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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 1710 by gezelter, Fri May 18 21:44:02 2012 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	+	#include "types/LennardJonesAdapter.hpp"
56
57	<	AtomType* ForceField::getMatchingAtomType(const string &at) {
57	>	namespace OpenMD {
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	>	ForceField::ForceField() {
60	>
61	>	char* tempPath;
62	>	tempPath = getenv("FORCE_PARAM_PATH");
63	>
64	>	if (tempPath == NULL) {
65	>	//convert a macro from compiler to a string in c++
66	>	STR_DEFINE(ffPath_, FRC_PATH );
67	>	} else {
68	>	ffPath_ = tempPath;
69	>	}
70		}
13	–	}
71
72	<	BondType* ForceField::getMatchingBondType(const string &at1,
73	<	const string &at2) {
72	>	/**
73	>	* getAtomType by string
74	>	*
75	>	* finds the requested atom type in this force field using the string
76	>	* name of the atom type.
77	>	*/
78	>	AtomType* ForceField::getAtomType(const std::string &at) {
79	>	std::vector<std::string> keys;
80	>	keys.push_back(at);
81	>	return atomTypeCont_.find(keys);
82	>	}
83
84	<	map<pair<string,string>, BondType*>::iterator iter;
85	<	vector<BondType*> foundTypes;
84	>	/**
85	>	* getAtomType by ident
86	>	*
87	>	* finds the requested atom type in this force field using the
88	>	* integer ident instead of the string name of the atom type.
89	>	*/
90	>	AtomType* ForceField::getAtomType(int ident) {
91	>	std::string at = atypeIdentToName.find(ident)->second;
92	>	return getAtomType(at);
93	>	}
94
95	<	iter = bondTypeMap.find(pair<at1, at2>);
96	<	if (iter != bondTypeMap.end()) {
97	<	// exact match, so just return it
98	<	return iter->second;
99	<	}
95	>	BondType* ForceField::getBondType(const std::string &at1,
96	>	const std::string &at2) {
97	>	std::vector<std::string> keys;
98	>	keys.push_back(at1);
99	>	keys.push_back(at2);
100
101	<	iter = bondTypeMap.find(pair<at2, at1>);
102	<	if (iter != bondTypeMap.end()) {
103	<	// exact match in reverse order, so just return it
104	<	return iter->second;
105	<	}
101	>	//try exact match first
102	>	BondType* bondType = bondTypeCont_.find(keys);
103	>	if (bondType) {
104	>	return bondType;
105	>	} else {
106	>	AtomType* atype1;
107	>	AtomType* atype2;
108	>	std::vector<std::string> at1key;
109	>	at1key.push_back(at1);
110	>	atype1 = atomTypeCont_.find(at1key);
111	>
112	>	std::vector<std::string> at2key;
113	>	at2key.push_back(at2);
114	>	atype2 = atomTypeCont_.find(at2key);
115
116	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
117	<	if (iter != bondTypeMap.end()) {
118	<	foundTypes.push_back(iter->second);
36	<	}
116	>	// query atom types for their chains of responsibility
117	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
118	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
119
120	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
121	<	if (iter != bondTypeMap.end()) {
40	<	foundTypes.push_back(iter->second);
41	<	}
120	>	std::vector<AtomType*>::iterator i;
121	>	std::vector<AtomType*>::iterator j;
122
123	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
124	<	if (iter != bondTypeMap.end()) {
125	<	foundTypes.push_back(iter->second);
46	<	}
123	>	int ii = 0;
124	>	int jj = 0;
125	>	int bondTypeScore;
126
127	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
128	<	if (iter != bondTypeMap.end()) {
129	<	foundTypes.push_back(iter->second);
127	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
128	>
129	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
130	>	jj = 0;
131	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
132	>
133	>	bondTypeScore = ii + jj;
134	>
135	>	std::vector<std::string> myKeys;
136	>	myKeys.push_back((*i)->getName());
137	>	myKeys.push_back((*j)->getName());
138	>
139	>	BondType* bondType = bondTypeCont_.find(myKeys);
140	>	if (bondType) {
141	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
142	>	}
143	>	jj++;
144	>	}
145	>	ii++;
146	>	}
147	>
148	>
149	>	if (foundBonds.size() > 0) {
150	>	// sort the foundBonds by the score:
151	>	std::sort(foundBonds.begin(), foundBonds.end());
