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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 1629 by gezelter, Wed Sep 14 21:15:17 2011 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	<
70	<	ForceField::~ForceField() {
71	<	deleteAtypes();
72	<	}
73	<
74	<	AtomType* ForceField::getAtomType(const std::string &at) {
69	>	/**
70	>	* getAtomType by string
71	>	*
72	>	* finds the requested atom type in this force field using the string
73	>	* name of the atom type.
74	>	*/
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	>	/**
82	>	* getAtomType by ident
83	>	*
84	>	* finds the requested atom type in this force field using the
85	>	* integer ident instead of the string name of the atom type.
86	>	*/
87	>	AtomType* ForceField::getAtomType(int ident) {
88	>	std::string at = atypeIdentToName.find(ident)->second;
89	>	return getAtomType(at);
90	>	}
91	>
92	>	BondType* ForceField::getBondType(const std::string &at1,
93	>	const std::string &at2) {
94		std::vector<std::string> keys;
95		keys.push_back(at1);
96		keys.push_back(at2);
#	Line 83 | Line 98 | BondType* ForceField::getBondType(const std::string &a
98		//try exact match first
99		BondType* bondType = bondTypeCont_.find(keys);
100		if (bondType) {
101	<	return bondType;
101	>	return bondType;
102		} else {
103	<	//if no exact match found, try wild card match
104	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
105	<	}
103	>	AtomType* atype1;
104	>	AtomType* atype2;
105	>	std::vector<std::string> at1key;
106	>	at1key.push_back(at1);
107	>	atype1 = atomTypeCont_.find(at1key);
108	>
109	>	std::vector<std::string> at2key;
110	>	at2key.push_back(at2);
111	>	atype2 = atomTypeCont_.find(at2key);
112
113	<	}
113	>	// query atom types for their chains of responsibility
114	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
115	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
116
117	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
118	<	const std::string &at3) {
117	>	std::vector<AtomType*>::iterator i;
118	>	std::vector<AtomType*>::iterator j;
119	>
120	>	int ii = 0;
121	>	int jj = 0;
122	>	int bondTypeScore;
123	>
124	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
125	>
126	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
127	>	jj = 0;
128	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
129	>
130	>	bondTypeScore = ii + jj;
131	>
132	>	std::vector<std::string> myKeys;
133	>	myKeys.push_back((*i)->getName());
134	>	myKeys.push_back((*j)->getName());
135	>
136	>	BondType* bondType = bondTypeCont_.find(myKeys);
137	>	if (bondType) {
138	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
139	>	}
140	>	jj++;
141	>	}
142	>	ii++;
143	>	}
144	>
145	>
146	>	if (foundBonds.size() > 0) {
147	>	// sort the foundBonds by the score:
148	>	std::sort(foundBonds.begin(), foundBonds.end());
149	>
150	>	int bestScore = foundBonds[0].first;
151	>	std::vector<std::string> theKeys = foundBonds[0].second;
152	>
153	>	BondType* bestType = bondTypeCont_.find(theKeys);
154	>
155	>	return bestType;
156	>	} else {
157	>	//if no exact match found, try wild card match
158	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
159	>	}
160	>	}
161	>	}
162	>
163	>	BendType* ForceField::getBendType(const std::string &at1,
164	>	const std::string &at2,
165	>	const std::string &at3) {
166		std::vector<std::string> keys;
167		keys.push_back(at1);
168		keys.push_back(at2);
#	Line 101 | Line 171 | BendType* ForceField::getBendType(const std::string &a
171		//try exact match first
172		BendType* bendType = bendTypeCont_.find(keys);
173		if (bendType) {
174	<	return bendType;
174	>	return bendType;
175		} else {
106	–	//if no exact match found, try wild card match
107	–	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
108	–	}
109	–	}
176
177	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
178	<	const std::string &at3, const std::string &at4) {
177	>	AtomType* atype1;
178	>	AtomType* atype2;
179	>	AtomType* atype3;
180	>	std::vector<std::string> at1key;
181	>	at1key.push_back(at1);
182	>	atype1 = atomTypeCont_.find(at1key);
183	>
184	>	std::vector<std::string> at2key;
185	>	at2key.push_back(at2);
186	>	atype2 = atomTypeCont_.find(at2key);
187	>
188	>	std::vector<std::string> at3key;
189	>	at3key.push_back(at3);
190	>	atype3 = atomTypeCont_.find(at3key);
191	>
