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

Comparing trunk/src/UseTheForce/ForceField.cpp (file contents):
Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 1 | Line 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
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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	+	*/
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	+	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56	+	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	+	namespace OpenMD {
58
59	<	AtomType* ForceField::getMatchingAtomType(const string &at) {
59	>	ForceField::ForceField() {
60	>	char* tempPath;
61	>	tempPath = getenv("FORCE_PARAM_PATH");
62
63	<	map<string, AtomType*>::iterator iter;
64	<
65	<	iter = atomTypeMap.find(at);
66	<	if (iter != atomTypeMap.end()) {
67	<	return iter->second;
10	<	} else {
11	<	return NULL;
63	>	if (tempPath == NULL) {
64	>	ffPath_ = "ORNULL(FRC_PATH)";
65	>	} else {
66	>	ffPath_ = tempPath;
67	>	}
68		}
13	–	}
69
15	–	BondType* ForceField::getMatchingBondType(const string &at1,
16	–	const string &at2) {
70
71	<	map<pair<string,string>, BondType*>::iterator iter;
72	<	vector<BondType*> foundTypes;
71	>	ForceField::~ForceField() {
72	>	deleteAtypes();
73	>	deleteSwitch();
74	>	}
75
76	<	iter = bondTypeMap.find(pair<at1, at2>);
77	<	if (iter != bondTypeMap.end()) {
78	<	// exact match, so just return it
79	<	return iter->second;
80	<	}
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	>	}
81
82	<	iter = bondTypeMap.find(pair<at2, at1>);
83	<	if (iter != bondTypeMap.end()) {
84	<	// exact match in reverse order, so just return it
85	<	return iter->second;
86	<	}
82	>	BondType* ForceField::getBondType(const std::string &at1,
83	>	const std::string &at2) {
84	>	std::vector<std::string> keys;
85	>	keys.push_back(at1);
86	>	keys.push_back(at2);
87
88	<	iter = bondTypeMap.find(pair<at1, wildCardAtomTypeName>);
89	<	if (iter != bondTypeMap.end()) {
90	<	foundTypes.push_back(iter->second);
91	<	}
88	>	//try exact match first
89	>	BondType* bondType = bondTypeCont_.find(keys);
90	>	if (bondType) {
91	>	return bondType;
92	>	} else {
93	>	AtomType* atype1;
94	>	AtomType* atype2;
95	>	std::vector<std::string> at1key;
96	>	at1key.push_back(at1);
97	>	atype1 = atomTypeCont_.find(at1key);
98	>
99	>	std::vector<std::string> at2key;
100	>	at2key.push_back(at2);
101	>	atype2 = atomTypeCont_.find(at2key);
102
103	<	iter = bondTypeMap.find(pair<at2, wildCardAtomTypeName>);
104	<	if (iter != bondTypeMap.end()) {
105	<	foundTypes.push_back(iter->second);
41	<	}
103	>	// query atom types for their chains of responsibility
104	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
105	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
106
107	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at1>);
108	<	if (iter != bondTypeMap.end()) {
45	<	foundTypes.push_back(iter->second);
46	<	}
107	>	std::vector<AtomType*>::iterator i;
108	>	std::vector<AtomType*>::iterator j;
109
110	<	iter = bondTypeMap.find(pair<wildCardAtomTypeName, at2>);
111	<	if (iter != bondTypeMap.end()) {
112	<	foundTypes.push_back(iter->second);
110	>	int ii = 0;
111	>	int jj = 0;
112	>	int bondTypeScore;
113	>
114	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
115	>
116	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
117	>	jj = 0;
118	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
119	>
120	>	bondTypeScore = ii + jj;
121	>
122	>	std::vector<std::string> myKeys;
123	>	myKeys.push_back((*i)->getName());
124	>	myKeys.push_back((*j)->getName());
125	>
126	>	BondType* bondType = bondTypeCont_.find(myKeys);
127	>	if (bondType) {
128	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
129	>	}
130	>	jj++;
131	>	}
132	>	ii++;
133	>	}
134	>
135	>
136	>	if (foundBonds.size() > 0) {
137	>	// sort the foundBonds by the score:
138	>	std::sort(foundBonds.begin(), foundBonds.end());
139	>
140	>	int bestScore = foundBonds[0].first;
141	>	std::vector<std::string> theKeys = foundBonds[0].second;
142	>
143	>	BondType* bestType = bondTypeCont_.find(theKeys);
144	>
145	>	return bestType;
146	>	} else {
147	>	//if no exact match found, try wild card match