152	>
153	>	int bestScore = foundBonds[0].first;
154	>	std::vector<std::string> theKeys = foundBonds[0].second;
155	>
156	>	BondType* bestType = bondTypeCont_.find(theKeys);
157	>
158	>	return bestType;
159	>	} else {
160	>	//if no exact match found, try wild card match
161	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
162	>	}
163	>	}
164		}
165
166	<	if (foundTypes.empty()) {
167	<	return NULL;
168	<	} else {
169	<
166	>	BendType* ForceField::getBendType(const std::string &at1,
167	>	const std::string &at2,
168	>	const std::string &at3) {
169	>	std::vector<std::string> keys;
170	>	keys.push_back(at1);
171	>	keys.push_back(at2);
172	>	keys.push_back(at3);
173
174	<
174	>	//try exact match first
175	>	BendType* bendType = bendTypeCont_.find(keys);
176	>	if (bendType) {
177	>	return bendType;
178	>	} else {
179
180	+	AtomType* atype1;
181	+	AtomType* atype2;
182	+	AtomType* atype3;
183	+	std::vector<std::string> at1key;
184	+	at1key.push_back(at1);
185	+	atype1 = atomTypeCont_.find(at1key);
186	+
187	+	std::vector<std::string> at2key;
188	+	at2key.push_back(at2);
189	+	atype2 = atomTypeCont_.find(at2key);
190
191	+	std::vector<std::string> at3key;
192	+	at3key.push_back(at3);
193	+	atype3 = atomTypeCont_.find(at3key);
194
195	+	// query atom types for their chains of responsibility
196	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
197	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
198	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
199	+
200	+	std::vector<AtomType*>::iterator i;
201	+	std::vector<AtomType*>::iterator j;
202	+	std::vector<AtomType*>::iterator k;
203	+
204	+	int ii = 0;
205	+	int jj = 0;
206	+	int kk = 0;
207	+	int IKscore;
208	+
209	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
210	+
211	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
212	+	ii = 0;
213	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
214	+	kk = 0;
215	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
216	+
217	+	IKscore = ii + kk;
218	+
219	+	std::vector<std::string> myKeys;
220	+	myKeys.push_back((*i)->getName());
221	+	myKeys.push_back((*j)->getName());
222	+	myKeys.push_back((*k)->getName());
223	+
224	+	BendType* bendType = bendTypeCont_.find(myKeys);
225	+	if (bendType) {
226	+	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
227	+	}
228	+	kk++;
229	+	}
230	+	ii++;
231	+	}
232	+	jj++;
233	+	}
234	+
235	+	if (foundBends.size() > 0) {
236	+	std::sort(foundBends.begin(), foundBends.end());
237	+	int jscore = foundBends[0].first;
238	+	int ikscore = foundBends[0].second;
239	+	std::vector<std::string> theKeys = foundBends[0].third;
240	+
241	+	BendType* bestType = bendTypeCont_.find(theKeys);
242	+	return bestType;
243	+	} else {
244	+	//if no exact match found, try wild card match
245	+	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
246	+	}
247	+	}
248	+	}
249	+
250	+	TorsionType* ForceField::getTorsionType(const std::string &at1,
251	+	const std::string &at2,
252	+	const std::string &at3,
253	+	const std::string &at4) {
254	+	std::vector<std::string> keys;
255	+	keys.push_back(at1);
256	+	keys.push_back(at2);
257	+	keys.push_back(at3);
258	+	keys.push_back(at4);
259	+
260	+
261	+	//try exact match first
262	+	TorsionType* torsionType = torsionTypeCont_.find(keys);
263	+	if (torsionType) {
264	+	return torsionType;
265	+	} else {
266	+
267	+	AtomType* atype1;
268	+	AtomType* atype2;
269	+	AtomType* atype3;
270	+	AtomType* atype4;
271	+	std::vector<std::string> at1key;
272	+	at1key.push_back(at1);
273	+	atype1 = atomTypeCont_.find(at1key);
274
275	+	std::vector<std::string> at2key;
276	+	at2key.push_back(at2);
277	+	atype2 = atomTypeCont_.find(at2key);
278
279	+	std::vector<std::string> at3key;
280	+	at3key.push_back(at3);
281	+	atype3 = atomTypeCont_.find(at3key);
282
283	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
284	<	const string &at3);
285	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
68	<	const string &at3, const string &at4);
283	>	std::vector<std::string> at4key;
284	>	at4key.push_back(at4);
285	>	atype4 = atomTypeCont_.find(at4key);