192	>	// query atom types for their chains of responsibility
193	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
194	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
195	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
196	>
197	>	std::vector<AtomType*>::iterator i;
198	>	std::vector<AtomType*>::iterator j;
199	>	std::vector<AtomType*>::iterator k;
200	>
201	>	int ii = 0;
202	>	int jj = 0;
203	>	int kk = 0;
204	>	int IKscore;
205	>
206	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
207	>
208	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
209	>	ii = 0;
210	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
211	>	kk = 0;
212	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
213	>
214	>	IKscore = ii + kk;
215	>
216	>	std::vector<std::string> myKeys;
217	>	myKeys.push_back((*i)->getName());
218	>	myKeys.push_back((*j)->getName());
219	>	myKeys.push_back((*k)->getName());
220	>
221	>	BendType* bendType = bendTypeCont_.find(myKeys);
222	>	if (bendType) {
223	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
224	>	}
225	>	kk++;
226	>	}
227	>	ii++;
228	>	}
229	>	jj++;
230	>	}
231	>
232	>	if (foundBends.size() > 0) {
233	>	std::sort(foundBends.begin(), foundBends.end());
234	>	int jscore = foundBends[0].first;
235	>	int ikscore = foundBends[0].second;
236	>	std::vector<std::string> theKeys = foundBends[0].third;
237	>
238	>	BendType* bestType = bendTypeCont_.find(theKeys);
239	>	return bestType;
240	>	} else {
241	>	//if no exact match found, try wild card match
242	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
243	>	}
244	>	}
245	>	}
246	>
247	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
248	>	const std::string &at2,
249	>	const std::string &at3,
250	>	const std::string &at4) {
251		std::vector<std::string> keys;
252		keys.push_back(at1);
253		keys.push_back(at2);
254		keys.push_back(at3);
255		keys.push_back(at4);
256
257	+
258	+	//try exact match first
259		TorsionType* torsionType = torsionTypeCont_.find(keys);
260		if (torsionType) {
261	<	return torsionType;
261	>	return torsionType;
262		} 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_);
263
264	<	}
264	>	AtomType* atype1;
265	>	AtomType* atype2;
266	>	AtomType* atype3;
267	>	AtomType* atype4;
268	>	std::vector<std::string> at1key;
269	>	at1key.push_back(at1);
270	>	atype1 = atomTypeCont_.find(at1key);
271	>
272	>	std::vector<std::string> at2key;
273	>	at2key.push_back(at2);
274	>	atype2 = atomTypeCont_.find(at2key);
275
276	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
276	>	std::vector<std::string> at3key;
277	>	at3key.push_back(at3);
278	>	atype3 = atomTypeCont_.find(at3key);
279	>
280	>	std::vector<std::string> at4key;
281	>	at4key.push_back(at4);
282	>	atype4 = atomTypeCont_.find(at4key);
283	>
284	>	// query atom types for their chains of responsibility
285	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
286	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
287	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
288	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
289	>
290	>	std::vector<AtomType*>::iterator i;
291	>	std::vector<AtomType*>::iterator j;
292	>	std::vector<AtomType*>::iterator k;
293	>	std::vector<AtomType*>::iterator l;
294	>
295	>	int ii = 0;
296	>	int jj = 0;
297	>	int kk = 0;
298	>	int ll = 0;
299	>	int ILscore;
300	>	int JKscore;
301	>
302	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
303	>
304	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
305	>	kk = 0;
306	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
307	>	ii = 0;
308	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
309	>	ll = 0;
310	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
311	>
312	>	ILscore = ii + ll;
313	>	JKscore = jj + kk;
314	>
315	>	std::vector<std::string> myKeys;
316	>	myKeys.push_back((*i)->getName());
317	>	myKeys.push_back((*j)->getName());
318	>	myKeys.push_back((*k)->getName());
319	>	myKeys.push_back((*l)->getName());
320	>
321	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
322	>	if (torsionType) {
323	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
324	>	}
325	>	ll++;
326	>	}
327	>	ii++;
328	>	}
329	>	kk++;
330	>	}
331	>	jj++;
332	>	}
333	>
334	>	if (foundTorsions.size() > 0) {
335	>	std::sort(foundTorsions.begin(), foundTorsions.end());
