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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.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 1 | Line 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
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 "UseTheForce/ForceField.hpp"
53	+	#include "utils/simError.h"
54	+	#include "utils/Tuple.hpp"
55	+	namespace OpenMD {
56
57	<	AtomType* ForceField::getMatchingAtomType(const string &at) {
57	>	ForceField::ForceField() {
58
59	<	map<string, AtomType*>::iterator iter;
60	<
61	<	iter = atomTypeMap.find(at);
62	<	if (iter != atomTypeMap.end()) {
63	<	return iter->second;
64	<	} else {
65	<	return NULL;
59	>	char* tempPath;
60	>	tempPath = getenv("FORCE_PARAM_PATH");
61	>
62	>	if (tempPath == NULL) {
63	>	//convert a macro from compiler to a string in c++
64	>	STR_DEFINE(ffPath_, FRC_PATH );
65	>	} else {
66	>	ffPath_ = tempPath;
67	>	}
68		}
13	–	}
69
70	<	BondType* ForceField::getMatchingBondType(const string &at1,
71	<	const string &at2) {
70	>	/**
71	>	* getAtomType by string
72	>	*
73	>	* finds the requested atom type in this force field using the string
74	>	* name of the atom type.
75	>	*/
76	>	AtomType* ForceField::getAtomType(const std::string &at) {
77	>	std::vector<std::string> keys;
78	>	keys.push_back(at);
79	>	return atomTypeCont_.find(keys);
80	>	}
81
82	<	map<pair<string,string>, BondType*>::iterator iter;
83	<	vector<BondType*> foundTypes;
82	>	/**
83	>	* getAtomType by ident
84	>	*
85	>	* finds the requested atom type in this force field using the
86	>	* integer ident instead of the string name of the atom type.
87	>	*/
88	>	AtomType* ForceField::getAtomType(int ident) {
89	>	std::string at = atypeIdentToName.find(ident)->second;
90	>	return getAtomType(at);
91	>	}
92
93	<	iter = bondTypeMap.find(pair<at1, at2>);
94	<	if (iter != bondTypeMap.end()) {
95	<	// exact match, so just return it
96	<	return iter->second;
97	<	}
93	>	BondType* ForceField::getBondType(const std::string &at1,
94	>	const std::string &at2) {
95	>	std::vector<std::string> keys;
96	>	keys.push_back(at1);
97	>	keys.push_back(at2);
98
99	<	iter = bondTypeMap.find(pair<at2, at1>);
100	<	if (iter != bondTypeMap.end()) {
101	<	// exact match in reverse order, so just return it
102	<	return iter->second;
103	<	}
99	>	//try exact match first
100	>	BondType* bondType = bondTypeCont_.find(keys);
101	>	if (bondType) {
102	>	return bondType;
103	>	} else {
104	>	AtomType* atype1;
105	>	AtomType* atype2;
106	>	std::vector<std::string> at1key;
107	>	at1key.push_back(at1);
108	>	atype1 = atomTypeCont_.find(at1key);
109	>
110	>	std::vector<std::string> at2key;
111	>	at2key.push_back(at2);
112	>	atype2 = atomTypeCont_.find(at2key);
113
114	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
115	<	if (iter != bondTypeMap.end()) {
116	<	foundTypes.push_back(iter->second);
36	<	}
114	>	// query atom types for their chains of responsibility
115	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
116	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
117
118	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
119	<	if (iter != bondTypeMap.end()) {
40	<	foundTypes.push_back(iter->second);
41	<	}
118	>	std::vector<AtomType*>::iterator i;
119	>	std::vector<AtomType*>::iterator j;
120
121	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
122	<	if (iter != bondTypeMap.end()) {
123	<	foundTypes.push_back(iter->second);
46	<	}
121	>	int ii = 0;
122	>	int jj = 0;
123	>	int bondTypeScore;
124
125	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
126	<	if (iter != bondTypeMap.end()) {
127	<	foundTypes.push_back(iter->second);
125	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
126	>
127	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
128	>	jj = 0;
129	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
130	>
131	>	bondTypeScore = ii + jj;
132	>
133	>	std::vector<std::string> myKeys;
134	>	myKeys.push_back((*i)->getName());
135	>	myKeys.push_back((*j)->getName());
136	>
137	>	BondType* bondType = bondTypeCont_.find(myKeys);
138	>	if (bondType) {
139	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
140	>	}
141	>	jj++;
142	>	}
143	>	ii++;
144	>	}
145	>
146	>
147	>	if (foundBonds.size() > 0) {
148	>	// sort the foundBonds by the score:
