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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 1530 by gezelter, Tue Dec 28 21:47:55 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 "utils/Tuple.hpp"
54		#include "UseTheForce/DarkSide/atype_interface.h"
55	<	namespace oopse {
55	>	namespace OpenMD {
56
57	<	ForceField::ForceField() {
57	>	ForceField::ForceField() {
58	>
59		char* tempPath;
60		tempPath = getenv("FORCE_PARAM_PATH");
61	<
61	>
62		if (tempPath == NULL) {
63	<	//convert a macro from compiler to a string in c++
64	<	STR_DEFINE(ffPath_, FRC_PATH );
63	>	//convert a macro from compiler to a string in c++
64	>	STR_DEFINE(ffPath_, FRC_PATH );
65		} else {
66	<	ffPath_ = tempPath;
66	>	ffPath_ = tempPath;
67		}
68	<	}
68	>	}
69
70
71	<	ForceField::~ForceField() {
71	>	ForceField::~ForceField() {
72		deleteAtypes();
73	<	}
73	>	}
74
75	<	AtomType* ForceField::getAtomType(const std::string &at) {
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	<	}
79	>	}
80
81	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
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);
#	Line 83 | Line 87 | BondType* ForceField::getBondType(const std::string &a
87		//try exact match first
88		BondType* bondType = bondTypeCont_.find(keys);
89		if (bondType) {
90	<	return bondType;
90	>	return bondType;
91		} else {
92	<	//if no exact match found, try wild card match
93	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
94	<	}
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	<	}
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	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
107	<	const std::string &at3) {
106	>	std::vector<AtomType*>::iterator i;
107	>	std::vector<AtomType*>::iterator j;
108	>
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	>	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);
#	Line 101 | Line 160 | BendType* ForceField::getBendType(const std::string &a
160		//try exact match first
161		BendType* bendType = bendTypeCont_.find(keys);
162		if (bendType) {
163	<	return bendType;
163	>	return bendType;
164		} else {
165	<	//if no exact match found, try wild card match
166	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
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	>	// 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	>	int ii = 0;
191	>	int jj = 0;
192	>	int kk = 0;
193	>	int IKscore;
194	>
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	>	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	>	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	<	}
234	>	}
235
236	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
237	<	const std::string &at3, const std::string &at4) {
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
246	+
247	+	//try exact match first
248		TorsionType* torsionType = torsionTypeCont_.find(keys);
249		if (torsionType) {
250	<	return torsionType;
250	>	return torsionType;
251		} 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_);
252
253	<	}
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	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
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	<	return bondTypeCont_.find(keys);
346	<	}
345	>	keys.push_back(at3);
346	>	keys.push_back(at4);
347
348	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
349	<	const std::string &at3){
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, const std::string &at2,
473	<	const std::string &at3, const std::string &at4){
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	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
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	<	}
508	>	}
509
510	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
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	<
525	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
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, const std::string &at2,
534	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
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	<	}
544	>	}
545
546	<	double ForceField::getRcutFromAtomType(AtomType* at) {
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	<	double rcut = 0.0;
572	<
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 = OOPSE_ERROR;
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	} else {
592	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
593	<	painCave.severity = OOPSE_ERROR;
594	<	painCave.isFatal = 1;
595	<	simError();
596	<	}
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		}
219	–
598		return rcut;
599	<	}
599	>	}
600	>
601
602	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
602	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
603		std::string forceFieldFilename(filename);
604		ifstrstream* ffStream = new ifstrstream();
605
#	Line 229 | Line 607 | ifstrstream* ForceField::openForceFieldFile(const std:
607		ffStream->open(forceFieldFilename.c_str());
608		if(!ffStream->is_open()){
609
610	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
611	<	ffStream->open( forceFieldFilename.c_str() );
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()){
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 = OOPSE_ERROR;
624	<	painCave.isFatal = 1;
625	<	simError();
626	<	}
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		}
250	–
628		return ffStream;
629	+	}
630
631	<	}
254	<
255	<	} //end namespace oopse
631	>	} //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 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

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