336	>	int jkscore = foundTorsions[0].first;
337	>	int ilscore = foundTorsions[0].second;
338	>	std::vector<std::string> theKeys = foundTorsions[0].third;
339	>
340	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
341	>	return bestType;
342	>	} else {
343	>	//if no exact match found, try wild card match
344	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
345	>	}
346	>	}
347	>	}
348	>
349	>	InversionType* ForceField::getInversionType(const std::string &at1,
350	>	const std::string &at2,
351	>	const std::string &at3,
352	>	const std::string &at4) {
353		std::vector<std::string> keys;
354		keys.push_back(at1);
355		keys.push_back(at2);
356	<	return bondTypeCont_.find(keys);
357	<	}
356	>	keys.push_back(at3);
357	>	keys.push_back(at4);
358
359	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
360	<	const std::string &at3){
359	>	//try exact match first
360	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
361	>	if (inversionType) {
362	>	return inversionType;
363	>	} else {
364	>
365	>	AtomType* atype1;
366	>	AtomType* atype2;
367	>	AtomType* atype3;
368	>	AtomType* atype4;
369	>	std::vector<std::string> at1key;
370	>	at1key.push_back(at1);
371	>	atype1 = atomTypeCont_.find(at1key);
372	>
373	>	std::vector<std::string> at2key;
374	>	at2key.push_back(at2);
375	>	atype2 = atomTypeCont_.find(at2key);
376	>
377	>	std::vector<std::string> at3key;
378	>	at3key.push_back(at3);
379	>	atype3 = atomTypeCont_.find(at3key);
380	>
381	>	std::vector<std::string> at4key;
382	>	at4key.push_back(at4);
383	>	atype4 = atomTypeCont_.find(at4key);
384	>
385	>	// query atom types for their chains of responsibility
386	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
387	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
388	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
389	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
390	>
391	>	std::vector<AtomType*>::iterator i;
392	>	std::vector<AtomType*>::iterator j;
393	>	std::vector<AtomType*>::iterator k;
394	>	std::vector<AtomType*>::iterator l;
395	>
396	>	int ii = 0;
397	>	int jj = 0;
398	>	int kk = 0;
399	>	int ll = 0;
400	>	int Iscore;
401	>	int JKLscore;
402	>
403	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
404	>
405	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
406	>	kk = 0;
407	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
408	>	ii = 0;
409	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
410	>	ll = 0;
411	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
412	>
413	>	Iscore = ii;
414	>	JKLscore = jj + kk + ll;
415	>
416	>	std::vector<std::string> myKeys;
417	>	myKeys.push_back((*i)->getName());
418	>	myKeys.push_back((*j)->getName());
419	>	myKeys.push_back((*k)->getName());
420	>	myKeys.push_back((*l)->getName());
421	>
422	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
423	>	if (inversionType) {
424	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
425	>	}
426	>	ll++;
427	>	}
428	>	ii++;
429	>	}
430	>	kk++;
431	>	}
432	>	jj++;
433	>	}
434	>
435	>	if (foundInversions.size() > 0) {
436	>	std::sort(foundInversions.begin(), foundInversions.end());
437	>	int iscore = foundInversions[0].first;
438	>	int jklscore = foundInversions[0].second;
439	>	std::vector<std::string> theKeys = foundInversions[0].third;
440	>
441	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
442	>	return bestType;
443	>	} else {
444	>	//if no exact match found, try wild card match
445	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
446	>	}
447	>	}
448	>	}
449	>
450	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
451	>
452		std::vector<std::string> keys;
453		keys.push_back(at1);
454		keys.push_back(at2);
455	+
456	+	//try exact match first
457	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
458	+	if (nbiType) {
459	+	return nbiType;
460	+	} else {
461	+	AtomType* atype1;
462	+	AtomType* atype2;
463	+	std::vector<std::string> at1key;
464	+	at1key.push_back(at1);
465	+	atype1 = atomTypeCont_.find(at1key);
466	+
467	+	std::vector<std::string> at2key;
468	+	at2key.push_back(at2);
469	+	atype2 = atomTypeCont_.find(at2key);
470	+
471	+	// query atom types for their chains of responsibility
472	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
473	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
474	+
475	+	std::vector<AtomType*>::iterator i;