286
287	<	double ForceField::getRcutForAtomType(AtomType* at);
287	>	// query atom types for their chains of responsibility
288	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
289	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
290	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
291	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
292
293	+	std::vector<AtomType*>::iterator i;
294	+	std::vector<AtomType*>::iterator j;
295	+	std::vector<AtomType*>::iterator k;
296	+	std::vector<AtomType*>::iterator l;
297
298	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
299	<
300	<	vector<vector<string> > results;
298	>	int ii = 0;
299	>	int jj = 0;
300	>	int kk = 0;
301	>	int ll = 0;
302	>	int ILscore;
303	>	int JKscore;
304
305	<
305	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
306
307	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
308	+	kk = 0;
309	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
310	+	ii = 0;
311	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
312	+	ll = 0;
313	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
314	+
315	+	ILscore = ii + ll;
316	+	JKscore = jj + kk;
317
318	<	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
319	<
320	<	int nStrings;
321	<	vector<string> oneResult;
322	<	vector<vector<string> > allResults;
318	>	std::vector<std::string> myKeys;
319	>	myKeys.push_back((*i)->getName());
320	>	myKeys.push_back((*j)->getName());
321	>	myKeys.push_back((*k)->getName());
322	>	myKeys.push_back((*l)->getName());
323
324	<	nStrings = myAts.size();
324	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
325	>	if (torsionType) {
326	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
327	>	}
328	>	ll++;
329	>	}
330	>	ii++;
331	>	}
332	>	kk++;
333	>	}
334	>	jj++;
335	>	}
336	>
337	>	if (foundTorsions.size() > 0) {
338	>	std::sort(foundTorsions.begin(), foundTorsions.end());
339	>	int jkscore = foundTorsions[0].first;
340	>	int ilscore = foundTorsions[0].second;
341	>	std::vector<std::string> theKeys = foundTorsions[0].third;
342	>
343	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
344	>	return bestType;
345	>	} else {
346	>	//if no exact match found, try wild card match
347	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
348	>	}
349	>	}
350	>	}
351
352	<	if (nStrings == 1) {
353	<	oneResult.push_back(wildcardCharacter);
354	<	allResults.push_back(oneResult);
355	<	return allResults;
356	<	} else {
357	<
358	<	for (i=0; i < nStrings; i++) {
359	<	oneResult = myAts;
360	<	replace(oneResult.begin(), oneResult.end(),
352	>	InversionType* ForceField::getInversionType(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	>	//try exact match first
363	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
364	>	if (inversionType) {
365	>	return inversionType;
366	>	} else {
367	>
368	>	AtomType* atype1;
369	>	AtomType* atype2;
370	>	AtomType* atype3;
371	>	AtomType* atype4;
372	>	std::vector<std::string> at1key;
373	>	at1key.push_back(at1);
374	>	atype1 = atomTypeCont_.find(at1key);
375	>
376	>	std::vector<std::string> at2key;
377	>	at2key.push_back(at2);
378	>	atype2 = atomTypeCont_.find(at2key);
379	>
380	>	std::vector<std::string> at3key;
381	>	at3key.push_back(at3);
382	>	atype3 = atomTypeCont_.find(at3key);
383	>
384	>	std::vector<std::string> at4key;
385	>	at4key.push_back(at4);
386	>	atype4 = atomTypeCont_.find(at4key);
387	>
388	>	// query atom types for their chains of responsibility
389	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
390	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
391	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
392	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
393	>
394	>	std::vector<AtomType*>::iterator i;
395	>	std::vector<AtomType*>::iterator j;
396	>	std::vector<AtomType*>::iterator k;
397	>	std::vector<AtomType*>::iterator l;
398	>
399	>	int ii = 0;
400	>	int jj = 0;
401	>	int kk = 0;
402	>	int ll = 0;
403	>	int Iscore;
404	>	int JKLscore;
405	>
406	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
407	>
408	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
