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

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trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

#	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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	+	#include <algorithm>
52		#include "UseTheForce/ForceField.hpp"
53		#include "utils/simError.h"
54	<	#include "UseTheForce/DarkSide/atype_interface.h"
55	<	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
54	<	#include "UseTheForce/DarkSide/switcheroo_interface.h"
55	<	namespace oopse {
54	>	#include "utils/Tuple.hpp"
55	>	#include "types/LennardJonesAdapter.hpp"
56
57	+	namespace OpenMD {
58	+
59		ForceField::ForceField() {
60	+
61		char* tempPath;
62		tempPath = getenv("FORCE_PARAM_PATH");
63	<
63	>
64		if (tempPath == NULL) {
65		//convert a macro from compiler to a string in c++
66		STR_DEFINE(ffPath_, FRC_PATH );
#	Line 66 | Line 69 | namespace oopse {
69		}
70		}
71
72	<
73	<	ForceField::~ForceField() {
74	<	deleteAtypes();
75	<	deleteSwitch();
76	<	}
77	<
72	>	/**
73	>	* getAtomType by string
74	>	*
75	>	* finds the requested atom type in this force field using the string
76	>	* name of the atom type.
77	>	*/
78		AtomType* ForceField::getAtomType(const std::string &at) {
79		std::vector<std::string> keys;
80		keys.push_back(at);
81		return atomTypeCont_.find(keys);
82		}
83
84	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
84	>	/**
85	>	* getAtomType by ident
86	>	*
87	>	* finds the requested atom type in this force field using the
88	>	* integer ident instead of the string name of the atom type.
89	>	*/
90	>	AtomType* ForceField::getAtomType(int ident) {
91	>	std::string at = atypeIdentToName.find(ident)->second;
92	>	return getAtomType(at);
93	>	}
94	>
95	>	BondType* ForceField::getBondType(const std::string &at1,
96	>	const std::string &at2) {
97		std::vector<std::string> keys;
98		keys.push_back(at1);
99		keys.push_back(at2);
#	Line 88 | Line 103 | namespace oopse {
103		if (bondType) {
104		return bondType;
105		} else {
106	<	//if no exact match found, try wild card match
107	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
108	<	}
106	>	AtomType* atype1;
107	>	AtomType* atype2;
108	>	std::vector<std::string> at1key;
109	>	at1key.push_back(at1);
110	>	atype1 = atomTypeCont_.find(at1key);
111	>
112	>	std::vector<std::string> at2key;
113	>	at2key.push_back(at2);
114	>	atype2 = atomTypeCont_.find(at2key);
115
116	<	}
116	>	// query atom types for their chains of responsibility
117	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
118	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
119
120	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
120	>	std::vector<AtomType*>::iterator i;
121	>	std::vector<AtomType*>::iterator j;
122	>
123	>	int ii = 0;
124	>	int jj = 0;
125	>	int bondTypeScore;
126	>
127	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
128	>
129	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
130	>	jj = 0;
131	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
132	>
133	>	bondTypeScore = ii + jj;
134	>
135	>	std::vector<std::string> myKeys;
136	>	myKeys.push_back((*i)->getName());
137	>	myKeys.push_back((*j)->getName());
138	>
139	>	BondType* bondType = bondTypeCont_.find(myKeys);
140	>	if (bondType) {
141	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
142	>	}
143	>	jj++;
144	>	}
145	>	ii++;
146	>	}
147	>
148	>
149	>	if (foundBonds.size() > 0) {
150	>	// sort the foundBonds by the score:
151	>	std::sort(foundBonds.begin(), foundBonds.end());
152	>
153	>	int bestScore = foundBonds[0].first;
154	>	std::vector<std::string> theKeys = foundBonds[0].second;
155	>
156	>	BondType* bestType = bondTypeCont_.find(theKeys);
157	>
158	>	return bestType;
159	>	} else {
160	>	//if no exact match found, try wild card match
161	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
162	>	}
163	>	}
164	>	}
165	>
166	>	BendType* ForceField::getBendType(const std::string &at1,
167	>	const std::string &at2,
168		const std::string &at3) {
169		std::vector<std::string> keys;
170		keys.push_back(at1);
