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

Comparing:
trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

#	Line 1 | Line 1
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
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  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	<	*/
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 "UseTheForce/DarkSide/atype_interface.h"
54	<	namespace oopse {
53	>	#include "utils/Tuple.hpp"
54	>	namespace OpenMD {
55
56	<	ForceField::ForceField() {
56	>	ForceField::ForceField() {
57	>
58		char* tempPath;
59		tempPath = getenv("FORCE_PARAM_PATH");
60	<
60	>
61		if (tempPath == NULL) {
62	<	//convert a macro from compiler to a string in c++
63	<	STR_DEFINE(ffPath_, FRC_PATH );
62	>	//convert a macro from compiler to a string in c++
63	>	STR_DEFINE(ffPath_, FRC_PATH );
64		} else {
65	<	ffPath_ = tempPath;
65	>	ffPath_ = tempPath;
66		}
67	<	}
67	>	}
68
69	<
68	<	ForceField::~ForceField() {
69	<	deleteAtypes();
70	<	}
71	<
72	<	AtomType* ForceField::getAtomType(const std::string &at) {
69	>	AtomType* ForceField::getAtomType(const std::string &at) {
70		std::vector<std::string> keys;
71		keys.push_back(at);
72		return atomTypeCont_.find(keys);
73	<	}
73	>	}
74
75	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
75	>	BondType* ForceField::getBondType(const std::string &at1,
76	>	const std::string &at2) {
77		std::vector<std::string> keys;
78		keys.push_back(at1);
79		keys.push_back(at2);
#	Line 83 | Line 81 | BondType* ForceField::getBondType(const std::string &a
81		//try exact match first
82		BondType* bondType = bondTypeCont_.find(keys);
83		if (bondType) {
84	<	return bondType;
84	>	return bondType;
85		} else {
86	<	//if no exact match found, try wild card match
87	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
88	<	}
86	>	AtomType* atype1;
87	>	AtomType* atype2;
88	>	std::vector<std::string> at1key;
89	>	at1key.push_back(at1);
90	>	atype1 = atomTypeCont_.find(at1key);
91	>
92	>	std::vector<std::string> at2key;
93	>	at2key.push_back(at2);
94	>	atype2 = atomTypeCont_.find(at2key);
95
96	<	}
96	>	// query atom types for their chains of responsibility
97	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
98	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
99
100	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
101	<	const std::string &at3) {
100	>	std::vector<AtomType*>::iterator i;
101	>	std::vector<AtomType*>::iterator j;
102	>
103	>	int ii = 0;
104	>	int jj = 0;
105	>	int bondTypeScore;
106	>
107	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
108	>
109	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
110	>	jj = 0;
111	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
112	>
113	>	bondTypeScore = ii + jj;
114	>
115	>	std::vector<std::string> myKeys;
116	>	myKeys.push_back((*i)->getName());
117	>	myKeys.push_back((*j)->getName());
118	>
119	>	BondType* bondType = bondTypeCont_.find(myKeys);
120	>	if (bondType) {
121	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
122	>	}
123	>	jj++;
124	>	}
125	>	ii++;
126	>	}
127	>
128	>
129	>	if (foundBonds.size() > 0) {
130	>	// sort the foundBonds by the score:
131	>	std::sort(foundBonds.begin(), foundBonds.end());
132	>
133	>	int bestScore = foundBonds[0].first;
134	>	std::vector<std::string> theKeys = foundBonds[0].second;
135	>
136	>	BondType* bestType = bondTypeCont_.find(theKeys);
137	>
138	>	return bestType;
139	>	} else {
140	>	//if no exact match found, try wild card match
141	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
142	>	}
143	>	}
144	>	}
145	>
146	>	BendType* ForceField::getBendType(const std::string &at1,
147	>	const std::string &at2,
148	>	const std::string &at3) {
149		std::vector<std::string> keys;
150		keys.push_back(at1);
151		keys.push_back(at2);
#	Line 101 | Line 154 | BendType* ForceField::getBendType(const std::string &a
154		//try exact match first
155		BendType* bendType = bendTypeCont_.find(keys);
156		if (bendType) {
157	<	return bendType;
157	>	return bendType;
158		} else {
159	<	//if no exact match found, try wild card match
