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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file ForceField.cpp
45	<	* @author tlin
46	<	* @date 11/04/2004
47	<	* @time 22:51am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file ForceField.cpp
45	>	* @author tlin
46	>	* @date 11/04/2004
47	>	* @time 22:51am
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	<	namespace oopse {
54	>	#include "utils/Tuple.hpp"
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() {
72	<	deleteAtypes();
73	<	}
74	<
75	<	AtomType* ForceField::getAtomType(const std::string &at) {
70	>	/**
71	>	* getAtomType by string
72	>	*
73	>	* finds the requested atom type in this force field using the string
74	>	* name of the atom type.
75	>	*/
76	>	AtomType* ForceField::getAtomType(const std::string &at) {
77		std::vector<std::string> keys;
78		keys.push_back(at);
79		return atomTypeCont_.find(keys);
80	<	}
80	>	}
81
82	<	BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) {
82	>	/**
83	>	* getAtomType by ident
84	>	*
85	>	* finds the requested atom type in this force field using the
86	>	* integer ident instead of the string name of the atom type.
87	>	*/
88	>	AtomType* ForceField::getAtomType(int ident) {
89	>	std::string at = atypeIdentToName.find(ident)->second;
90	>	return getAtomType(at);
91	>	}
92	>
93	>	BondType* ForceField::getBondType(const std::string &at1,
94	>	const std::string &at2) {
95		std::vector<std::string> keys;
96		keys.push_back(at1);
97		keys.push_back(at2);
#	Line 83 | Line 99 | BondType* ForceField::getBondType(const std::string &a
99		//try exact match first
100		BondType* bondType = bondTypeCont_.find(keys);
101		if (bondType) {
102	<	return bondType;
102	>	return bondType;
103		} else {
104	<	//if no exact match found, try wild card match
105	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
106	<	}
104	>	AtomType* atype1;
105	>	AtomType* atype2;
106	>	std::vector<std::string> at1key;
107	>	at1key.push_back(at1);
108	>	atype1 = atomTypeCont_.find(at1key);
109	>
110	>	std::vector<std::string> at2key;
111	>	at2key.push_back(at2);
112	>	atype2 = atomTypeCont_.find(at2key);
113
114	<	}
114	>	// query atom types for their chains of responsibility
115	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
116	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
117
118	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
119	<	const std::string &at3) {
118	>	std::vector<AtomType*>::iterator i;
119	>	std::vector<AtomType*>::iterator j;
120	>
121	>	int ii = 0;
122	>	int jj = 0;
123	>	int bondTypeScore;
124	>
125	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
126	>
127	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
128	>	jj = 0;
129	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
130	>
131	>	bondTypeScore = ii + jj;
132	>
133	>	std::vector<std::string> myKeys;
134	>	myKeys.push_back((*i)->getName());
135	>	myKeys.push_back((*j)->getName());
136	>
137	>	BondType* bondType = bondTypeCont_.find(myKeys);
138	>	if (bondType) {
139	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
140	>	}
141	>	jj++;
142	>	}
143	>	ii++;
144	>	}
145	>
146	>
147	>	if (foundBonds.size() > 0) {
148	>	// sort the foundBonds by the score:
149	>	std::sort(foundBonds.begin(), foundBonds.end());
150	>
151	>	int bestScore = foundBonds[0].first;
152	>	std::vector<std::string> theKeys = foundBonds[0].second;
153	>
154	>	BondType* bestType = bondTypeCont_.find(theKeys);
155	>
156	>	return bestType;
157	>	} else {
158	>	//if no exact match found, try wild card match
159	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
160	>	}
161	>	}
162	>	}
163	>
164	>	BendType* ForceField::getBendType(const std::string &at1,
165	>	const std::string &at2,
166	>	const std::string &at3) {
167		std::vector<std::string> keys;
168		keys.push_back(at1);
169		keys.push_back(at2);
#	Line 101 | Line 172 | BendType* ForceField::getBendType(const std::string &a
172		//try exact match first
173		BendType* bendType = bendTypeCont_.find(keys);
174		if (bendType) {
175	<	return bendType;
175	>	return bendType;
176		} else {
106	–	//if no exact match found, try wild card match
107	–	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
108	–	}
109	–	}
177
178	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
179	<	const std::string &at3, const std::string &at4) {
178	>	AtomType* atype1;
179	>	AtomType* atype2;
180	>	AtomType* atype3;