#	Line 106 | Line 176 | namespace oopse {
176		if (bendType) {
177		return bendType;
178		} else {
179	<	//if no exact match found, try wild card match
180	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
179	>
180	>	AtomType* atype1;
181	>	AtomType* atype2;
182	>	AtomType* atype3;
183	>	std::vector<std::string> at1key;
184	>	at1key.push_back(at1);
185	>	atype1 = atomTypeCont_.find(at1key);
186	>
187	>	std::vector<std::string> at2key;
188	>	at2key.push_back(at2);
189	>	atype2 = atomTypeCont_.find(at2key);
190	>
191	>	std::vector<std::string> at3key;
192	>	at3key.push_back(at3);
193	>	atype3 = atomTypeCont_.find(at3key);
194	>
195	>	// query atom types for their chains of responsibility
196	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
197	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
198	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
199	>
200	>	std::vector<AtomType*>::iterator i;
201	>	std::vector<AtomType*>::iterator j;
202	>	std::vector<AtomType*>::iterator k;
203	>
204	>	int ii = 0;
205	>	int jj = 0;
206	>	int kk = 0;
207	>	int IKscore;
208	>
209	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
210	>
211	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
212	>	ii = 0;
213	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
214	>	kk = 0;
215	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
216	>
217	>	IKscore = ii + kk;
218	>
219	>	std::vector<std::string> myKeys;
220	>	myKeys.push_back((*i)->getName());
221	>	myKeys.push_back((*j)->getName());
222	>	myKeys.push_back((*k)->getName());
223	>
224	>	BendType* bendType = bendTypeCont_.find(myKeys);
225	>	if (bendType) {
226	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
227	>	}
228	>	kk++;
229	>	}
230	>	ii++;
231	>	}
232	>	jj++;
233	>	}
234	>
235	>	if (foundBends.size() > 0) {
236	>	std::sort(foundBends.begin(), foundBends.end());
237	>	int jscore = foundBends[0].first;
238	>	int ikscore = foundBends[0].second;
239	>	std::vector<std::string> theKeys = foundBends[0].third;
240	>
241	>	BendType* bestType = bendTypeCont_.find(theKeys);
242	>	return bestType;
243	>	} else {
244	>	//if no exact match found, try wild card match
245	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
246	>	}
247		}
248		}
249
250	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
251	<	const std::string &at3, const std::string &at4) {
250	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
251	>	const std::string &at2,
252	>	const std::string &at3,
253	>	const std::string &at4) {
254		std::vector<std::string> keys;
255		keys.push_back(at1);
256		keys.push_back(at2);
257		keys.push_back(at3);
258		keys.push_back(at4);
259
260	+
261	+	//try exact match first
262		TorsionType* torsionType = torsionTypeCont_.find(keys);
263		if (torsionType) {
264		return torsionType;
265		} else {
126	–	//if no exact match found, try wild card match
127	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
128	–	}
129	–
130	–	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
266
267	+	AtomType* atype1;
268	+	AtomType* atype2;
269	+	AtomType* atype3;
270	+	AtomType* atype4;
271	+	std::vector<std::string> at1key;
272	+	at1key.push_back(at1);
273	+	atype1 = atomTypeCont_.find(at1key);
274	+
275	+	std::vector<std::string> at2key;
276	+	at2key.push_back(at2);
277	+	atype2 = atomTypeCont_.find(at2key);
278	+
279	+	std::vector<std::string> at3key;
280	+	at3key.push_back(at3);
281	+	atype3 = atomTypeCont_.find(at3key);
282	+
283	+	std::vector<std::string> at4key;
284	+	at4key.push_back(at4);
285	+	atype4 = atomTypeCont_.find(at4key);
286	+
287	+	// query atom types for their chains of responsibility
288	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
289	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
290	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
291	+	std::vector<AtomType*> at4Chain = atype4->allYourBase();
292	+
293	+	std::vector<AtomType*>::iterator i;
294	+	std::vector<AtomType*>::iterator j;
295	+	std::vector<AtomType*>::iterator k;
296	+	std::vector<AtomType*>::iterator l;
297	+
298	+	int ii = 0;
299	+	int jj = 0;
300	+	int kk = 0;
301	+	int ll = 0;
