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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 1530 by gezelter, Tue Dec 28 21:47:55 2010 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]  Vardeman & Gezelter, in progress (2009).
40	+	*/
41	+
42	+	/**
43	+	* @file ForceField.cpp
44	+	* @author tlin
45	+	* @date 11/04/2004
46	+	* @time 22:51am
47	+	* @version 1.0
48	+	*/
49	+
50	+	#include <algorithm>
51		#include "UseTheForce/ForceField.hpp"
52	+	#include "utils/simError.h"
53	+	#include "utils/Tuple.hpp"
54	+	#include "UseTheForce/DarkSide/atype_interface.h"
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
15	–	BondType* ForceField::getMatchingBondType(const string &at1,
16	–	const string &at2) {
70
71	<	map<pair<string,string>, BondType*>::iterator iter;
72	<	vector<BondType*> foundTypes;
71	>	ForceField::~ForceField() {
72	>	deleteAtypes();
73	>	}
74
75	<	iter = bondTypeMap.find(pair<at1, at2>);
76	<	if (iter != bondTypeMap.end()) {
77	<	// exact match, so just return it
78	<	return iter->second;
79	<	}
75	>	AtomType* ForceField::getAtomType(const std::string &at) {
76	>	std::vector<std::string> keys;
77	>	keys.push_back(at);
78	>	return atomTypeCont_.find(keys);
79	>	}
80
81	<	iter = bondTypeMap.find(pair<at2, at1>);
82	<	if (iter != bondTypeMap.end()) {
83	<	// exact match in reverse order, so just return it
84	<	return iter->second;
85	<	}
81	>	BondType* ForceField::getBondType(const std::string &at1,
82	>	const std::string &at2) {
83	>	std::vector<std::string> keys;
84	>	keys.push_back(at1);
85	>	keys.push_back(at2);
86
87	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
88	<	if (iter != bondTypeMap.end()) {
89	<	foundTypes.push_back(iter->second);
90	<	}
87	>	//try exact match first
88	>	BondType* bondType = bondTypeCont_.find(keys);
89	>	if (bondType) {
90	>	return bondType;
91	>	} else {
92	>	AtomType* atype1;
93	>	AtomType* atype2;
94	>	std::vector<std::string> at1key;
95	>	at1key.push_back(at1);
96	>	atype1 = atomTypeCont_.find(at1key);
97	>
98	>	std::vector<std::string> at2key;
99	>	at2key.push_back(at2);
100	>	atype2 = atomTypeCont_.find(at2key);
101
102	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
103	<	if (iter != bondTypeMap.end()) {
104	<	foundTypes.push_back(iter->second);
41	<	}
102	>	// query atom types for their chains of responsibility
103	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
104	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
105
106	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
107	<	if (iter != bondTypeMap.end()) {
45	<	foundTypes.push_back(iter->second);
46	<	}
106	>	std::vector<AtomType*>::iterator i;
107	>	std::vector<AtomType*>::iterator j;
108
109	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
110	<	if (iter != bondTypeMap.end()) {
111	<	foundTypes.push_back(iter->second);
109	>	int ii = 0;
110	>	int jj = 0;
111	>	int bondTypeScore;
112	>
113	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
114	>
115	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
116	>	jj = 0;
117	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
118	>
119	>	bondTypeScore = ii + jj;
120	>
121	>	std::vector<std::string> myKeys;
122	>	myKeys.push_back((*i)->getName());
123	>	myKeys.push_back((*j)->getName());
124	>
125	>	BondType* bondType = bondTypeCont_.find(myKeys);
126	>	if (bondType) {
127	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
128	>	}
129	>	jj++;
130	>	}
131	>	ii++;
132	>	}
133	>
134	>
135	>	if (foundBonds.size() > 0) {
136	>	// sort the foundBonds by the score:
137	>	std::sort(foundBonds.begin(), foundBonds.end());
138	>
139	>	int bestScore = foundBonds[0].first;
140	>	std::vector<std::string> theKeys = foundBonds[0].second;
141	>
142	>	BondType* bestType = bondTypeCont_.find(theKeys);
143	>
144	>	return bestType;
145	>	} else {