148	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
149	>	}
150	>	}
151		}
152
153	<	if (foundTypes.empty()) {
154	<	return NULL;
155	<	} else {
156	<
153	>	BendType* ForceField::getBendType(const std::string &at1,
154	>	const std::string &at2,
155	>	const std::string &at3) {
156	>	std::vector<std::string> keys;
157	>	keys.push_back(at1);
158	>	keys.push_back(at2);
159	>	keys.push_back(at3);
160
161	<
161	>	//try exact match first
162	>	BendType* bendType = bendTypeCont_.find(keys);
163	>	if (bendType) {
164	>	return bendType;
165	>	} else {
166
167	+	AtomType* atype1;
168	+	AtomType* atype2;
169	+	AtomType* atype3;
170	+	std::vector<std::string> at1key;
171	+	at1key.push_back(at1);
172	+	atype1 = atomTypeCont_.find(at1key);
173	+
174	+	std::vector<std::string> at2key;
175	+	at2key.push_back(at2);
176	+	atype2 = atomTypeCont_.find(at2key);
177
178	+	std::vector<std::string> at3key;
179	+	at3key.push_back(at3);
180	+	atype3 = atomTypeCont_.find(at3key);
181
182	<
182	>	// query atom types for their chains of responsibility
183	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
184	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
185	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
186
187	+	std::vector<AtomType*>::iterator i;
188	+	std::vector<AtomType*>::iterator j;
189	+	std::vector<AtomType*>::iterator k;
190
191	<	BendType* ForceField::getMatchingBendType(const string &at1, const string &at2,
192	<	const string &at3);
193	<	TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2,
194	<	const string &at3, const string &at4);
191	>	int ii = 0;
192	>	int jj = 0;
193	>	int kk = 0;
194	>	int IKscore;
195
196	<	double ForceField::getRcutForAtomType(AtomType* at);
196	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
197
198	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
199	+	ii = 0;
200	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
201	+	kk = 0;
202	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
203	+
204	+	IKscore = ii + kk;
205
206	<	vector<vector<string> > generateWildcardSequence(const vector<string> atomTypes) {
207	<
208	<	vector<vector<string> > results;
206	>	std::vector<std::string> myKeys;
207	>	myKeys.push_back((*i)->getName());
208	>	myKeys.push_back((*j)->getName());
209	>	myKeys.push_back((*k)->getName());
210
211	<
211	>	BendType* bendType = bendTypeCont_.find(myKeys);
212	>	if (bendType) {
213	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
214	>	}
215	>	kk++;
216	>	}
217	>	ii++;
218	>	}
219	>	jj++;
220	>	}
221	>
222	>	if (foundBends.size() > 0) {
223	>	std::sort(foundBends.begin(), foundBends.end());
224	>	int jscore = foundBends[0].first;
225	>	int ikscore = foundBends[0].second;
226	>	std::vector<std::string> theKeys = foundBends[0].third;
227	>
228	>	BendType* bestType = bendTypeCont_.find(theKeys);
229	>	return bestType;
230	>	} else {
231	>	//if no exact match found, try wild card match
232	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
233	>	}
234	>	}
235	>	}
236
237	+	TorsionType* ForceField::getTorsionType(const std::string &at1,
238	+	const std::string &at2,
239	+	const std::string &at3,
240	+	const std::string &at4) {
241	+	std::vector<std::string> keys;
242	+	keys.push_back(at1);
243	+	keys.push_back(at2);
244	+	keys.push_back(at3);
245	+	keys.push_back(at4);
246
80	–	vector<vector< string> > getAllWildcardPermutations(const vector<string> myAts) {
81	–
82	–	int nStrings;
83	–	vector<string> oneResult;
84	–	vector<vector<string> > allResults;
247
248	<	nStrings = myAts.size();
248	>	//try exact match first
249	>	TorsionType* torsionType = torsionTypeCont_.find(keys);
250	>	if (torsionType) {
251	>	return torsionType;
252	>	} else {
253
254	<	if (nStrings == 1) {
255	<	oneResult.push_back(wildcardCharacter);
256	<	allResults.push_back(oneResult);
257	<	return allResults;
258	<	} else {
259	<
260	<	for (i=0; i < nStrings; i++) {
261	<	oneResult = myAts;
262	<	replace(oneResult.begin(), oneResult.end(),
254	>	AtomType* atype1;
255	>	AtomType* atype2;
256	>	AtomType* atype3;
257	>	AtomType* atype4;
258	>	std::vector<std::string> at1key;
259	>	at1key.push_back(at1);
260	>	atype1 = atomTypeCont_.find(at1key);