302	+	int ILscore;
303	+	int JKscore;
304	+
305	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
306	+
307	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
308	+	kk = 0;
309	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
310	+	ii = 0;
311	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
312	+	ll = 0;
313	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
314	+
315	+	ILscore = ii + ll;
316	+	JKscore = jj + kk;
317	+
318	+	std::vector<std::string> myKeys;
319	+	myKeys.push_back((*i)->getName());
320	+	myKeys.push_back((*j)->getName());
321	+	myKeys.push_back((*k)->getName());
322	+	myKeys.push_back((*l)->getName());
323	+
324	+	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
325	+	if (torsionType) {
326	+	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
327	+	}
328	+	ll++;
329	+	}
330	+	ii++;
331	+	}
332	+	kk++;
333	+	}
334	+	jj++;
335	+	}
336	+
337	+	if (foundTorsions.size() > 0) {
338	+	std::sort(foundTorsions.begin(), foundTorsions.end());
339	+	int jkscore = foundTorsions[0].first;
340	+	int ilscore = foundTorsions[0].second;
341	+	std::vector<std::string> theKeys = foundTorsions[0].third;
342	+
343	+	TorsionType* bestType = torsionTypeCont_.find(theKeys);
344	+	return bestType;
345	+	} else {
346	+	//if no exact match found, try wild card match
347	+	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
348	+	}
349	+	}
350		}
351
352	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
352	>	InversionType* ForceField::getInversionType(const std::string &at1,
353	>	const std::string &at2,
354	>	const std::string &at3,
355	>	const std::string &at4) {
356	>	std::vector<std::string> keys;
357	>	keys.push_back(at1);
358	>	keys.push_back(at2);
359	>	keys.push_back(at3);
360	>	keys.push_back(at4);
361	>
362	>	//try exact match first
363	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
364	>	if (inversionType) {
365	>	return inversionType;
366	>	} else {
367	>
368	>	AtomType* atype1;
369	>	AtomType* atype2;
370	>	AtomType* atype3;
371	>	AtomType* atype4;
372	>	std::vector<std::string> at1key;
373	>	at1key.push_back(at1);
374	>	atype1 = atomTypeCont_.find(at1key);
375	>
376	>	std::vector<std::string> at2key;
377	>	at2key.push_back(at2);
378	>	atype2 = atomTypeCont_.find(at2key);
379	>
380	>	std::vector<std::string> at3key;
381	>	at3key.push_back(at3);
382	>	atype3 = atomTypeCont_.find(at3key);
383	>
384	>	std::vector<std::string> at4key;
385	>	at4key.push_back(at4);
386	>	atype4 = atomTypeCont_.find(at4key);
387	>
388	>	// query atom types for their chains of responsibility
389	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
390	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
391	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
392	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
393	>
394	>	std::vector<AtomType*>::iterator i;
395	>	std::vector<AtomType*>::iterator j;
396	>	std::vector<AtomType*>::iterator k;
397	>	std::vector<AtomType*>::iterator l;
398	>
399	>	int ii = 0;
400	>	int jj = 0;
401	>	int kk = 0;
402	>	int ll = 0;
403	>	int Iscore;
404	>	int JKLscore;
405	>
406	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
407	>
408	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
409	>	kk = 0;
410	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
411	>	ii = 0;
412	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
413	>	ll = 0;
414	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
415	>
416	>	Iscore = ii;
417	>	JKLscore = jj + kk + ll;
418	>
419	>	std::vector<std::string> myKeys;
420	>	myKeys.push_back((*i)->getName());
421	>	myKeys.push_back((*j)->getName());
422	>	myKeys.push_back((*k)->getName());
423	>	myKeys.push_back((*l)->getName());
424	>
425	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
426	>	if (inversionType) {
427	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
428	>	}
429	>	ll++;
430	>	}
431	>	ii++;
432	>	}
433	>	kk++;
434	>	}
435	>	jj++;
436	>	}
437	>
438	>	if (foundInversions.size() > 0) {
439	>	std::sort(foundInversions.begin(), foundInversions.end());
440	>	int iscore = foundInversions[0].first;
