2);
355		keys.push_back(at3);
356		keys.push_back(at4);
357
358	+
359	+	//try exact match first
360		TorsionType* torsionType = torsionTypeCont_.find(keys);
361		if (torsionType) {
362	<	return torsionType;
362	>	return torsionType;
363		} 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_);
364
365	<	}
365	>	AtomType* atype1;
366	>	AtomType* atype2;
367	>	AtomType* atype3;
368	>	AtomType* atype4;
369	>	std::vector<std::string> at1key;
370	>	at1key.push_back(at1);
371	>	atype1 = atomTypeCont_.find(at1key);
372	>
373	>	std::vector<std::string> at2key;
374	>	at2key.push_back(at2);
375	>	atype2 = atomTypeCont_.find(at2key);
376
377	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
377	>	std::vector<std::string> at3key;
378	>	at3key.push_back(at3);
379	>	atype3 = atomTypeCont_.find(at3key);
380	>
381	>	std::vector<std::string> at4key;
382	>	at4key.push_back(at4);
383	>	atype4 = atomTypeCont_.find(at4key);
384	>
385	>	// query atom types for their chains of responsibility
386	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
387	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
388	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
389	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
390	>
391	>	std::vector<AtomType*>::iterator i;
392	>	std::vector<AtomType*>::iterator j;
393	>	std::vector<AtomType*>::iterator k;
394	>	std::vector<AtomType*>::iterator l;
395	>
396	>	int ii = 0;
397	>	int jj = 0;
398	>	int kk = 0;
399	>	int ll = 0;
400	>	int ILscore;
401	>	int JKscore;
402	>
403	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
404	>
405	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
406	>	kk = 0;
407	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
408	>	ii = 0;
409	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
410	>	ll = 0;
411	>	for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
412	>
413	>	ILscore = ii + ll;
414	>	JKscore = jj + kk;
415	>
416	>	std::vector<std::string> myKeys;
417	>	myKeys.push_back((*i)->getName());
418	>	myKeys.push_back((*j)->getName());
419	>	myKeys.push_back((*k)->getName());
420	>	myKeys.push_back((*l)->getName());
421	>
422	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
423	>	if (torsionType) {
424	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
425	>	}
426	>	ll++;
427	>	}
428	>	ii++;
429	>	}
430	>	kk++;
431	>	}
432	>	jj++;
433	>	}
434	>
435	>	if (!foundTorsions.empty()) {
436	>	std::sort(foundTorsions.begin(), foundTorsions.end());
437	>	std::vector<std::string> theKeys = foundTorsions[0].third;
438	>
439	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
440	>	return bestType;
441	>	} else {
442	>	//if no exact match found, try wild card match
443	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
444	>	}
445	>	}
446	>	}
447	>
448	>	InversionType* ForceField::getInversionType(const std::string &at1,
449	>	const std::string &at2,
450	>	const std::string &at3,
451	>	const std::string &at4) {
452		std::vector<std::string> keys;
453		keys.push_back(at1);
454		keys.push_back(at2);
455	<	return bondTypeCont_.find(keys);
456	<	}
455	>	keys.push_back(at3);
456	>	keys.push_back(at4);
457
458	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
459	<	const std::string &at3){
458	>	//try exact match first
459	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
460	>	if (inversionType) {
461	>	return inversionType;
462	>	} else {
463	>
464	>	AtomType* atype1;
465	>	AtomType* atype2;
466	>	AtomType* atype3;
467	>	AtomType* atype4;
468	>	std::vector<std::string> at1key;
469	>	at1key.push_back(at1);
470	>	atype1 = atomTypeCont_.find(at1key);
471	>
472	>	std::vector<std::string> at2key;
473	>	at2key.push_back(at2);
474	>	atype2 = atomTypeCont_.find(at2key);
475	>
476	>	std::vector<std::string> at3key;
477	>	at3key.push_back(at3);
478	>	atype3 = atomTypeCont_.find(at3key);
479	>
480	>	std::vector<std::string> at4key;
481	>	at4key.push_back(at4);
482	>	atype4 = atomTypeCont_.find(at4key);
483	>
484	>	// query atom types for their chains of responsibility
485	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
486	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
487	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