149	>	std::sort(foundBonds.begin(), foundBonds.end());
150	>
151	>	int bestScore = foundBonds[0].first;
152	>	std::vector<std::string> theKeys = foundBonds[0].second;
153	>
154	>	BondType* bestType = bondTypeCont_.find(theKeys);
155	>
156	>	return bestType;
157	>	} else {
158	>	//if no exact match found, try wild card match
159	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
160	>	}
161	>	}
162		}
163
164	<	if (foundTypes.empty()) {
165	<	return NULL;
166	<	} else {
167	<
164	>	BendType* ForceField::getBendType(const std::string &at1,
165	>	const std::string &at2,
166	>	const std::string &at3) {
167	>	std::vector<std::string> keys;
168	>	keys.push_back(at1);
169	>	keys.push_back(at2);
170	>	keys.push_back(at3);
171
172	<
172	>	//try exact match first
173	>	BendType* bendType = bendTypeCont_.find(keys);
174	>	if (bendType) {
175	>	return bendType;
176	>	} else {
177
178	+	AtomType* atype1;
179	+	AtomType* atype2;
180	+	AtomType* atype3;
181	+	std::vector<std::string> at1key;
182	+	at1key.push_back(at1);
183	+	atype1 = atomTypeCont_.find(at1key);
184	+
185	+	std::vector<std::string> at2key;
186	+	at2key.push_back(at2);
187	+	atype2 = atomTypeCont_.find(at2key);
188
189	+	std::vector<std::string> at3key;
190	+	at3key.push_back(at3);
191	+	atype3 = atomTypeCont_.find(at3key);
192
193	+	// query atom types for their chains of responsibility
194	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
195	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
196	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
197	+
198	+	std::vector<AtomType*>::iterator i;
199	+	std::vector<AtomType*>::iterator j;
200	+	std::vector<AtomType*>::iterator k;
201	+
202	+	int ii = 0;
203	+	int jj = 0;
204	+	int kk = 0;
205	+	int IKscore;
206	+
207	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
208	+
209	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
210	+	ii = 0;
211	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
212	+	kk = 0;
213	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
214	+
215	+	IKscore = ii + kk;
216	+
217	+	std::vector<std::string> myKeys;
218	+	myKeys.push_back((*i)->getName());
219	+	myKeys.push_back((*j)->getName());
220	+	myKeys.push_back((*k)->getName());
221	+
222	+	BendType* bendType = bendTypeCont_.find(myKeys);
223	+	if (bendType) {
224	+	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
225	+	}
226	+	kk++;
227	+	}
228	+	ii++;
229	+	}
230	+	jj++;
231	+	}
232	+
233	+	if (foundBends.size() > 0) {
234	+	std::sort(foundBends.begin(), foundBends.end());
235	+	int jscore = foundBends[0].first;
236	+	int ikscore = foundBends[0].second;
237	+	std::vector<std::string> theKeys = foundBends[0].third;
238	+
239	+	BendType* bestType = bendTypeCont_.find(theKeys);
240	+	return bestType;
241	+	} else {
242	+	//if no exact match found, try wild card match
243	+	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
244	+	}
245	+	}
246	+	}
247	+
248	+	TorsionType* ForceField::getTorsionType(const std::string &at1,
249	+	const std::string &at2,
250	+	const std::string &at3,
251	+	const std::string &at4) {
252	+	std::vector<std::string> keys;
253	+	keys.push_back(at1);
254	+	keys.push_back(at2);
255	+	keys.push_back(at3);
256	+	keys.push_back(at4);
257	+
258	+
259	+	//try exact match first
260	+	TorsionType* torsionType = torsionTypeCont_.find(keys);
261	+	if (torsionType) {
262	+	return torsionType;
263	+	} else {
264	+
265	+	AtomType* atype1;
266	+	AtomType* atype2;
267	+	AtomType* atype3;
268	+	AtomType* atype4;
269	+	std::vector<std::string> at1key;
270	+	at1key.push_back(at1);
271	+	atype1 = atomTypeCont_.find(at1key);
272
273	+	std::vector<std::string> at2key;
274	+	at2key.push_back(at2);
275	+	atype2 = atomTypeCont_.find(at2key);
276
277	+	std::vector<std::string> at3key;
278	+	at3key.push_back(at3);
279	+	atype3 = atomTypeCont_.find(at3key);
280
281	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
282	<	const string &at3);
283	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
68	<	const string &at3, const string &at4);
281	>	std::vector<std::string> at4key;
282	>	at4key.push_back(at4);
283	>	atype4 = atomTypeCont_.find(at4key);
284
285	<	double ForceField::getRcutForAtomType(AtomType* at);
285	>	// query atom types for their chains of responsibility
286	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