261	>
262	>	std::vector<std::string> at2key;
263	>	at2key.push_back(at2);
264	>	atype2 = atomTypeCont_.find(at2key);
265	>
266	>	std::vector<std::string> at3key;
267	>	at3key.push_back(at3);
268	>	atype3 = atomTypeCont_.find(at3key);
269	>
270	>	std::vector<std::string> at4key;
271	>	at4key.push_back(at4);
272	>	atype4 = atomTypeCont_.find(at4key);
273	>
274	>	// query atom types for their chains of responsibility
275	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
276	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
277	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
278	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
279	>
280	>	std::vector<AtomType*>::iterator i;
281	>	std::vector<AtomType*>::iterator j;
282	>	std::vector<AtomType*>::iterator k;
283	>	std::vector<AtomType*>::iterator l;
284	>
285	>	int ii = 0;
286	>	int jj = 0;
287	>	int kk = 0;
288	>	int ll = 0;
289	>	int ILscore;
290	>	int JKscore;
291	>
292	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
293	>
294	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
295	>	kk = 0;
296	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
297	>	ii = 0;
298	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
299	>	ll = 0;
300	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
301	>
302	>	ILscore = ii + ll;
303	>	JKscore = jj + kk;
304	>
305	>	std::vector<std::string> myKeys;
306	>	myKeys.push_back((*i)->getName());
307	>	myKeys.push_back((*j)->getName());
308	>	myKeys.push_back((*k)->getName());
309	>	myKeys.push_back((*l)->getName());
310	>
311	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
312	>	if (torsionType) {
313	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
314	>	}
315	>	ll++;
316	>	}
317	>	ii++;
318	>	}
319	>	kk++;
320	>	}
321	>	jj++;
322	>	}
323	>
324	>	if (foundTorsions.size() > 0) {
325	>	std::sort(foundTorsions.begin(), foundTorsions.end());
326	>	int jkscore = foundTorsions[0].first;
327	>	int ilscore = foundTorsions[0].second;
328	>	std::vector<std::string> theKeys = foundTorsions[0].third;
329	>
330	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
331	>	return bestType;
332	>	} else {
333	>	//if no exact match found, try wild card match
334	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
335	>	}
336	>	}
337	>	}
338	>
339	>	InversionType* ForceField::getInversionType(const std::string &at1,
340	>	const std::string &at2,
341	>	const std::string &at3,
342	>	const std::string &at4) {
343	>	std::vector<std::string> keys;
344	>	keys.push_back(at1);
345	>	keys.push_back(at2);
346	>	keys.push_back(at3);
347	>	keys.push_back(at4);
348	>
349	>	//try exact match first
350	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
351	>	if (inversionType) {
352	>	return inversionType;
353	>	} else {
354	>
355	>	AtomType* atype1;
356	>	AtomType* atype2;
357	>	AtomType* atype3;
358	>	AtomType* atype4;
359	>	std::vector<std::string> at1key;
360	>	at1key.push_back(at1);
361	>	atype1 = atomTypeCont_.find(at1key);
362	>
363	>	std::vector<std::string> at2key;
364	>	at2key.push_back(at2);
365	>	atype2 = atomTypeCont_.find(at2key);
366	>
367	>	std::vector<std::string> at3key;
368	>	at3key.push_back(at3);
369	>	atype3 = atomTypeCont_.find(at3key);
370	>
371	>	std::vector<std::string> at4key;
372	>	at4key.push_back(at4);
373	>	atype4 = atomTypeCont_.find(at4key);
374	>
375	>	// query atom types for their chains of responsibility
376	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
377	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
378	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
379	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
380	>
381	>	std::vector<AtomType*>::iterator i;
382	>	std::vector<AtomType*>::iterator j;
383	>	std::vector<AtomType*>::iterator k;
384	>	std::vector<AtomType*>::iterator l;
385	>
386	>	int ii = 0;
387	>	int jj = 0;
388	>	int kk = 0;
389	>	int ll = 0;
390	>	int Iscore;
391	>	int JKLscore;
392	>
393	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
394	>
395	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
396	>	kk = 0;
397	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
398	>	ii = 0;