488	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
489	>
490	>	std::vector<AtomType*>::iterator i;
491	>	std::vector<AtomType*>::iterator j;
492	>	std::vector<AtomType*>::iterator k;
493	>	std::vector<AtomType*>::iterator l;
494	>
495	>	int ii = 0;
496	>	int jj = 0;
497	>	int kk = 0;
498	>	int ll = 0;
499	>	int Iscore;
500	>	int JKLscore;
501	>
502	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
503	>
504	>	for (j = at2Chain.begin(); j != at2Chain.end(); ++j) {
505	>	kk = 0;
506	>	for (k = at3Chain.begin(); k != at3Chain.end(); ++k) {
507	>	ii = 0;
508	>	for (i = at1Chain.begin(); i != at1Chain.end(); ++i) {
509	>	ll = 0;
510	>	for (l = at4Chain.begin(); l != at4Chain.end(); ++l) {
511	>
512	>	Iscore = ii;
513	>	JKLscore = jj + kk + ll;
514	>
515	>	std::vector<std::string> myKeys;
516	>	myKeys.push_back((*i)->getName());
517	>	myKeys.push_back((*j)->getName());
518	>	myKeys.push_back((*k)->getName());
519	>	myKeys.push_back((*l)->getName());
520	>
521	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
522	>	if (inversionType) {
523	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
524	>	}
525	>	ll++;
526	>	}
527	>	ii++;
528	>	}
529	>	kk++;
530	>	}
531	>	jj++;
532	>	}
533	>
534	>	if (!foundInversions.empty()) {
535	>	std::sort(foundInversions.begin(), foundInversions.end());
536	>	std::vector<std::string> theKeys = foundInversions[0].third;
537	>
538	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
539	>	return bestType;
540	>	} else {
541	>	//if no exact match found, try wild card match
542	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
543	>	}
544	>	}
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);
552	+
553	+	//try exact match first
554	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
555	+	if (nbiType) {
556	+	return nbiType;
557	+	} else {
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,
616	+	const std::string &at2){
617	+	std::vector<std::string> keys;
618	+	keys.push_back(at1);
619	+	keys.push_back(at2);
620	+	return bondTypeCont_.find(keys);
621	+	}
622	+
623	+	BendType* ForceField::getExactBendType(const std::string &at1,
624	+	const std::string &at2,
625	+	const std::string &at3){
626	+	std::vector<std::string> keys;
627	+	keys.push_back(at1);
628	+	keys.push_back(at2);
629		keys.push_back(at3);
630		return bendTypeCont_.find(keys);
631	<	}
632	<
633	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
634	<	const std::string &at3, const std::string &at4){
631	>	}
632	>
633	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
634	>	const std::string &at2,
635	>	const std::string &at3,
636	>	const std::string &at4){
637		std::vector<std::string> keys;
638		keys.push_back(at1);
639		keys.push_back(at2);
640		keys.push_back(at3);
641		keys.push_back(at4);
642		return torsionTypeCont_.find(keys);
643	<	}
644	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
643	>	}
644	>
645	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
646	>	const std::string &at2,
647	>	const std::string &at3,
648	>	const std::string &at4){
649		std::vector<std::string> keys;
650	+	keys.push_back(at1);
651	+	keys.push_back(at2);
652	+	keys.push_back(at3);
653	+	keys.push_back(at4);
654	+	return inversionTypeCont_.find(keys);
655	+	}
656	+
657	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
658	+	std::vector<std::string> keys;
659	+	keys.push_back(at1);
660	+	keys.push_back(at2);
661	+	return nonBondedInteractionTypeCont_.find(keys);
662	+	}
663	+
664	+
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	<	}
670	>	}
671
672	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
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	+
679	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
680	+	BondType* bondType) {
681	+	std::vector<std::string> keys;
682		keys.push_back(at1);
683		keys.push_back(at2);
684	<	return bondTypeCont_.add(keys, bondType);
685	<
686	<	}
687	<
688	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
684	>	return bondTypeCont_.add(keys, bondType);
685	>	}
686	>
687	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
688	>	const std::string &at3, BendType* bendType) {
689		std::vector<std::string> keys;
690		keys.push_back(at1);