287	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
288	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
289	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
290
291	+	std::vector<AtomType*>::iterator i;
292	+	std::vector<AtomType*>::iterator j;
293	+	std::vector<AtomType*>::iterator k;
294	+	std::vector<AtomType*>::iterator l;
295
296	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
297	<
298	<	vector<vector<string> > results;
296	>	int ii = 0;
297	>	int jj = 0;
298	>	int kk = 0;
299	>	int ll = 0;
300	>	int ILscore;
301	>	int JKscore;
302
303	<
303	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
304
305	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
306	+	kk = 0;
307	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
308	+	ii = 0;
309	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
310	+	ll = 0;
311	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
312	+
313	+	ILscore = ii + ll;
314	+	JKscore = jj + kk;
315
316	<	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
317	<
318	<	int nStrings;
319	<	vector<string> oneResult;
320	<	vector<vector<string> > allResults;
316	>	std::vector<std::string> myKeys;
317	>	myKeys.push_back((*i)->getName());
318	>	myKeys.push_back((*j)->getName());
319	>	myKeys.push_back((*k)->getName());
320	>	myKeys.push_back((*l)->getName());
321
322	<	nStrings = myAts.size();
322	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
323	>	if (torsionType) {
324	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
325	>	}
326	>	ll++;
327	>	}
328	>	ii++;
329	>	}
330	>	kk++;
331	>	}
332	>	jj++;
333	>	}
334	>
335	>	if (foundTorsions.size() > 0) {
336	>	std::sort(foundTorsions.begin(), foundTorsions.end());
337	>	int jkscore = foundTorsions[0].first;
338	>	int ilscore = foundTorsions[0].second;
339	>	std::vector<std::string> theKeys = foundTorsions[0].third;
340	>
341	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
342	>	return bestType;
343	>	} else {
344	>	//if no exact match found, try wild card match
345	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
346	>	}
347	>	}
348	>	}
349
350	<	if (nStrings == 1) {
351	<	oneResult.push_back(wildcardCharacter);
352	<	allResults.push_back(oneResult);
353	<	return allResults;
354	<	} else {
355	<
356	<	for (i=0; i < nStrings; i++) {
357	<	oneResult = myAts;
358	<	replace(oneResult.begin(), oneResult.end(),
350	>	InversionType* ForceField::getInversionType(const std::string &at1,
351	>	const std::string &at2,
352	>	const std::string &at3,
353	>	const std::string &at4) {
354	>	std::vector<std::string> keys;
355	>	keys.push_back(at1);
356	>	keys.push_back(at2);
357	>	keys.push_back(at3);
358	>	keys.push_back(at4);
359	>
360	>	//try exact match first
361	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
362	>	if (inversionType) {
363	>	return inversionType;
364	>	} else {
365	>
366	>	AtomType* atype1;
367	>	AtomType* atype2;
368	>	AtomType* atype3;
369	>	AtomType* atype4;
370	>	std::vector<std::string> at1key;
371	>	at1key.push_back(at1);
372	>	atype1 = atomTypeCont_.find(at1key);
373	>
374	>	std::vector<std::string> at2key;
375	>	at2key.push_back(at2);
376	>	atype2 = atomTypeCont_.find(at2key);
377	>
378	>	std::vector<std::string> at3key;
379	>	at3key.push_back(at3);
380	>	atype3 = atomTypeCont_.find(at3key);
381	>
382	>	std::vector<std::string> at4key;
383	>	at4key.push_back(at4);
384	>	atype4 = atomTypeCont_.find(at4key);
385	>
386	>	// query atom types for their chains of responsibility
387	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
388	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
389	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
390	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
391	>
392	>	std::vector<AtomType*>::iterator i;
393	>	std::vector<AtomType*>::iterator j;
394	>	std::vector<AtomType*>::iterator k;
395	>	std::vector<AtomType*>::iterator l;
396	>
397	>	int ii = 0;
398	>	int jj = 0;
399	>	int kk = 0;
400	>	int ll = 0;
401	>	int Iscore;
402	>	int JKLscore;
403	>
404	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
405	>
406	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
407	>	kk = 0;
408	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
409	>	ii = 0;
410	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