476	+	std::vector<AtomType*>::iterator j;
477	+
478	+	int ii = 0;
479	+	int jj = 0;
480	+	int nbiTypeScore;
481	+
482	+	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
483	+
484	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
485	+	jj = 0;
486	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
487	+
488	+	nbiTypeScore = ii + jj;
489	+
490	+	std::vector<std::string> myKeys;
491	+	myKeys.push_back((*i)->getName());
492	+	myKeys.push_back((*j)->getName());
493	+
494	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
495	+	if (nbiType) {
496	+	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
497	+	}
498	+	jj++;
499	+	}
500	+	ii++;
501	+	}
502	+
503	+
504	+	if (foundNBI.size() > 0) {
505	+	// sort the foundNBI by the score:
506	+	std::sort(foundNBI.begin(), foundNBI.end());
507	+
508	+	int bestScore = foundNBI[0].first;
509	+	std::vector<std::string> theKeys = foundNBI[0].second;
510	+
511	+	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
512	+	return bestType;
513	+	} else {
514	+	//if no exact match found, try wild card match
515	+	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
516	+	}
517	+	}
518	+	}
519	+
520	+	BondType* ForceField::getExactBondType(const std::string &at1,
521	+	const std::string &at2){
522	+	std::vector<std::string> keys;
523	+	keys.push_back(at1);
524	+	keys.push_back(at2);
525	+	return bondTypeCont_.find(keys);
526	+	}
527	+
528	+	BendType* ForceField::getExactBendType(const std::string &at1,
529	+	const std::string &at2,
530	+	const std::string &at3){
531	+	std::vector<std::string> keys;
532	+	keys.push_back(at1);
533	+	keys.push_back(at2);
534		keys.push_back(at3);
535		return bendTypeCont_.find(keys);
536	<	}
537	<
538	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
539	<	const std::string &at3, const std::string &at4){
536	>	}
537	>
538	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
539	>	const std::string &at2,
540	>	const std::string &at3,
541	>	const std::string &at4){
542		std::vector<std::string> keys;
543		keys.push_back(at1);
544		keys.push_back(at2);
545		keys.push_back(at3);
546		keys.push_back(at4);
547		return torsionTypeCont_.find(keys);
548	<	}
549	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
548	>	}
549	>
550	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
551	>	const std::string &at2,
552	>	const std::string &at3,
553	>	const std::string &at4){
554		std::vector<std::string> keys;
555	+	keys.push_back(at1);
556	+	keys.push_back(at2);
557	+	keys.push_back(at3);
558	+	keys.push_back(at4);
559	+	return inversionTypeCont_.find(keys);
560	+	}
561	+
562	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
563	+	std::vector<std::string> keys;
564	+	keys.push_back(at1);
565	+	keys.push_back(at2);
566	+	return nonBondedInteractionTypeCont_.find(keys);
567	+	}
568	+
569	+
570	+	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
571	+	std::vector<std::string> keys;
572		keys.push_back(at);
573	+	atypeIdentToName[atomType->getIdent()] = at;
574		return atomTypeCont_.add(keys, atomType);
575	<	}
575	>	}
576
577	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
577	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
578		std::vector<std::string> keys;
579	+	keys.push_back(at);
580	+	atypeIdentToName[atomType->getIdent()] = at;
581	+	return atomTypeCont_.replace(keys, atomType);
582	+	}
583	+
584	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
585	+	BondType* bondType) {
586	+	std::vector<std::string> keys;
587		keys.push_back(at1);
588		keys.push_back(at2);
589	<	return bondTypeCont_.add(keys, bondType);
590	<
591	<	}
592	<
593	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
589	>	return bondTypeCont_.add(keys, bondType);
590	>	}
591	>
592	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
593	>	const std::string &at3, BendType* bendType) {
594		std::vector<std::string> keys;
595		keys.push_back(at1);
596		keys.push_back(at2);
597		keys.push_back(at3);
598		return bendTypeCont_.add(keys, bendType);
599	<	}
600	<
601	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
602	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
599	>	}
600	>
601	>	bool ForceField::addTorsionType(const std::string &at1,
602	>	const std::string &at2,
603	>	const std::string &at3,
604	>	const std::string &at4,
605	>	TorsionType* torsionType) {