409	>	kk = 0;
410	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
411	>	ii = 0;
412	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
413	>	ll = 0;
414	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
415	>
416	>	Iscore = ii;
417	>	JKLscore = jj + kk + ll;
418	>
419	>	std::vector<std::string> myKeys;
420	>	myKeys.push_back((*i)->getName());
421	>	myKeys.push_back((*j)->getName());
422	>	myKeys.push_back((*k)->getName());
423	>	myKeys.push_back((*l)->getName());
424	>
425	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
426	>	if (inversionType) {
427	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
428	>	}
429	>	ll++;
430	>	}
431	>	ii++;
432	>	}
433	>	kk++;
434	>	}
435	>	jj++;
436	>	}
437	>
438	>	if (foundInversions.size() > 0) {
439	>	std::sort(foundInversions.begin(), foundInversions.end());
440	>	int iscore = foundInversions[0].first;
441	>	int jklscore = foundInversions[0].second;
442	>	std::vector<std::string> theKeys = foundInversions[0].third;
443	>
444	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
445	>	return bestType;
446	>	} else {
447	>	//if no exact match found, try wild card match
448	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
449	>	}
450	>	}
451	>	}
452	>
453	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
454	>
455	>	std::vector<std::string> keys;
456	>	keys.push_back(at1);
457	>	keys.push_back(at2);
458	>
459	>	//try exact match first
460	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
461	>	if (nbiType) {
462	>	return nbiType;
463	>	} else {
464	>	AtomType* atype1;
465	>	AtomType* atype2;
466	>	std::vector<std::string> at1key;
467	>	at1key.push_back(at1);
468	>	atype1 = atomTypeCont_.find(at1key);
469	>
470	>	std::vector<std::string> at2key;
471	>	at2key.push_back(at2);
472	>	atype2 = atomTypeCont_.find(at2key);
473	>
474	>	// query atom types for their chains of responsibility
475	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
476	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
477	>
478	>	std::vector<AtomType*>::iterator i;
479	>	std::vector<AtomType*>::iterator j;
480	>
481	>	int ii = 0;
482	>	int jj = 0;
483	>	int nbiTypeScore;
484	>
485	>	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
486	>
487	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
488	>	jj = 0;
489	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
490	>
491	>	nbiTypeScore = ii + jj;
492	>
493	>	std::vector<std::string> myKeys;
494	>	myKeys.push_back((*i)->getName());
495	>	myKeys.push_back((*j)->getName());
496	>
497	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
498	>	if (nbiType) {
499	>	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
500	>	}
501	>	jj++;
502	>	}
503	>	ii++;
504	>	}
505	>
506	>
507	>	if (foundNBI.size() > 0) {
508	>	// sort the foundNBI by the score:
509	>	std::sort(foundNBI.begin(), foundNBI.end());
510	>
511	>	int bestScore = foundNBI[0].first;
512	>	std::vector<std::string> theKeys = foundNBI[0].second;
513	>
514	>	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
515	>	return bestType;
516	>	} else {
517	>	//if no exact match found, try wild card match
518	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
519	>	}
520	>	}
521	>	}
522	>
523	>	BondType* ForceField::getExactBondType(const std::string &at1,
524	>	const std::string &at2){
525	>	std::vector<std::string> keys;
526	>	keys.push_back(at1);
527	>	keys.push_back(at2);
528	>	return bondTypeCont_.find(keys);
529	>	}
530	>
531	>	BendType* ForceField::getExactBendType(const std::string &at1,
532	>	const std::string &at2,
533	>	const std::string &at3){
534	>	std::vector<std::string> keys;
535	>	keys.push_back(at1);
536	>	keys.push_back(at2);
537	>	keys.push_back(at3);
538	>	return bendTypeCont_.find(keys);
539	>	}
540	>
541	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
542	>	const std::string &at2,
543	>	const std::string &at3,
544	>	const std::string &at4){
545	>	std::vector<std::string> keys;
546	>	keys.push_back(at1);
547	>	keys.push_back(at2);
548	>	keys.push_back(at3);
549	>	keys.push_back(at4);
550	>	return torsionTypeCont_.find(keys);