411	>	ll = 0;
412	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
413	>
414	>	Iscore = ii;
415	>	JKLscore = jj + kk + ll;
416	>
417	>	std::vector<std::string> myKeys;
418	>	myKeys.push_back((*i)->getName());
419	>	myKeys.push_back((*j)->getName());
420	>	myKeys.push_back((*k)->getName());
421	>	myKeys.push_back((*l)->getName());
422	>
423	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
424	>	if (inversionType) {
425	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
426	>	}
427	>	ll++;
428	>	}
429	>	ii++;
430	>	}
431	>	kk++;
432	>	}
433	>	jj++;
434	>	}
435	>
436	>	if (foundInversions.size() > 0) {
437	>	std::sort(foundInversions.begin(), foundInversions.end());
438	>	int iscore = foundInversions[0].first;
439	>	int jklscore = foundInversions[0].second;
440	>	std::vector<std::string> theKeys = foundInversions[0].third;
441	>
442	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
443	>	return bestType;
444	>	} else {
445	>	//if no exact match found, try wild card match
446	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
447	>	}
448	>	}
449	>	}
450	>
451	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
452	>
453	>	std::vector<std::string> keys;
454	>	keys.push_back(at1);
455	>	keys.push_back(at2);
456	>
457	>	//try exact match first
458	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
459	>	if (nbiType) {
460	>	return nbiType;
461	>	} else {
462	>	AtomType* atype1;
463	>	AtomType* atype2;
464	>	std::vector<std::string> at1key;
465	>	at1key.push_back(at1);
466	>	atype1 = atomTypeCont_.find(at1key);
467	>
468	>	std::vector<std::string> at2key;
469	>	at2key.push_back(at2);
470	>	atype2 = atomTypeCont_.find(at2key);
471	>
472	>	// query atom types for their chains of responsibility
473	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
474	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
475	>
476	>	std::vector<AtomType*>::iterator i;
477	>	std::vector<AtomType*>::iterator j;
478	>
479	>	int ii = 0;
480	>	int jj = 0;
481	>	int nbiTypeScore;
482	>
483	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
484	>
485	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
486	>	jj = 0;
487	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
488	>
489	>	nbiTypeScore = ii + jj;
490	>
491	>	std::vector<std::string> myKeys;
492	>	myKeys.push_back((*i)->getName());
493	>	myKeys.push_back((*j)->getName());
494	>
495	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
496	>	if (nbiType) {
497	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
498	>	}
499	>	jj++;
500	>	}
501	>	ii++;
502	>	}
503	>
504	>
505	>	if (foundNBI.size() > 0) {
506	>	// sort the foundNBI by the score:
507	>	std::sort(foundNBI.begin(), foundNBI.end());
508	>
509	>	int bestScore = foundNBI[0].first;
510	>	std::vector<std::string> theKeys = foundNBI[0].second;
511	>
512	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
513	>	return bestType;
514	>	} else {
515	>	//if no exact match found, try wild card match
516	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
517	>	}
518	>	}
519	>	}
520	>
521	>	BondType* ForceField::getExactBondType(const std::string &at1,
522	>	const std::string &at2){
523	>	std::vector<std::string> keys;
524	>	keys.push_back(at1);
525	>	keys.push_back(at2);
526	>	return bondTypeCont_.find(keys);
527	>	}
528	>
529	>	BendType* ForceField::getExactBendType(const std::string &at1,
530	>	const std::string &at2,
531	>	const std::string &at3){
532	>	std::vector<std::string> keys;
533	>	keys.push_back(at1);
534	>	keys.push_back(at2);
535	>	keys.push_back(at3);
536	>	return bendTypeCont_.find(keys);
537	>	}
538	>
539	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
540	>	const std::string &at2,
541	>	const std::string &at3,
542	>	const std::string &at4){
543	>	std::vector<std::string> keys;
544	>	keys.push_back(at1);
545	>	keys.push_back(at2);
546	>	keys.push_back(at3);
547	>	keys.push_back(at4);
548	>	return torsionTypeCont_.find(keys);
549	>	}
550	>
551	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
552	>	const std::string &at2,
553	>	const std::string &at3,
554	>	const std::string &at4){
555	>	std::vector<std::string> keys;
556	>	keys.push_back(at1);
557	>	keys.push_back(at2);
558	>	keys.push_back(at3);
559	>	keys.push_back(at4);
560	>	return inversionTypeCont_.find(keys);
