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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 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		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	<	#include "UseTheForce/ForceField.hpp"
51	>	#include <algorithm>
52	>	#include "brains/ForceField.hpp"
53		#include "utils/simError.h"
52	–	#include "UseTheForce/DarkSide/atype_interface.h"
53	–	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	–	namespace oopse {
54
55	<	ForceField::ForceField() {
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	>	#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	>	namespace OpenMD {
83	>
84	>	ForceField::ForceField(std::string ffName) {
85	>
86		char* tempPath;
87		tempPath = getenv("FORCE_PARAM_PATH");
88	<
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	+	setForceFieldFileName(ffName + ".frc");
97	+
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	+	void ForceField::parse(const std::string& filename) {
146	+	ifstrstream* ffStream;
147
148	<	ForceField::~ForceField() {
149	<	deleteAtypes();
150	<	deleteSwitch();
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	+	/**
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	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
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);
#	Line 88 | Line 205 | namespace oopse {
205		if (bondType) {
206		return bondType;
207		} else {
208	<	//if no exact match found, try wild card match
209	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
210	<	}
208	>	AtomType* atype1;
209	>	AtomType* atype2;
210	>	std::vector<std::string> at1key;
211	>	at1key.push_back(at1);
212	>	atype1 = atomTypeCont_.find(at1key);
213	>
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	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
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);
#	Line 106 | Line 278 | namespace oopse {
278		if (bendType) {
279		return bendType;
280		} else {
281	<	//if no exact match found, try wild card match
282	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
281	>
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	>	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	>	std::vector<AtomType*>::iterator i;
303	>	std::vector<AtomType*>::iterator j;
304	>	std::vector<AtomType*>::iterator k;
305	>
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	>	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	>	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	>	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, const std::string &at2,
353	<	const std::string &at3, const std::string &at4) {
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 {
126	–	//if no exact match found, try wild card match
127	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
128	–	}
129	–
130	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
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	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
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, const std::string &at2,
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);
#	Line 146 | Line 639 | namespace oopse {
639		keys.push_back(at3);
640		return bendTypeCont_.find(keys);
641		}
642	<
643	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
644	<	const std::string &at3, const std::string &at4){
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);
#	Line 156 | Line 651 | namespace oopse {
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::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
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);
170	<
694	>	return bondTypeCont_.add(keys, bondType);
695		}
696	<
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;
#	Line 178 | Line 702 | namespace oopse {
702		keys.push_back(at3);
703		return bendTypeCont_.add(keys, bendType);
704		}
705	<
706	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
707	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
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);
#	Line 189 | Line 716 | namespace oopse {
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	<	/**@todo */
743	<	GenericData* data;
744	<	RealType rcut = 0.0;
745	<
746	<	if (at->isLennardJones()) {
198	<	data = at->getPropertyByName("LennardJones");
199	<	if (data != NULL) {
200	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
201	<
202	<	if (ljData != NULL) {
203	<	LJParam ljParam = ljData->getData();
204	<
205	<	//by default use 2.5*sigma as cutoff radius
206	<	rcut = 2.5 * ljParam.sigma;
207	<
208	<	} else {
209	<	sprintf( painCave.errMsg,
210	<	"Can not cast GenericData to LJParam\n");
211	<	painCave.severity = OOPSE_ERROR;
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
215	<	} else {
216	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
217	<	painCave.severity = OOPSE_ERROR;
218	<	painCave.isFatal = 1;
219	<	simError();
220	<	}
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
226	–
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());
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() );
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
#	Line 245 | Line 789 | namespace oopse {
789		"\tHave you tried setting the FORCE_PARAM_PATH environment "
790		"variable?\n",
791		forceFieldFilename.c_str() );
792	<	painCave.severity = OOPSE_ERROR;
792	>	painCave.severity = OPENMD_ERROR;
793		painCave.isFatal = 1;
794		simError();
795		}
796		}
253	–
797		return ffStream;
255	–
798		}
799
800	<	void ForceField::setFortranForceOptions(){
259	<	ForceOptions theseFortranOptions;
260	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
261	<	setfForceOptions(&theseFortranOptions);
262	<	}
263	<	} //end namespace oopse
800	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 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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