551	>	}
552	>
553	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
554	>	const std::string &at2,
555	>	const std::string &at3,
556	>	const std::string &at4){
557	>	std::vector<std::string> keys;
558	>	keys.push_back(at1);
559	>	keys.push_back(at2);
560	>	keys.push_back(at3);
561	>	keys.push_back(at4);
562	>	return inversionTypeCont_.find(keys);
563	>	}
564	>
565	>	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
566	>	std::vector<std::string> keys;
567	>	keys.push_back(at1);
568	>	keys.push_back(at2);
569	>	return nonBondedInteractionTypeCont_.find(keys);
570	>	}
571	>
572	>
573	>	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
574	>	std::vector<std::string> keys;
575	>	keys.push_back(at);
576	>	atypeIdentToName[atomType->getIdent()] = at;
577	>	return atomTypeCont_.add(keys, atomType);
578	>	}
579	>
580	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
581	>	std::vector<std::string> keys;
582	>	keys.push_back(at);
583	>	atypeIdentToName[atomType->getIdent()] = at;
584	>	return atomTypeCont_.replace(keys, atomType);
585	>	}
586	>
587	>	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
588	>	BondType* bondType) {
589	>	std::vector<std::string> keys;
590	>	keys.push_back(at1);
591	>	keys.push_back(at2);
592	>	return bondTypeCont_.add(keys, bondType);
593	>	}
594	>
595	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
596	>	const std::string &at3, BendType* bendType) {
597	>	std::vector<std::string> keys;
598	>	keys.push_back(at1);
599	>	keys.push_back(at2);
600	>	keys.push_back(at3);
601	>	return bendTypeCont_.add(keys, bendType);
602	>	}
603	>
604	>	bool ForceField::addTorsionType(const std::string &at1,
605	>	const std::string &at2,
606	>	const std::string &at3,
607	>	const std::string &at4,
608	>	TorsionType* torsionType) {
609	>	std::vector<std::string> keys;
610	>	keys.push_back(at1);
611	>	keys.push_back(at2);
612	>	keys.push_back(at3);
613	>	keys.push_back(at4);
614	>	return torsionTypeCont_.add(keys, torsionType);
615	>	}
616	>
617	>	bool ForceField::addInversionType(const std::string &at1,
618	>	const std::string &at2,
619	>	const std::string &at3,
620	>	const std::string &at4,
621	>	InversionType* inversionType) {
622	>	std::vector<std::string> keys;
623	>	keys.push_back(at1);
624	>	keys.push_back(at2);
625	>	keys.push_back(at3);
626	>	keys.push_back(at4);
627	>	return inversionTypeCont_.add(keys, inversionType);
628	>	}
629	>
630	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
631	>	const std::string &at2,
632	>	NonBondedInteractionType* nbiType) {
633	>	std::vector<std::string> keys;
634	>	keys.push_back(at1);
635	>	keys.push_back(at2);
636	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
637	>	}
638	>
639	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
640	>	RealType rcut = 0.0;
641	>
642	>	LennardJonesAdapter lja = LennardJonesAdapter(at);
643	>	if (lja.isLennardJones()) {
644	>	rcut = 2.5 * lja.getSigma();
645	>	}
646	>	return rcut;
647	>	}
648	>
649	>
650	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
651	>	std::string forceFieldFilename(filename);
652	>	ifstrstream* ffStream = new ifstrstream();
653	>
654	>	//try to open the force filed file in current directory first
655	>	ffStream->open(forceFieldFilename.c_str());
656	>	if(!ffStream->is_open()){
657	>
658	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
659	>	ffStream->open( forceFieldFilename.c_str() );
660	>
661	>	//if current directory does not contain the force field file,
662	>	//try to open it in the path
663	>	if(!ffStream->is_open()){
664	>
665	>	sprintf( painCave.errMsg,
666	>	"Error opening the force field parameter file:\n"
667	>	"\t%s\n"
668	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
669	>	"variable?\n",
670	>	forceFieldFilename.c_str() );
671	>	painCave.severity = OPENMD_ERROR;
672	>	painCave.isFatal = 1;
673	>	simError();
674	>	}
675	>	}
676	>	return ffStream;
677	>	}
678	>
679	>	} //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 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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