146	>	//if no exact match found, try wild card match
147	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
148	>	}
149	>	}
150		}
151
152	<	if (foundTypes.empty()) {
153	<	return NULL;
154	<	} else {
155	<
152	>	BendType* ForceField::getBendType(const std::string &at1,
153	>	const std::string &at2,
154	>	const std::string &at3) {
155	>	std::vector<std::string> keys;
156	>	keys.push_back(at1);
157	>	keys.push_back(at2);
158	>	keys.push_back(at3);
159
160	<
160	>	//try exact match first
161	>	BendType* bendType = bendTypeCont_.find(keys);
162	>	if (bendType) {
163	>	return bendType;
164	>	} else {
165
166	+	AtomType* atype1;
167	+	AtomType* atype2;
168	+	AtomType* atype3;
169	+	std::vector<std::string> at1key;
170	+	at1key.push_back(at1);
171	+	atype1 = atomTypeCont_.find(at1key);
172	+
173	+	std::vector<std::string> at2key;
174	+	at2key.push_back(at2);
175	+	atype2 = atomTypeCont_.find(at2key);
176
177	+	std::vector<std::string> at3key;
178	+	at3key.push_back(at3);
179	+	atype3 = atomTypeCont_.find(at3key);
180
181	<
181	>	// query atom types for their chains of responsibility
182	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
183	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
184	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
185
186	+	std::vector<AtomType*>::iterator i;
187	+	std::vector<AtomType*>::iterator j;
188	+	std::vector<AtomType*>::iterator k;
189
190	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
191	<	const string &at3);
192	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
193	<	const string &at3, const string &at4);
190	>	int ii = 0;
191	>	int jj = 0;
192	>	int kk = 0;
193	>	int IKscore;
194
195	<	double ForceField::getRcutForAtomType(AtomType* at);
195	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
196
197	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
198	+	ii = 0;
199	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
200	+	kk = 0;
201	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
202	+
203	+	IKscore = ii + kk;
204
205	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
206	<
207	<	vector<vector<string> > results;
205	>	std::vector<std::string> myKeys;
206	>	myKeys.push_back((*i)->getName());
207	>	myKeys.push_back((*j)->getName());
208	>	myKeys.push_back((*k)->getName());
209
210	<
210	>	BendType* bendType = bendTypeCont_.find(myKeys);
211	>	if (bendType) {
212	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
213	>	}
214	>	kk++;
215	>	}
216	>	ii++;
217	>	}
218	>	jj++;
219	>	}
220	>
221	>	if (foundBends.size() > 0) {
222	>	std::sort(foundBends.begin(), foundBends.end());
223	>	int jscore = foundBends[0].first;
224	>	int ikscore = foundBends[0].second;
225	>	std::vector<std::string> theKeys = foundBends[0].third;
226	>
227	>	BendType* bestType = bendTypeCont_.find(theKeys);
228	>	return bestType;
229	>	} else {
230	>	//if no exact match found, try wild card match
231	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
232	>	}
233	>	}
234	>	}
235
236	+	TorsionType* ForceField::getTorsionType(const std::string &at1,
237	+	const std::string &at2,
238	+	const std::string &at3,
239	+	const std::string &at4) {
240	+	std::vector<std::string> keys;
241	+	keys.push_back(at1);
242	+	keys.push_back(at2);
243	+	keys.push_back(at3);
244	+	keys.push_back(at4);
245
80	–	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
81	–
82	–	int nStrings;
83	–	vector<string> oneResult;
84	–	vector<vector<string> > allResults;
246
247	<	nStrings = myAts.size();
247	>	//try exact match first
248	>	TorsionType* torsionType = torsionTypeCont_.find(keys);
249	>	if (torsionType) {
250	>	return torsionType;
251	>	} else {
252
253	<	if (nStrings == 1) {
254	<	oneResult.push_back(wildcardCharacter);
255	<	allResults.push_back(oneResult);
256	<	return allResults;
257	<	} else {
258	<
259	<	for (i=0; i < nStrings; i++) {