160	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
159	>
160	>	AtomType* atype1;
161	>	AtomType* atype2;
162	>	AtomType* atype3;
163	>	std::vector<std::string> at1key;
164	>	at1key.push_back(at1);
165	>	atype1 = atomTypeCont_.find(at1key);
166	>
167	>	std::vector<std::string> at2key;
168	>	at2key.push_back(at2);
169	>	atype2 = atomTypeCont_.find(at2key);
170	>
171	>	std::vector<std::string> at3key;
172	>	at3key.push_back(at3);
173	>	atype3 = atomTypeCont_.find(at3key);
174	>
175	>	// query atom types for their chains of responsibility
176	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
177	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
178	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
179	>
180	>	std::vector<AtomType*>::iterator i;
181	>	std::vector<AtomType*>::iterator j;
182	>	std::vector<AtomType*>::iterator k;
183	>
184	>	int ii = 0;
185	>	int jj = 0;
186	>	int kk = 0;
187	>	int IKscore;
188	>
189	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
190	>
191	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
192	>	ii = 0;
193	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
194	>	kk = 0;
195	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
196	>
197	>	IKscore = ii + kk;
198	>
199	>	std::vector<std::string> myKeys;
200	>	myKeys.push_back((*i)->getName());
201	>	myKeys.push_back((*j)->getName());
202	>	myKeys.push_back((*k)->getName());
203	>
204	>	BendType* bendType = bendTypeCont_.find(myKeys);
205	>	if (bendType) {
206	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
207	>	}
208	>	kk++;
209	>	}
210	>	ii++;
211	>	}
212	>	jj++;
213	>	}
214	>
215	>	if (foundBends.size() > 0) {
216	>	std::sort(foundBends.begin(), foundBends.end());
217	>	int jscore = foundBends[0].first;
218	>	int ikscore = foundBends[0].second;
219	>	std::vector<std::string> theKeys = foundBends[0].third;
220	>
221	>	BendType* bestType = bendTypeCont_.find(theKeys);
222	>	return bestType;
223	>	} else {
224	>	//if no exact match found, try wild card match
225	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
226	>	}
227		}
228	<	}
228	>	}
229
230	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
231	<	const std::string &at3, const std::string &at4) {
230	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
231	>	const std::string &at2,
232	>	const std::string &at3,
233	>	const std::string &at4) {
234		std::vector<std::string> keys;
235		keys.push_back(at1);
236		keys.push_back(at2);
237		keys.push_back(at3);
238		keys.push_back(at4);
239
240	+
241	+	//try exact match first
242		TorsionType* torsionType = torsionTypeCont_.find(keys);
243		if (torsionType) {
244	<	return torsionType;
244	>	return torsionType;
245		} else {
123	–	//if no exact match found, try wild card match
124	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
125	–	}
126	–
127	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
246
247	<	}
247	>	AtomType* atype1;
248	>	AtomType* atype2;
249	>	AtomType* atype3;
250	>	AtomType* atype4;
251	>	std::vector<std::string> at1key;
252	>	at1key.push_back(at1);
253	>	atype1 = atomTypeCont_.find(at1key);
254	>
255	>	std::vector<std::string> at2key;
256	>	at2key.push_back(at2);
257	>	atype2 = atomTypeCont_.find(at2key);
258
259	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
259	>	std::vector<std::string> at3key;
260	>	at3key.push_back(at3);
261	>	atype3 = atomTypeCont_.find(at3key);
262	>
263	>	std::vector<std::string> at4key;
264	>	at4key.push_back(at4);
265	>	atype4 = atomTypeCont_.find(at4key);
266	>
267	>	// query atom types for their chains of responsibility
268	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
269	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
270	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
271	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
272	>
273	>	std::vector<AtomType*>::iterator i;
274	>	std::vector<AtomType*>::iterator j;
275	>	std::vector<AtomType*>::iterator k;
276	>	std::vector<AtomType*>::iterator l;
277	>
278	>	int ii = 0;
279	>	int jj = 0;
280	>	int kk = 0;
281	>	int ll = 0;