441	>	int jklscore = foundInversions[0].second;
442	>	std::vector<std::string> theKeys = foundInversions[0].third;
443	>
444	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
445	>	return bestType;
446	>	} else {
447	>	//if no exact match found, try wild card match
448	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
449	>	}
450	>	}
451	>	}
452	>
453	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
454	>
455		std::vector<std::string> keys;
456		keys.push_back(at1);
457		keys.push_back(at2);
458	+
459	+	//try exact match first
460	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
461	+	if (nbiType) {
462	+	return nbiType;
463	+	} else {
464	+	AtomType* atype1;
465	+	AtomType* atype2;
466	+	std::vector<std::string> at1key;
467	+	at1key.push_back(at1);
468	+	atype1 = atomTypeCont_.find(at1key);
469	+
470	+	std::vector<std::string> at2key;
471	+	at2key.push_back(at2);
472	+	atype2 = atomTypeCont_.find(at2key);
473	+
474	+	// query atom types for their chains of responsibility
475	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
476	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
477	+
478	+	std::vector<AtomType*>::iterator i;
479	+	std::vector<AtomType*>::iterator j;
480	+
481	+	int ii = 0;
482	+	int jj = 0;
483	+	int nbiTypeScore;
484	+
485	+	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
486	+
487	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
488	+	jj = 0;
489	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
490	+
491	+	nbiTypeScore = ii + jj;
492	+
493	+	std::vector<std::string> myKeys;
494	+	myKeys.push_back((*i)->getName());
495	+	myKeys.push_back((*j)->getName());
496	+
497	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
498	+	if (nbiType) {
499	+	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
500	+	}
501	+	jj++;
502	+	}
503	+	ii++;
504	+	}
505	+
506	+
507	+	if (foundNBI.size() > 0) {
508	+	// sort the foundNBI by the score:
509	+	std::sort(foundNBI.begin(), foundNBI.end());
510	+
511	+	int bestScore = foundNBI[0].first;
512	+	std::vector<std::string> theKeys = foundNBI[0].second;
513	+
514	+	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
515	+	return bestType;
516	+	} else {
517	+	//if no exact match found, try wild card match
518	+	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
519	+	}
520	+	}
521	+	}
522	+
523	+	BondType* ForceField::getExactBondType(const std::string &at1,
524	+	const std::string &at2){
525	+	std::vector<std::string> keys;
526	+	keys.push_back(at1);
527	+	keys.push_back(at2);
528		return bondTypeCont_.find(keys);
529		}
530	<
531	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
530	>
531	>	BendType* ForceField::getExactBendType(const std::string &at1,
532	>	const std::string &at2,
533		const std::string &at3){
534		std::vector<std::string> keys;
535		keys.push_back(at1);
#	Line 146 | Line 537 | namespace oopse {
537		keys.push_back(at3);
538		return bendTypeCont_.find(keys);
539		}
540	<
541	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
542	<	const std::string &at3, const std::string &at4){
540	>
541	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
542	>	const std::string &at2,
543	>	const std::string &at3,
544	>	const std::string &at4){
545		std::vector<std::string> keys;
546		keys.push_back(at1);
547		keys.push_back(at2);
#	Line 156 | Line 549 | namespace oopse {
549		keys.push_back(at4);
550		return torsionTypeCont_.find(keys);
551		}
552	+
553	+	InversionType* ForceField::getExactInversionType(const std::string &at1,
554	+	const std::string &at2,
555	+	const std::string &at3,
556	+	const std::string &at4){
557	+	std::vector<std::string> keys;
558	+	keys.push_back(at1);
559	+	keys.push_back(at2);
560	+	keys.push_back(at3);
561	+	keys.push_back(at4);
562	+	return inversionTypeCont_.find(keys);
563	+	}
564	+
565	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
566	+	std::vector<std::string> keys;
567	+	keys.push_back(at1);
568	+	keys.push_back(at2);
569	+	return nonBondedInteractionTypeCont_.find(keys);
570	+	}
571	+
572	+
573		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
574		std::vector<std::string> keys;