260	<	oneResult = myAts;
261	<	replace(oneResult.begin(), oneResult.end(),
253	>	AtomType* atype1;
254	>	AtomType* atype2;
255	>	AtomType* atype3;
256	>	AtomType* atype4;
257	>	std::vector<std::string> at1key;
258	>	at1key.push_back(at1);
259	>	atype1 = atomTypeCont_.find(at1key);
260	>
261	>	std::vector<std::string> at2key;
262	>	at2key.push_back(at2);
263	>	atype2 = atomTypeCont_.find(at2key);
264	>
265	>	std::vector<std::string> at3key;
266	>	at3key.push_back(at3);
267	>	atype3 = atomTypeCont_.find(at3key);
268	>
269	>	std::vector<std::string> at4key;
270	>	at4key.push_back(at4);
271	>	atype4 = atomTypeCont_.find(at4key);
272	>
273	>	// query atom types for their chains of responsibility
274	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
275	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
276	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
277	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
278	>
279	>	std::vector<AtomType*>::iterator i;
280	>	std::vector<AtomType*>::iterator j;
281	>	std::vector<AtomType*>::iterator k;
282	>	std::vector<AtomType*>::iterator l;
283	>
284	>	int ii = 0;
285	>	int jj = 0;
286	>	int kk = 0;
287	>	int ll = 0;
288	>	int ILscore;
289	>	int JKscore;
290	>
291	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
292	>
293	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
294	>	kk = 0;
295	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
296	>	ii = 0;
297	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
298	>	ll = 0;
299	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
300	>
301	>	ILscore = ii + ll;
302	>	JKscore = jj + kk;
303	>
304	>	std::vector<std::string> myKeys;
305	>	myKeys.push_back((*i)->getName());
306	>	myKeys.push_back((*j)->getName());
307	>	myKeys.push_back((*k)->getName());
308	>	myKeys.push_back((*l)->getName());
309	>
310	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
311	>	if (torsionType) {
312	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
313	>	}
314	>	ll++;
315	>	}
316	>	ii++;
317	>	}
318	>	kk++;
319	>	}
320	>	jj++;
321	>	}
322	>
323	>	if (foundTorsions.size() > 0) {
324	>	std::sort(foundTorsions.begin(), foundTorsions.end());
325	>	int jkscore = foundTorsions[0].first;
326	>	int ilscore = foundTorsions[0].second;
327	>	std::vector<std::string> theKeys = foundTorsions[0].third;
328	>
329	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
330	>	return bestType;
331	>	} else {
332	>	//if no exact match found, try wild card match
333	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
334	>	}
335	>	}
336	>	}
337	>
338	>	InversionType* ForceField::getInversionType(const std::string &at1,
339	>	const std::string &at2,
340	>	const std::string &at3,
341	>	const std::string &at4) {
342	>	std::vector<std::string> keys;
343	>	keys.push_back(at1);
344	>	keys.push_back(at2);
345	>	keys.push_back(at3);
346	>	keys.push_back(at4);
347	>
348	>	//try exact match first
349	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
350	>	if (inversionType) {
351	>	return inversionType;
352	>	} else {
353	>
354	>	AtomType* atype1;
355	>	AtomType* atype2;
356	>	AtomType* atype3;
357	>	AtomType* atype4;
358	>	std::vector<std::string> at1key;
359	>	at1key.push_back(at1);
360	>	atype1 = atomTypeCont_.find(at1key);
361	>
362	>	std::vector<std::string> at2key;
363	>	at2key.push_back(at2);
364	>	atype2 = atomTypeCont_.find(at2key);
365	>
366	>	std::vector<std::string> at3key;
367	>	at3key.push_back(at3);
368	>	atype3 = atomTypeCont_.find(at3key);
369	>
370	>	std::vector<std::string> at4key;
371	>	at4key.push_back(at4);
372	>	atype4 = atomTypeCont_.find(at4key);
373	>
374	>	// query atom types for their chains of responsibility
375	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
376	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