282	>	int ILscore;
283	>	int JKscore;
284	>
285	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
286	>
287	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
288	>	kk = 0;
289	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
290	>	ii = 0;
291	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
292	>	ll = 0;
293	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
294	>
295	>	ILscore = ii + ll;
296	>	JKscore = jj + kk;
297	>
298	>	std::vector<std::string> myKeys;
299	>	myKeys.push_back((*i)->getName());
300	>	myKeys.push_back((*j)->getName());
301	>	myKeys.push_back((*k)->getName());
302	>	myKeys.push_back((*l)->getName());
303	>
304	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
305	>	if (torsionType) {
306	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
307	>	}
308	>	ll++;
309	>	}
310	>	ii++;
311	>	}
312	>	kk++;
313	>	}
314	>	jj++;
315	>	}
316	>
317	>	if (foundTorsions.size() > 0) {
318	>	std::sort(foundTorsions.begin(), foundTorsions.end());
319	>	int jkscore = foundTorsions[0].first;
320	>	int ilscore = foundTorsions[0].second;
321	>	std::vector<std::string> theKeys = foundTorsions[0].third;
322	>
323	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
324	>	return bestType;
325	>	} else {
326	>	//if no exact match found, try wild card match
327	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
328	>	}
329	>	}
330	>	}
331	>
332	>	InversionType* ForceField::getInversionType(const std::string &at1,
333	>	const std::string &at2,
334	>	const std::string &at3,
335	>	const std::string &at4) {
336		std::vector<std::string> keys;
337		keys.push_back(at1);
338		keys.push_back(at2);
339	<	return bondTypeCont_.find(keys);
340	<	}
339	>	keys.push_back(at3);
340	>	keys.push_back(at4);
341
342	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
343	<	const std::string &at3){
342	>	//try exact match first
343	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
344	>	if (inversionType) {
345	>	return inversionType;
346	>	} else {
347	>
348	>	AtomType* atype1;
349	>	AtomType* atype2;
350	>	AtomType* atype3;
351	>	AtomType* atype4;
352	>	std::vector<std::string> at1key;
353	>	at1key.push_back(at1);
354	>	atype1 = atomTypeCont_.find(at1key);
355	>
356	>	std::vector<std::string> at2key;
357	>	at2key.push_back(at2);
358	>	atype2 = atomTypeCont_.find(at2key);
359	>
360	>	std::vector<std::string> at3key;
361	>	at3key.push_back(at3);
362	>	atype3 = atomTypeCont_.find(at3key);
363	>
364	>	std::vector<std::string> at4key;
365	>	at4key.push_back(at4);
366	>	atype4 = atomTypeCont_.find(at4key);
367	>
368	>	// query atom types for their chains of responsibility
369	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
370	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
371	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
372	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
373	>
374	>	std::vector<AtomType*>::iterator i;
375	>	std::vector<AtomType*>::iterator j;
376	>	std::vector<AtomType*>::iterator k;
377	>	std::vector<AtomType*>::iterator l;
378	>
379	>	int ii = 0;
380	>	int jj = 0;
381	>	int kk = 0;
382	>	int ll = 0;
383	>	int Iscore;
384	>	int JKLscore;
385	>
386	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
387	>
388	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
389	>	kk = 0;
390	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
391	>	ii = 0;
392	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
393	>	ll = 0;
394	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
395	>
396	>	Iscore = ii;
397	>	JKLscore = jj + kk + ll;
398	>
399	>	std::vector<std::string> myKeys;
400	>	myKeys.push_back((*i)->getName());
401	>	myKeys.push_back((*j)->getName());
402	>	myKeys.push_back((*k)->getName());
403	>	myKeys.push_back((*l)->getName());
404	>
405	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
406	>	if (inversionType) {
407	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
408	>	}
409	>	ll++;
410	>	}
411	>	ii++;
412	>	}
413	>	kk++;
414	>	}
415	>	jj++;
416	>	}
417	>
418	>	if (foundInversions.size() > 0) {