181	>	std::vector<std::string> at1key;
182	>	at1key.push_back(at1);
183	>	atype1 = atomTypeCont_.find(at1key);
184	>
185	>	std::vector<std::string> at2key;
186	>	at2key.push_back(at2);
187	>	atype2 = atomTypeCont_.find(at2key);
188	>
189	>	std::vector<std::string> at3key;
190	>	at3key.push_back(at3);
191	>	atype3 = atomTypeCont_.find(at3key);
192	>
193	>	// query atom types for their chains of responsibility
194	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
195	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
196	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
197	>
198	>	std::vector<AtomType*>::iterator i;
199	>	std::vector<AtomType*>::iterator j;
200	>	std::vector<AtomType*>::iterator k;
201	>
202	>	int ii = 0;
203	>	int jj = 0;
204	>	int kk = 0;
205	>	int IKscore;
206	>
207	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
208	>
209	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
210	>	ii = 0;
211	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
212	>	kk = 0;
213	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
214	>
215	>	IKscore = ii + kk;
216	>
217	>	std::vector<std::string> myKeys;
218	>	myKeys.push_back((*i)->getName());
219	>	myKeys.push_back((*j)->getName());
220	>	myKeys.push_back((*k)->getName());
221	>
222	>	BendType* bendType = bendTypeCont_.find(myKeys);
223	>	if (bendType) {
224	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
225	>	}
226	>	kk++;
227	>	}
228	>	ii++;
229	>	}
230	>	jj++;
231	>	}
232	>
233	>	if (foundBends.size() > 0) {
234	>	std::sort(foundBends.begin(), foundBends.end());
235	>	int jscore = foundBends[0].first;
236	>	int ikscore = foundBends[0].second;
237	>	std::vector<std::string> theKeys = foundBends[0].third;
238	>
239	>	BendType* bestType = bendTypeCont_.find(theKeys);
240	>	return bestType;
241	>	} else {
242	>	//if no exact match found, try wild card match
243	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
244	>	}
245	>	}
246	>	}
247	>
248	>	TorsionType* ForceField::getTorsionType(const std::string &at1,
249	>	const std::string &at2,
250	>	const std::string &at3,
251	>	const std::string &at4) {
252		std::vector<std::string> keys;
253		keys.push_back(at1);
254		keys.push_back(at2);
255		keys.push_back(at3);
256		keys.push_back(at4);
257
258	+
259	+	//try exact match first
260		TorsionType* torsionType = torsionTypeCont_.find(keys);
261		if (torsionType) {
262	<	return torsionType;
262	>	return torsionType;
263		} 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_);
264
265	<	}
265	>	AtomType* atype1;
266	>	AtomType* atype2;
267	>	AtomType* atype3;
268	>	AtomType* atype4;
269	>	std::vector<std::string> at1key;
270	>	at1key.push_back(at1);
271	>	atype1 = atomTypeCont_.find(at1key);
272	>
273	>	std::vector<std::string> at2key;
274	>	at2key.push_back(at2);
275	>	atype2 = atomTypeCont_.find(at2key);
276
277	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
277	>	std::vector<std::string> at3key;
278	>	at3key.push_back(at3);
279	>	atype3 = atomTypeCont_.find(at3key);
280	>
281	>	std::vector<std::string> at4key;
282	>	at4key.push_back(at4);
283	>	atype4 = atomTypeCont_.find(at4key);
284	>
285	>	// query atom types for their chains of responsibility
286	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
287	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
288	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
289	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
290	>
291	>	std::vector<AtomType*>::iterator i;
292	>	std::vector<AtomType*>::iterator j;
293	>	std::vector<AtomType*>::iterator k;
294	>	std::vector<AtomType*>::iterator l;
295	>
296	>	int ii = 0;
297	>	int jj = 0;
298	>	int kk = 0;
299	>	int ll = 0;
300	>	int ILscore;
301	>	int JKscore;
302	>
303	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
304	>
305	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
306	>	kk = 0;
307	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
308	>	ii = 0;
309	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
310	>	ll = 0;
311	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
312	>
313	>	ILscore = ii + ll;
314	>	JKscore = jj + kk;
315	>
316	>	std::vector<std::string> myKeys;
317	>	myKeys.push_back((*i)->getName());
318	>	myKeys.push_back((*j)->getName());
319	>	myKeys.push_back((*k)->getName());
320	>	myKeys.push_back((*l)->getName());
321	>
322	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
323	>	if (torsionType) {