575		keys.push_back(at);
576	+	atypeIdentToName[atomType->getIdent()] = at;
577		return atomTypeCont_.add(keys, atomType);
578		}
579
580	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
580	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
581		std::vector<std::string> keys;
582	+	keys.push_back(at);
583	+	atypeIdentToName[atomType->getIdent()] = at;
584	+	return atomTypeCont_.replace(keys, atomType);
585	+	}
586	+
587	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
588	+	BondType* bondType) {
589	+	std::vector<std::string> keys;
590		keys.push_back(at1);
591		keys.push_back(at2);
592	<	return bondTypeCont_.add(keys, bondType);
170	<
592	>	return bondTypeCont_.add(keys, bondType);
593		}
594	<
594	>
595		bool ForceField::addBendType(const std::string &at1, const std::string &at2,
596		const std::string &at3, BendType* bendType) {
597		std::vector<std::string> keys;
#	Line 178 | Line 600 | namespace oopse {
600		keys.push_back(at3);
601		return bendTypeCont_.add(keys, bendType);
602		}
603	<
604	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
605	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
603	>
604	>	bool ForceField::addTorsionType(const std::string &at1,
605	>	const std::string &at2,
606	>	const std::string &at3,
607	>	const std::string &at4,
608	>	TorsionType* torsionType) {
609		std::vector<std::string> keys;
610		keys.push_back(at1);
611		keys.push_back(at2);
#	Line 189 | Line 614 | namespace oopse {
614		return torsionTypeCont_.add(keys, torsionType);
615		}
616
617	+	bool ForceField::addInversionType(const std::string &at1,
618	+	const std::string &at2,
619	+	const std::string &at3,
620	+	const std::string &at4,
621	+	InversionType* inversionType) {
622	+	std::vector<std::string> keys;
623	+	keys.push_back(at1);
624	+	keys.push_back(at2);
625	+	keys.push_back(at3);
626	+	keys.push_back(at4);
627	+	return inversionTypeCont_.add(keys, inversionType);
628	+	}
629	+
630	+	bool ForceField::addNonBondedInteractionType(const std::string &at1,
631	+	const std::string &at2,
632	+	NonBondedInteractionType* nbiType) {
633	+	std::vector<std::string> keys;
634	+	keys.push_back(at1);
635	+	keys.push_back(at2);
636	+	return nonBondedInteractionTypeCont_.add(keys, nbiType);
637	+	}
638	+
639		RealType ForceField::getRcutFromAtomType(AtomType* at) {
193	–	/**@todo */
194	–	GenericData* data;
640		RealType rcut = 0.0;
641	<
642	<	if (at->isLennardJones()) {
643	<	data = at->getPropertyByName("LennardJones");
644	<	if (data != NULL) {
200	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
201	<
202	<	if (ljData != NULL) {
203	<	LJParam ljParam = ljData->getData();
204	<
205	<	//by default use 2.5*sigma as cutoff radius
206	<	rcut = 2.5 * ljParam.sigma;
207	<
208	<	} else {
209	<	sprintf( painCave.errMsg,
210	<	"Can not cast GenericData to LJParam\n");
211	<	painCave.severity = OOPSE_ERROR;
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
215	<	} else {
216	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
217	<	painCave.severity = OOPSE_ERROR;
218	<	painCave.isFatal = 1;
219	<	simError();
220	<	}
641	>
642	>	LennardJonesAdapter lja = LennardJonesAdapter(at);
643	>	if (lja.isLennardJones()) {
644	>	rcut = 2.5 * lja.getSigma();
645		}
222	–
646		return rcut;
647		}
648	+
649
226	–
650		ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
651		std::string forceFieldFilename(filename);
652		ifstrstream* ffStream = new ifstrstream();
#	Line 245 | Line 668 | namespace oopse {
668		"\tHave you tried setting the FORCE_PARAM_PATH environment "
669		"variable?\n",
670		forceFieldFilename.c_str() );
671	<	painCave.severity = OOPSE_ERROR;
671	>	painCave.severity = OPENMD_ERROR;
672		painCave.isFatal = 1;
673		simError();
674		}
675		}
253	–
676		return ffStream;
255	–
677		}
678
679	<	void ForceField::setFortranForceOptions(){
259	<	ForceOptions theseFortranOptions;
260	<	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
261	<	setfForceOptions(&theseFortranOptions);
262	<	}
263	<	} //end namespace oopse
679	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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