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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 939 by gezelter, Thu Apr 20 18:24:24 2006 UTC vs.
trunk/src/brains/ForceField.cpp (file contents), Revision 1880 by gezelter, Mon Jun 17 18:28:30 2013 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, 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
46	–	* @time 22:51am
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	–	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	–	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	–	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 );
91		} else {
92		ffPath_ = tempPath;
93		}
94	+
95	+	setForceFieldFileName(ffName + ".frc");
96	+
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	+	void ForceField::parse(const std::string& filename) {
145	+	ifstrstream* ffStream;
146
147	<	ForceField::~ForceField() {
148	<	deleteAtypes();
149	<	deleteSwitch();
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		}
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 88 | Line 204 | namespace oopse {
204		if (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,
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);
#	Line 106 | Line 276 | namespace oopse {
276		if (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		}
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;
363		} 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_);
364
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	+	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	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
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	+	keys.push_back(at3);
456	+	keys.push_back(at4);
457	+
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, const std::string &at2,
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);
#	Line 146 | Line 629 | namespace oopse {
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){
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);
#	Line 156 | Line 641 | namespace oopse {
641		keys.push_back(at4);
642		return torsionTypeCont_.find(keys);
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		}
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);
170	<
684	>	return bondTypeCont_.add(keys, bondType);
685		}
686	<
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;
#	Line 178 | Line 692 | namespace oopse {
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) {
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);
#	Line 189 | Line 706 | namespace oopse {
706		return torsionTypeCont_.add(keys, torsionType);
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();
220	<	}
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		}
757	+
758
226	–
759		ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
760		std::string forceFieldFilename(filename);
761		ifstrstream* ffStream = new ifstrstream();
#	Line 245 | Line 777 | namespace oopse {
777		"\tHave you tried setting the FORCE_PARAM_PATH environment "
778		"variable?\n",
779		forceFieldFilename.c_str() );
780	<	painCave.severity = OOPSE_ERROR;
780	>	painCave.severity = OPENMD_ERROR;
781		painCave.isFatal = 1;
782		simError();
783		}
784		}
253	–
785		return ffStream;
255	–
786		}
787
788	<	void ForceField::setFortranForceOptions(){
259	<	ForceOptions theseFortranOptions;
260	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
261	<	setfForceOptions(&theseFortranOptions);
262	<	}
263	<	} //end namespace oopse
788	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 939 by gezelter, Thu Apr 20 18:24:24 2006 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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