324	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
325	>	}
326	>	ll++;
327	>	}
328	>	ii++;
329	>	}
330	>	kk++;
331	>	}
332	>	jj++;
333	>	}
334	>
335	>	if (foundTorsions.size() > 0) {
336	>	std::sort(foundTorsions.begin(), foundTorsions.end());
337	>	int jkscore = foundTorsions[0].first;
338	>	int ilscore = foundTorsions[0].second;
339	>	std::vector<std::string> theKeys = foundTorsions[0].third;
340	>
341	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
342	>	return bestType;
343	>	} else {
344	>	//if no exact match found, try wild card match
345	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
346	>	}
347	>	}
348	>	}
349	>
350	>	InversionType* ForceField::getInversionType(const std::string &at1,
351	>	const std::string &at2,
352	>	const std::string &at3,
353	>	const std::string &at4) {
354		std::vector<std::string> keys;
355		keys.push_back(at1);
356		keys.push_back(at2);
357	<	return bondTypeCont_.find(keys);
358	<	}
357	>	keys.push_back(at3);
358	>	keys.push_back(at4);
359
360	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
361	<	const std::string &at3){
360	>	//try exact match first
361	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
362	>	if (inversionType) {
363	>	return inversionType;
364	>	} else {
365	>
366	>	AtomType* atype1;
367	>	AtomType* atype2;
368	>	AtomType* atype3;
369	>	AtomType* atype4;
370	>	std::vector<std::string> at1key;
371	>	at1key.push_back(at1);
372	>	atype1 = atomTypeCont_.find(at1key);
373	>
374	>	std::vector<std::string> at2key;
375	>	at2key.push_back(at2);
376	>	atype2 = atomTypeCont_.find(at2key);
377	>
378	>	std::vector<std::string> at3key;
379	>	at3key.push_back(at3);
380	>	atype3 = atomTypeCont_.find(at3key);
381	>
382	>	std::vector<std::string> at4key;
383	>	at4key.push_back(at4);
384	>	atype4 = atomTypeCont_.find(at4key);
385	>
386	>	// query atom types for their chains of responsibility
387	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
388	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
389	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
390	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
391	>
392	>	std::vector<AtomType*>::iterator i;
393	>	std::vector<AtomType*>::iterator j;
394	>	std::vector<AtomType*>::iterator k;
395	>	std::vector<AtomType*>::iterator l;
396	>
397	>	int ii = 0;
398	>	int jj = 0;
399	>	int kk = 0;
400	>	int ll = 0;
401	>	int Iscore;
402	>	int JKLscore;
403	>
404	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
405	>
406	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
407	>	kk = 0;
408	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
409	>	ii = 0;
410	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
411	>	ll = 0;
412	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
413	>
414	>	Iscore = ii;
415	>	JKLscore = jj + kk + ll;
416	>
417	>	std::vector<std::string> myKeys;
418	>	myKeys.push_back((*i)->getName());
419	>	myKeys.push_back((*j)->getName());
420	>	myKeys.push_back((*k)->getName());
421	>	myKeys.push_back((*l)->getName());
422	>
423	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
424	>	if (inversionType) {
425	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
426	>	}
427	>	ll++;
428	>	}
429	>	ii++;
430	>	}
431	>	kk++;
432	>	}
433	>	jj++;
434	>	}
435	>
436	>	if (foundInversions.size() > 0) {
437	>	std::sort(foundInversions.begin(), foundInversions.end());
438	>	int iscore = foundInversions[0].first;
439	>	int jklscore = foundInversions[0].second;
440	>	std::vector<std::string> theKeys = foundInversions[0].third;
441	>
442	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
443	>	return bestType;
444	>	} else {
445	>	//if no exact match found, try wild card match
446	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
447	>	}
448	>	}
449	>	}
450	>
451	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
452	>
453		std::vector<std::string> keys;
454		keys.push_back(at1);
455		keys.push_back(at2);
456	+
457	+	//try exact match first
458	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
459	+	if (nbiType) {
460	+	return nbiType;
461	+	} else {
462	+	AtomType* atype1;
463	+	AtomType* atype2;
464	+	std::vector<std::string> at1key;
465	+	at1key.push_back(at1);
466	+	atype1 = atomTypeCont_.find(at1key);
467	+
468	+	std::vector<std::string> at2key;
469	+	at2key.push_back(at2);
470	+	atype2 = atomTypeCont_.find(at2key);
471	+
472	+	// query atom types for their chains of responsibility