606		std::vector<std::string> keys;
607		keys.push_back(at1);
608		keys.push_back(at2);
609		keys.push_back(at3);
610		keys.push_back(at4);
611		return torsionTypeCont_.add(keys, torsionType);
612	<	}
612	>	}
613
614	<	double ForceField::getRcutFromAtomType(AtomType* at) {
614	>	bool ForceField::addInversionType(const std::string &at1,
615	>	const std::string &at2,
616	>	const std::string &at3,
617	>	const std::string &at4,
618	>	InversionType* inversionType) {
619	>	std::vector<std::string> keys;
620	>	keys.push_back(at1);
621	>	keys.push_back(at2);
622	>	keys.push_back(at3);
623	>	keys.push_back(at4);
624	>	return inversionTypeCont_.add(keys, inversionType);
625	>	}
626	>
627	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
628	>	const std::string &at2,
629	>	NonBondedInteractionType* nbiType) {
630	>	std::vector<std::string> keys;
631	>	keys.push_back(at1);
632	>	keys.push_back(at2);
633	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
634	>	}
635	>
636	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
637		/**@todo */
638		GenericData* data;
639	<	double rcut = 0.0;
640	<
639	>	RealType rcut = 0.0;
640	>
641		if (at->isLennardJones()) {
642	<	data = at->getPropertyByName("LennardJones");
643	<	if (data != NULL) {
644	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
645	<
646	<	if (ljData != NULL) {
647	<	LJParam ljParam = ljData->getData();
648	<
649	<	//by default use 2.5*sigma as cutoff radius
650	<	rcut = 2.5 * ljParam.sigma;
651	<
652	<	} else {
653	<	sprintf( painCave.errMsg,
654	<	"Can not cast GenericData to LJParam\n");
655	<	painCave.severity = OOPSE_ERROR;
656	<	painCave.isFatal = 1;
657	<	simError();
658	<	}
659	<	} else {
660	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
661	<	painCave.severity = OOPSE_ERROR;
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
642	>	data = at->getPropertyByName("LennardJones");
643	>	if (data != NULL) {
644	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
645	>
646	>	if (ljData != NULL) {
647	>	LJParam ljParam = ljData->getData();
648	>
649	>	//by default use 2.5*sigma as cutoff radius
650	>	rcut = 2.5 * ljParam.sigma;
651	>
652	>	} else {
653	>	sprintf( painCave.errMsg,
654	>	"Can not cast GenericData to LJParam\n");
655	>	painCave.severity = OPENMD_ERROR;
656	>	painCave.isFatal = 1;
657	>	simError();
658	>	}
659	>	} else {
660	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
661	>	painCave.severity = OPENMD_ERROR;
662	>	painCave.isFatal = 1;
663	>	simError();
664	>	}
665		}
219	–
666		return rcut;
667	<	}
667	>	}
668	>
669
670	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
670	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
671		std::string forceFieldFilename(filename);
672		ifstrstream* ffStream = new ifstrstream();
673
#	Line 229 | Line 675 | ifstrstream* ForceField::openForceFieldFile(const std:
675		ffStream->open(forceFieldFilename.c_str());
676		if(!ffStream->is_open()){
677
678	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
679	<	ffStream->open( forceFieldFilename.c_str() );
678	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
679	>	ffStream->open( forceFieldFilename.c_str() );
680
681	<	//if current directory does not contain the force field file,
682	<	//try to open it in the path
683	<	if(!ffStream->is_open()){
681	>	//if current directory does not contain the force field file,
682	>	//try to open it in the path
683	>	if(!ffStream->is_open()){
684
685	<	sprintf( painCave.errMsg,
686	<	"Error opening the force field parameter file:\n"
687	<	"\t%s\n"
688	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
689	<	"variable?\n",
690	<	forceFieldFilename.c_str() );
691	<	painCave.severity = OOPSE_ERROR;
692	<	painCave.isFatal = 1;
693	<	simError();
694	<	}
685	>	sprintf( painCave.errMsg,
686	>	"Error opening the force field parameter file:\n"
687	>	"\t%s\n"
688	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
689	>	"variable?\n",
690	>	forceFieldFilename.c_str() );
691	>	painCave.severity = OPENMD_ERROR;
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695		}
250	–
696		return ffStream;
697	+	}
698
699	<	}
254	<
255	<	} //end namespace oopse
699	>	} //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 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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