691		keys.push_back(at2);
692		keys.push_back(at3);
693		return bendTypeCont_.add(keys, bendType);
694	<	}
695	<
696	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
697	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
694	>	}
695	>
696	>	bool ForceField::addTorsionType(const std::string &at1,
697	>	const std::string &at2,
698	>	const std::string &at3,
699	>	const std::string &at4,
700	>	TorsionType* torsionType) {
701		std::vector<std::string> keys;
702		keys.push_back(at1);
703		keys.push_back(at2);
704		keys.push_back(at3);
705		keys.push_back(at4);
706		return torsionTypeCont_.add(keys, torsionType);
707	<	}
707	>	}
708
709	<	double ForceField::getRcutFromAtomType(AtomType* at) {
710	<	/**@todo */
711	<	GenericData* data;
712	<	double rcut = 0.0;
713	<
714	<	if (at->isLennardJones()) {
715	<	data = at->getPropertyByName("LennardJones");
716	<	if (data != NULL) {
717	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
718	<
719	<	if (ljData != NULL) {
720	<	LJParam ljParam = ljData->getData();
721	<
722	<	//by default use 2.5*sigma as cutoff radius
723	<	rcut = 2.5 * ljParam.sigma;
724	<
725	<	} else {
726	<	sprintf( painCave.errMsg,
727	<	"Can not cast GenericData to LJParam\n");
728	<	painCave.severity = OOPSE_ERROR;
729	<	painCave.isFatal = 1;
730	<	simError();
731	<	}
732	<	} else {
733	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
734	<	painCave.severity = OOPSE_ERROR;
735	<	painCave.isFatal = 1;
736	<	simError();
217	<	}
709	>	bool ForceField::addInversionType(const std::string &at1,
710	>	const std::string &at2,
711	>	const std::string &at3,
712	>	const std::string &at4,
713	>	InversionType* inversionType) {
714	>	std::vector<std::string> keys;
715	>	keys.push_back(at1);
716	>	keys.push_back(at2);
717	>	keys.push_back(at3);
718	>	keys.push_back(at4);
719	>	return inversionTypeCont_.add(keys, inversionType);
720	>	}
721	>
722	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
723	>	const std::string &at2,
724	>	NonBondedInteractionType* nbiType) {
725	>	std::vector<std::string> keys;
726	>	keys.push_back(at1);
727	>	keys.push_back(at2);
728	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
729	>	}
730	>
731	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
732	>	RealType rcut(0.0);
733	>
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	<	}
756	>	}
757	>
758
759	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
759	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
760		std::string forceFieldFilename(filename);
761		ifstrstream* ffStream = new ifstrstream();
762
#	Line 229 | Line 764 | ifstrstream* ForceField::openForceFieldFile(const std:
764		ffStream->open(forceFieldFilename.c_str());
765		if(!ffStream->is_open()){
766
767	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
768	<	ffStream->open( forceFieldFilename.c_str() );
767	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
768	>	ffStream->open( forceFieldFilename.c_str() );
769
770	<	//if current directory does not contain the force field file,
771	<	//try to open it in the path
772	<	if(!ffStream->is_open()){
770	>	//if current directory does not contain the force field file,
771	>	//try to open it in the path
772	>	if(!ffStream->is_open()){
773
774	<	sprintf( painCave.errMsg,
775	<	"Error opening the force field parameter file:\n"
776	<	"\t%s\n"
777	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
778	<	"variable?\n",
779	<	forceFieldFilename.c_str() );
780	<	painCave.severity = OOPSE_ERROR;
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
774	>	sprintf( painCave.errMsg,
775	>	"Error opening the force field parameter file:\n"
776	>	"\t%s\n"
777	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
778	>	"variable?\n",
779	>	forceFieldFilename.c_str() );
780	>	painCave.severity = OPENMD_ERROR;
781	>	painCave.isFatal = 1;
782	>	simError();
783	>	}
784		}
250	–
785		return ffStream;
786	+	}
787
788	<	}
254	<
255	<	} //end namespace oopse
788	>	} //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.
trunk/src/brains/ForceField.cpp (property svn:keywords), Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 UTC

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