473	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
474	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
475	+
476	+	std::vector<AtomType*>::iterator i;
477	+	std::vector<AtomType*>::iterator j;
478	+
479	+	int ii = 0;
480	+	int jj = 0;
481	+	int nbiTypeScore;
482	+
483	+	std::vector<std::pair<int, std::vector<std::string> > > foundNBI;
484	+
485	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
486	+	jj = 0;
487	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
488	+
489	+	nbiTypeScore = ii + jj;
490	+
491	+	std::vector<std::string> myKeys;
492	+	myKeys.push_back((*i)->getName());
493	+	myKeys.push_back((*j)->getName());
494	+
495	+	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys);
496	+	if (nbiType) {
497	+	foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys));
498	+	}
499	+	jj++;
500	+	}
501	+	ii++;
502	+	}
503	+
504	+
505	+	if (foundNBI.size() > 0) {
506	+	// sort the foundNBI by the score:
507	+	std::sort(foundNBI.begin(), foundNBI.end());
508	+
509	+	int bestScore = foundNBI[0].first;
510	+	std::vector<std::string> theKeys = foundNBI[0].second;
511	+
512	+	NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys);
513	+	return bestType;
514	+	} else {
515	+	//if no exact match found, try wild card match
516	+	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
517	+	}
518	+	}
519	+	}
520	+
521	+	BondType* ForceField::getExactBondType(const std::string &at1,
522	+	const std::string &at2){
523	+	std::vector<std::string> keys;
524	+	keys.push_back(at1);
525	+	keys.push_back(at2);
526	+	return bondTypeCont_.find(keys);
527	+	}
528	+
529	+	BendType* ForceField::getExactBendType(const std::string &at1,
530	+	const std::string &at2,
531	+	const std::string &at3){
532	+	std::vector<std::string> keys;
533	+	keys.push_back(at1);
534	+	keys.push_back(at2);
535		keys.push_back(at3);
536		return bendTypeCont_.find(keys);
537	<	}
538	<
539	<	TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2,
540	<	const std::string &at3, const std::string &at4){
537	>	}
538	>
539	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
540	>	const std::string &at2,
541	>	const std::string &at3,
542	>	const std::string &at4){
543		std::vector<std::string> keys;
544		keys.push_back(at1);
545		keys.push_back(at2);
546		keys.push_back(at3);
547		keys.push_back(at4);
548		return torsionTypeCont_.find(keys);
549	<	}
550	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
549	>	}
550	>
551	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
552	>	const std::string &at2,
553	>	const std::string &at3,
554	>	const std::string &at4){
555		std::vector<std::string> keys;
556	+	keys.push_back(at1);
557	+	keys.push_back(at2);
558	+	keys.push_back(at3);
559	+	keys.push_back(at4);
560	+	return inversionTypeCont_.find(keys);
561	+	}
562	+
563	+	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
564	+	std::vector<std::string> keys;
565	+	keys.push_back(at1);
566	+	keys.push_back(at2);
567	+	return nonBondedInteractionTypeCont_.find(keys);
568	+	}
569	+
570	+
571	+	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
572	+	std::vector<std::string> keys;
573		keys.push_back(at);
574	+	atypeIdentToName[atomType->getIdent()] = at;
575		return atomTypeCont_.add(keys, atomType);
576	<	}
576	>	}
577
578	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
578	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
579		std::vector<std::string> keys;
580	+	keys.push_back(at);
581	+	atypeIdentToName[atomType->getIdent()] = at;
582	+	return atomTypeCont_.replace(keys, atomType);
583	+	}
584	+
585	+	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
586	+	BondType* bondType) {
587	+	std::vector<std::string> keys;
588		keys.push_back(at1);
589		keys.push_back(at2);
590	<	return bondTypeCont_.add(keys, bondType);
591	<
592	<	}
593	<
594	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
590	>	return bondTypeCont_.add(keys, bondType);
591	>	}
592	>
593	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
594	>	const std::string &at3, BendType* bendType) {
595		std::vector<std::string> keys;
596		keys.push_back(at1);
597		keys.push_back(at2);
598		keys.push_back(at3);
599		return bendTypeCont_.add(keys, bendType);
600	<	}
601	<
602	<	bool ForceField::addTorsionType(const std::string &at1, const std::string &at2,
603	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
600	>	}
601	>
602	>	bool ForceField::addTorsionType(const std::string &at1,