419	>	std::sort(foundInversions.begin(), foundInversions.end());
420	>	int iscore = foundInversions[0].first;
421	>	int jklscore = foundInversions[0].second;
422	>	std::vector<std::string> theKeys = foundInversions[0].third;
423	>
424	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
425	>	return bestType;
426	>	} else {
427	>	//if no exact match found, try wild card match
428	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
429	>	}
430	>	}
431	>	}
432	>
433	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
434		std::vector<std::string> keys;
435		keys.push_back(at1);
436		keys.push_back(at2);
437	+
438	+	//try exact match first
439	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
440	+	if (nbiType) {
441	+	return nbiType;
442	+	} else {
443	+	//if no exact match found, try wild card match
444	+	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
445	+	}
446	+	}
447	+
448	+	BondType* ForceField::getExactBondType(const std::string &at1,
449	+	const std::string &at2){
450	+	std::vector<std::string> keys;
451	+	keys.push_back(at1);
452	+	keys.push_back(at2);
453	+	return bondTypeCont_.find(keys);
454	+	}
455	+
456	+	BendType* ForceField::getExactBendType(const std::string &at1,
457	+	const std::string &at2,
458	+	const std::string &at3){
459	+	std::vector<std::string> keys;
460	+	keys.push_back(at1);
461	+	keys.push_back(at2);
462		keys.push_back(at3);
463		return bendTypeCont_.find(keys);
464	<	}
465	<
466	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
467	<	const std::string &at3, const std::string &at4){
464	>	}
465	>
466	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
467	>	const std::string &at2,
468	>	const std::string &at3,
469	>	const std::string &at4){
470		std::vector<std::string> keys;
471		keys.push_back(at1);
472		keys.push_back(at2);
473		keys.push_back(at3);
474		keys.push_back(at4);
475		return torsionTypeCont_.find(keys);
476	<	}
477	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
476	>	}
477	>
478	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
479	>	const std::string &at2,
480	>	const std::string &at3,
481	>	const std::string &at4){
482		std::vector<std::string> keys;
483	+	keys.push_back(at1);
484	+	keys.push_back(at2);
485	+	keys.push_back(at3);
486	+	keys.push_back(at4);
487	+	return inversionTypeCont_.find(keys);
488	+	}
489	+
490	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
491	+	std::vector<std::string> keys;
492	+	keys.push_back(at1);
493	+	keys.push_back(at2);
494	+	return nonBondedInteractionTypeCont_.find(keys);
495	+	}
496	+
497	+
498	+	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
499	+	std::vector<std::string> keys;
500		keys.push_back(at);
501		return atomTypeCont_.add(keys, atomType);
502	<	}
502	>	}
503
504	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
504	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
505		std::vector<std::string> keys;
506	+	keys.push_back(at);
507	+	return atomTypeCont_.replace(keys, atomType);
508	+	}
509	+
510	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
511	+	BondType* bondType) {
512	+	std::vector<std::string> keys;
513		keys.push_back(at1);
514		keys.push_back(at2);
515	<	return bondTypeCont_.add(keys, bondType);
516	<
517	<	}
518	<
519	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
515	>	return bondTypeCont_.add(keys, bondType);
516	>	}
517	>
518	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
519	>	const std::string &at3, BendType* bendType) {
520		std::vector<std::string> keys;
521		keys.push_back(at1);
522		keys.push_back(at2);
523		keys.push_back(at3);
524		return bendTypeCont_.add(keys, bendType);
525	<	}
526	<
527	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
528	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
525	>	}
526	>
527	>	bool ForceField::addTorsionType(const std::string &at1,
528	>	const std::string &at2,
529	>	const std::string &at3,
530	>	const std::string &at4,
531	>	TorsionType* torsionType) {
532		std::vector<std::string> keys;
533		keys.push_back(at1);
534		keys.push_back(at2);
535		keys.push_back(at3);
536		keys.push_back(at4);