377	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
378	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
379	>
380	>	std::vector<AtomType*>::iterator i;
381	>	std::vector<AtomType*>::iterator j;
382	>	std::vector<AtomType*>::iterator k;
383	>	std::vector<AtomType*>::iterator l;
384	>
385	>	int ii = 0;
386	>	int jj = 0;
387	>	int kk = 0;
388	>	int ll = 0;
389	>	int Iscore;
390	>	int JKLscore;
391	>
392	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
393	>
394	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
395	>	kk = 0;
396	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
397	>	ii = 0;
398	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
399	>	ll = 0;
400	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
401	>
402	>	Iscore = ii;
403	>	JKLscore = jj + kk + ll;
404	>
405	>	std::vector<std::string> myKeys;
406	>	myKeys.push_back((*i)->getName());
407	>	myKeys.push_back((*j)->getName());
408	>	myKeys.push_back((*k)->getName());
409	>	myKeys.push_back((*l)->getName());
410	>
411	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
412	>	if (inversionType) {
413	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
414	>	}
415	>	ll++;
416	>	}
417	>	ii++;
418	>	}
419	>	kk++;
420	>	}
421	>	jj++;
422	>	}
423	>
424	>	if (foundInversions.size() > 0) {
425	>	std::sort(foundInversions.begin(), foundInversions.end());
426	>	int iscore = foundInversions[0].first;
427	>	int jklscore = foundInversions[0].second;
428	>	std::vector<std::string> theKeys = foundInversions[0].third;
429	>
430	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
431	>	return bestType;
432	>	} else {
433	>	//if no exact match found, try wild card match
434	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
435	>	}
436	>	}
437	>	}
438	>
439	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
440	>	std::vector<std::string> keys;
441	>	keys.push_back(at1);
442	>	keys.push_back(at2);
443	>
444	>	//try exact match first
445	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
446	>	if (nbiType) {
447	>	return nbiType;
448	>	} else {
449	>	//if no exact match found, try wild card match
450	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
451	>	}
452	>	}
453	>
454	>	BondType* ForceField::getExactBondType(const std::string &at1,
455	>	const std::string &at2){
456	>	std::vector<std::string> keys;
457	>	keys.push_back(at1);
458	>	keys.push_back(at2);
459	>	return bondTypeCont_.find(keys);
460	>	}
461	>
462	>	BendType* ForceField::getExactBendType(const std::string &at1,
463	>	const std::string &at2,
464	>	const std::string &at3){
465	>	std::vector<std::string> keys;
466	>	keys.push_back(at1);
467	>	keys.push_back(at2);
468	>	keys.push_back(at3);
469	>	return bendTypeCont_.find(keys);
470	>	}
471	>
472	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
473	>	const std::string &at2,
474	>	const std::string &at3,
475	>	const std::string &at4){
476	>	std::vector<std::string> keys;
477	>	keys.push_back(at1);
478	>	keys.push_back(at2);
479	>	keys.push_back(at3);
480	>	keys.push_back(at4);
481	>	return torsionTypeCont_.find(keys);
482	>	}
483	>
484	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
485	>	const std::string &at2,
486	>	const std::string &at3,
487	>	const std::string &at4){
488	>	std::vector<std::string> keys;
489	>	keys.push_back(at1);
490	>	keys.push_back(at2);
491	>	keys.push_back(at3);
492	>	keys.push_back(at4);
493	>	return inversionTypeCont_.find(keys);
494	>	}
495	>
496	>	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
497	>	std::vector<std::string> keys;
498	>	keys.push_back(at1);
499	>	keys.push_back(at2);
500	>	return nonBondedInteractionTypeCont_.find(keys);
501	>	}
502	>
503	>
504	>	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
505	>	std::vector<std::string> keys;
506	>	keys.push_back(at);
507	>	return atomTypeCont_.add(keys, atomType);