603	>	const std::string &at2,
604	>	const std::string &at3,
605	>	const std::string &at4,
606	>	TorsionType* torsionType) {
607		std::vector<std::string> keys;
608		keys.push_back(at1);
609		keys.push_back(at2);
610		keys.push_back(at3);
611		keys.push_back(at4);
612		return torsionTypeCont_.add(keys, torsionType);
613	<	}
613	>	}
614
615	<	double ForceField::getRcutFromAtomType(AtomType* at) {
615	>	bool ForceField::addInversionType(const std::string &at1,
616	>	const std::string &at2,
617	>	const std::string &at3,
618	>	const std::string &at4,
619	>	InversionType* inversionType) {
620	>	std::vector<std::string> keys;
621	>	keys.push_back(at1);
622	>	keys.push_back(at2);
623	>	keys.push_back(at3);
624	>	keys.push_back(at4);
625	>	return inversionTypeCont_.add(keys, inversionType);
626	>	}
627	>
628	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
629	>	const std::string &at2,
630	>	NonBondedInteractionType* nbiType) {
631	>	std::vector<std::string> keys;
632	>	keys.push_back(at1);
633	>	keys.push_back(at2);
634	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
635	>	}
636	>
637	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
638		/**@todo */
639		GenericData* data;
640	<	double rcut = 0.0;
641	<
640	>	RealType rcut = 0.0;
641	>
642		if (at->isLennardJones()) {
643	<	data = at->getPropertyByName("LennardJones");
644	<	if (data != NULL) {
645	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
646	<
647	<	if (ljData != NULL) {
648	<	LJParam ljParam = ljData->getData();
649	<
650	<	//by default use 2.5*sigma as cutoff radius
651	<	rcut = 2.5 * ljParam.sigma;
652	<
653	<	} else {
654	<	sprintf( painCave.errMsg,
655	<	"Can not cast GenericData to LJParam\n");
656	<	painCave.severity = OOPSE_ERROR;
657	<	painCave.isFatal = 1;
658	<	simError();
659	<	}
660	<	} else {
661	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662	<	painCave.severity = OOPSE_ERROR;
663	<	painCave.isFatal = 1;
664	<	simError();
665	<	}
643	>	data = at->getPropertyByName("LennardJones");
644	>	if (data != NULL) {
645	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
646	>
647	>	if (ljData != NULL) {
648	>	LJParam ljParam = ljData->getData();
649	>
650	>	//by default use 2.5*sigma as cutoff radius
651	>	rcut = 2.5 * ljParam.sigma;
652	>
653	>	} else {
654	>	sprintf( painCave.errMsg,
655	>	"Can not cast GenericData to LJParam\n");
656	>	painCave.severity = OPENMD_ERROR;
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660	>	} else {
661	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
662	>	painCave.severity = OPENMD_ERROR;
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666		}
219	–
667		return rcut;
668	<	}
668	>	}
669	>
670
671	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
671	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
672		std::string forceFieldFilename(filename);
673		ifstrstream* ffStream = new ifstrstream();
674
#	Line 229 | Line 676 | ifstrstream* ForceField::openForceFieldFile(const std:
676		ffStream->open(forceFieldFilename.c_str());
677		if(!ffStream->is_open()){
678
679	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
680	<	ffStream->open( forceFieldFilename.c_str() );
679	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
680	>	ffStream->open( forceFieldFilename.c_str() );
681
682	<	//if current directory does not contain the force field file,
683	<	//try to open it in the path
684	<	if(!ffStream->is_open()){
682	>	//if current directory does not contain the force field file,
683	>	//try to open it in the path
684	>	if(!ffStream->is_open()){
685
686	<	sprintf( painCave.errMsg,
687	<	"Error opening the force field parameter file:\n"
688	<	"\t%s\n"
689	<	"\tHave you tried setting the FORCE_PARAM_PATH environment "
690	<	"variable?\n",
691	<	forceFieldFilename.c_str() );
692	<	painCave.severity = OOPSE_ERROR;
693	<	painCave.isFatal = 1;
694	<	simError();
695	<	}
686	>	sprintf( painCave.errMsg,
687	>	"Error opening the force field parameter file:\n"
688	>	"\t%s\n"
689	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
690	>	"variable?\n",
691	>	forceFieldFilename.c_str() );
692	>	painCave.severity = OPENMD_ERROR;
693	>	painCave.isFatal = 1;
694	>	simError();
695	>	}
696		}
250	–
697		return ffStream;
698	+	}
699
700	<	}
254	<
255	<	} //end namespace oopse
700	>	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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