537		return torsionTypeCont_.add(keys, torsionType);
538	<	}
538	>	}
539
540	<	double ForceField::getRcutFromAtomType(AtomType* at) {
540	>	bool ForceField::addInversionType(const std::string &at1,
541	>	const std::string &at2,
542	>	const std::string &at3,
543	>	const std::string &at4,
544	>	InversionType* inversionType) {
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 inversionTypeCont_.add(keys, inversionType);
551	>	}
552	>
553	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
554	>	const std::string &at2,
555	>	NonBondedInteractionType* nbiType) {
556	>	std::vector<std::string> keys;
557	>	keys.push_back(at1);
558	>	keys.push_back(at2);
559	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
560	>	}
561	>
562	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
563		/**@todo */
564		GenericData* data;
565	<	double rcut = 0.0;
566	<
565	>	RealType rcut = 0.0;
566	>
567		if (at->isLennardJones()) {
568	<	data = at->getPropertyByName("LennardJones");
569	<	if (data != NULL) {
570	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
571	<
572	<	if (ljData != NULL) {
573	<	LJParam ljParam = ljData->getData();
574	<
575	<	//by default use 2.5*sigma as cutoff radius
576	<	rcut = 2.5 * ljParam.sigma;
577	<
578	<	} else {
579	<	sprintf( painCave.errMsg,
580	<	"Can not cast GenericData to LJParam\n");
581	<	painCave.severity = OOPSE_ERROR;
582	<	painCave.isFatal = 1;
583	<	simError();
584	<	}
585	<	} else {
586	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
587	<	painCave.severity = OOPSE_ERROR;
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
568	>	data = at->getPropertyByName("LennardJones");
569	>	if (data != NULL) {
570	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
571	>
572	>	if (ljData != NULL) {
573	>	LJParam ljParam = ljData->getData();
574	>
575	>	//by default use 2.5*sigma as cutoff radius
576	>	rcut = 2.5 * ljParam.sigma;
577	>
578	>	} else {
579	>	sprintf( painCave.errMsg,
580	>	"Can not cast GenericData to LJParam\n");
581	>	painCave.severity = OPENMD_ERROR;
582	>	painCave.isFatal = 1;
583	>	simError();
584	>	}
585	>	} else {
586	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
587	>	painCave.severity = OPENMD_ERROR;
588	>	painCave.isFatal = 1;
589	>	simError();
590	>	}
591		}
219	–
592		return rcut;
593	<	}
593	>	}
594	>
595
596	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
596	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
597		std::string forceFieldFilename(filename);
598		ifstrstream* ffStream = new ifstrstream();
599
#	Line 229 | Line 601 | ifstrstream* ForceField::openForceFieldFile(const std:
601		ffStream->open(forceFieldFilename.c_str());
602		if(!ffStream->is_open()){
603
604	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
605	<	ffStream->open( forceFieldFilename.c_str() );
604	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
605	>	ffStream->open( forceFieldFilename.c_str() );
606
607	<	//if current directory does not contain the force field file,
608	<	//try to open it in the path
609	<	if(!ffStream->is_open()){
607	>	//if current directory does not contain the force field file,
608	>	//try to open it in the path
609	>	if(!ffStream->is_open()){
610
611	<	sprintf( painCave.errMsg,
612	<	"Error opening the force field parameter file:\n"
613	<	"\t%s\n"
614	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
615	<	"variable?\n",
616	<	forceFieldFilename.c_str() );
617	<	painCave.severity = OOPSE_ERROR;
618	<	painCave.isFatal = 1;
619	<	simError();
620	<	}
611	>	sprintf( painCave.errMsg,
612	>	"Error opening the force field parameter file:\n"
613	>	"\t%s\n"
614	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
615	>	"variable?\n",
616	>	forceFieldFilename.c_str() );
617	>	painCave.severity = OPENMD_ERROR;
618	>	painCave.isFatal = 1;
619	>	simError();
620	>	}
621		}
250	–
622		return ffStream;
623	+	}
624
625	<	}
254	<
255	<	} //end namespace oopse
625	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1532 by gezelter, Wed Dec 29 19:59:21 2010 UTC

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