561	>	}
562	>
563	>	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
564	>	std::vector<std::string> keys;
565	>	keys.push_back(at1);
566	>	keys.push_back(at2);
567	>	return nonBondedInteractionTypeCont_.find(keys);
568	>	}
569	>
570	>
571	>	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
572	>	std::vector<std::string> keys;
573	>	keys.push_back(at);
574	>	atypeIdentToName[atomType->getIdent()] = at;
575	>	return atomTypeCont_.add(keys, atomType);
576	>	}
577	>
578	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
579	>	std::vector<std::string> keys;
580	>	keys.push_back(at);
581	>	atypeIdentToName[atomType->getIdent()] = at;
582	>	return atomTypeCont_.replace(keys, atomType);
583	>	}
584	>
585	>	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
586	>	BondType* bondType) {
587	>	std::vector<std::string> keys;
588	>	keys.push_back(at1);
589	>	keys.push_back(at2);
590	>	return bondTypeCont_.add(keys, bondType);
591	>	}
592	>
593	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
594	>	const std::string &at3, BendType* bendType) {
595	>	std::vector<std::string> keys;
596	>	keys.push_back(at1);
597	>	keys.push_back(at2);
598	>	keys.push_back(at3);
599	>	return bendTypeCont_.add(keys, bendType);
600	>	}
601	>
602	>	bool ForceField::addTorsionType(const std::string &at1,
603	>	const std::string &at2,
604	>	const std::string &at3,
605	>	const std::string &at4,
606	>	TorsionType* torsionType) {
607	>	std::vector<std::string> keys;
608	>	keys.push_back(at1);
609	>	keys.push_back(at2);
610	>	keys.push_back(at3);
611	>	keys.push_back(at4);
612	>	return torsionTypeCont_.add(keys, torsionType);
613	>	}
614	>
615	>	bool ForceField::addInversionType(const std::string &at1,
616	>	const std::string &at2,
617	>	const std::string &at3,
618	>	const std::string &at4,
619	>	InversionType* inversionType) {
620	>	std::vector<std::string> keys;
621	>	keys.push_back(at1);
622	>	keys.push_back(at2);
623	>	keys.push_back(at3);
624	>	keys.push_back(at4);
625	>	return inversionTypeCont_.add(keys, inversionType);
626	>	}
627	>
628	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
629	>	const std::string &at2,
630	>	NonBondedInteractionType* nbiType) {
631	>	std::vector<std::string> keys;
632	>	keys.push_back(at1);
633	>	keys.push_back(at2);
634	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
635	>	}
636	>
637	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
638	>	/**@todo */
639	>	GenericData* data;
640	>	RealType rcut = 0.0;
641	>
642	>	if (at->isLennardJones()) {
643	>	data = at->getPropertyByName("LennardJones");
644	>	if (data != NULL) {
645	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
646	>
647	>	if (ljData != NULL) {
648	>	LJParam ljParam = ljData->getData();
649	>
650	>	//by default use 2.5*sigma as cutoff radius
651	>	rcut = 2.5 * ljParam.sigma;
652	>
653	>	} else {
654	>	sprintf( painCave.errMsg,
655	>	"Can not cast GenericData to LJParam\n");
656	>	painCave.severity = OPENMD_ERROR;
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>	} else {
661	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662	>	painCave.severity = OPENMD_ERROR;
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666	>	}
667	>	return rcut;
668	>	}
669	>
670	>
671	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
672	>	std::string forceFieldFilename(filename);
673	>	ifstrstream* ffStream = new ifstrstream();
674	>
675	>	//try to open the force filed file in current directory first
676	>	ffStream->open(forceFieldFilename.c_str());
677	>	if(!ffStream->is_open()){
678	>
679	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
680	>	ffStream->open( forceFieldFilename.c_str() );
681	>
682	>	//if current directory does not contain the force field file,
683	>	//try to open it in the path
684	>	if(!ffStream->is_open()){
685	>
686	>	sprintf( painCave.errMsg,
687	>	"Error opening the force field parameter file:\n"
688	>	"\t%s\n"
689	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
690	>	"variable?\n",
691	>	forceFieldFilename.c_str() );
692	>	painCave.severity = OPENMD_ERROR;
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696	>	}
697	>	return ffStream;
698	>	}
699	>
700	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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