508	>	}
509	>
510	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
511	>	std::vector<std::string> keys;
512	>	keys.push_back(at);
513	>	return atomTypeCont_.replace(keys, atomType);
514	>	}
515	>
516	>	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
517	>	BondType* bondType) {
518	>	std::vector<std::string> keys;
519	>	keys.push_back(at1);
520	>	keys.push_back(at2);
521	>	return bondTypeCont_.add(keys, bondType);
522	>	}
523	>
524	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
525	>	const std::string &at3, BendType* bendType) {
526	>	std::vector<std::string> keys;
527	>	keys.push_back(at1);
528	>	keys.push_back(at2);
529	>	keys.push_back(at3);
530	>	return bendTypeCont_.add(keys, bendType);
531	>	}
532	>
533	>	bool ForceField::addTorsionType(const std::string &at1,
534	>	const std::string &at2,
535	>	const std::string &at3,
536	>	const std::string &at4,
537	>	TorsionType* torsionType) {
538	>	std::vector<std::string> keys;
539	>	keys.push_back(at1);
540	>	keys.push_back(at2);
541	>	keys.push_back(at3);
542	>	keys.push_back(at4);
543	>	return torsionTypeCont_.add(keys, torsionType);
544	>	}
545	>
546	>	bool ForceField::addInversionType(const std::string &at1,
547	>	const std::string &at2,
548	>	const std::string &at3,
549	>	const std::string &at4,
550	>	InversionType* inversionType) {
551	>	std::vector<std::string> keys;
552	>	keys.push_back(at1);
553	>	keys.push_back(at2);
554	>	keys.push_back(at3);
555	>	keys.push_back(at4);
556	>	return inversionTypeCont_.add(keys, inversionType);
557	>	}
558	>
559	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
560	>	const std::string &at2,
561	>	NonBondedInteractionType* nbiType) {
562	>	std::vector<std::string> keys;
563	>	keys.push_back(at1);
564	>	keys.push_back(at2);
565	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
566	>	}
567	>
568	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
569	>	/**@todo */
570	>	GenericData* data;
571	>	RealType rcut = 0.0;
572	>
573	>	if (at->isLennardJones()) {
574	>	data = at->getPropertyByName("LennardJones");
575	>	if (data != NULL) {
576	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
577	>
578	>	if (ljData != NULL) {
579	>	LJParam ljParam = ljData->getData();
580	>
581	>	//by default use 2.5*sigma as cutoff radius
582	>	rcut = 2.5 * ljParam.sigma;
583	>
584	>	} else {
585	>	sprintf( painCave.errMsg,
586	>	"Can not cast GenericData to LJParam\n");
587	>	painCave.severity = OPENMD_ERROR;
588	>	painCave.isFatal = 1;
589	>	simError();
590	>	}
591	>	} else {
592	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
593	>	painCave.severity = OPENMD_ERROR;
594	>	painCave.isFatal = 1;
595	>	simError();
596	>	}
597	>	}
598	>	return rcut;
599	>	}
600	>
601	>
602	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
603	>	std::string forceFieldFilename(filename);
604	>	ifstrstream* ffStream = new ifstrstream();
605	>
606	>	//try to open the force filed file in current directory first
607	>	ffStream->open(forceFieldFilename.c_str());
608	>	if(!ffStream->is_open()){
609	>
610	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
611	>	ffStream->open( forceFieldFilename.c_str() );
612	>
613	>	//if current directory does not contain the force field file,
614	>	//try to open it in the path
615	>	if(!ffStream->is_open()){
616	>
617	>	sprintf( painCave.errMsg,
618	>	"Error opening the force field parameter file:\n"
619	>	"\t%s\n"
620	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
621	>	"variable?\n",
622	>	forceFieldFilename.c_str() );
623	>	painCave.severity = OPENMD_ERROR;
624	>	painCave.isFatal = 1;
625	>	simError();
626	>	}
627	>	}
628	>	return ffStream;
629	>	}
630	>
631	>	} //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 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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