399	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
400	>	ll = 0;
401	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
402	>
403	>	Iscore = ii;
404	>	JKLscore = jj + kk + ll;
405	>
406	>	std::vector<std::string> myKeys;
407	>	myKeys.push_back((*i)->getName());
408	>	myKeys.push_back((*j)->getName());
409	>	myKeys.push_back((*k)->getName());
410	>	myKeys.push_back((*l)->getName());
411	>
412	>	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
413	>	if (inversionType) {
414	>	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
415	>	}
416	>	ll++;
417	>	}
418	>	ii++;
419	>	}
420	>	kk++;
421	>	}
422	>	jj++;
423	>	}
424	>
425	>	if (foundInversions.size() > 0) {
426	>	std::sort(foundInversions.begin(), foundInversions.end());
427	>	int iscore = foundInversions[0].first;
428	>	int jklscore = foundInversions[0].second;
429	>	std::vector<std::string> theKeys = foundInversions[0].third;
430	>
431	>	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
432	>	return bestType;
433	>	} else {
434	>	//if no exact match found, try wild card match
435	>	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
436	>	}
437	>	}
438	>	}
439	>
440	>	NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
441	>	std::vector<std::string> keys;
442	>	keys.push_back(at1);
443	>	keys.push_back(at2);
444	>
445	>	//try exact match first
446	>	NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys);
447	>	if (nbiType) {
448	>	return nbiType;
449	>	} else {
450	>	//if no exact match found, try wild card match
451	>	return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_);
452	>	}
453	>	}
454	>
455	>	BondType* ForceField::getExactBondType(const std::string &at1,
456	>	const std::string &at2){
457	>	std::vector<std::string> keys;
458	>	keys.push_back(at1);
459	>	keys.push_back(at2);
460	>	return bondTypeCont_.find(keys);
461	>	}
462	>
463	>	BendType* ForceField::getExactBendType(const std::string &at1,
464	>	const std::string &at2,
465	>	const std::string &at3){
466	>	std::vector<std::string> keys;
467	>	keys.push_back(at1);
468	>	keys.push_back(at2);
469	>	keys.push_back(at3);
470	>	return bendTypeCont_.find(keys);
471	>	}
472	>
473	>	TorsionType* ForceField::getExactTorsionType(const std::string &at1,
474	>	const std::string &at2,
475	>	const std::string &at3,
476	>	const std::string &at4){
477	>	std::vector<std::string> keys;
478	>	keys.push_back(at1);
479	>	keys.push_back(at2);
480	>	keys.push_back(at3);
481	>	keys.push_back(at4);
482	>	return torsionTypeCont_.find(keys);
483	>	}
484	>
485	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
486	>	const std::string &at2,
487	>	const std::string &at3,
488	>	const std::string &at4){
489	>	std::vector<std::string> keys;
490	>	keys.push_back(at1);
491	>	keys.push_back(at2);
492	>	keys.push_back(at3);
493	>	keys.push_back(at4);
494	>	return inversionTypeCont_.find(keys);
495	>	}
496	>
497	>	NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
498	>	std::vector<std::string> keys;
499	>	keys.push_back(at1);
500	>	keys.push_back(at2);
501	>	return nonBondedInteractionTypeCont_.find(keys);
502	>	}
503	>
504	>
505	>	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
506	>	std::vector<std::string> keys;
507	>	keys.push_back(at);
508	>	return atomTypeCont_.add(keys, atomType);
509	>	}
510	>
511	>	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
512	>	std::vector<std::string> keys;
513	>	keys.push_back(at);
514	>	return atomTypeCont_.replace(keys, atomType);
515	>	}
516	>
517	>	bool ForceField::addBondType(const std::string &at1, const std::string &at2,
518	>	BondType* bondType) {
519	>	std::vector<std::string> keys;
520	>	keys.push_back(at1);
521	>	keys.push_back(at2);
522	>	return bondTypeCont_.add(keys, bondType);
523	>	}
524	>
525	>	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
526	>	const std::string &at3, BendType* bendType) {
527	>	std::vector<std::string> keys;
528	>	keys.push_back(at1);
529	>	keys.push_back(at2);
530	>	keys.push_back(at3);
531	>	return bendTypeCont_.add(keys, bendType);
532	>	}
533	>
534	>	bool ForceField::addTorsionType(const std::string &at1,
535	>	const std::string &at2,
536	>	const std::string &at3,
537	>	const std::string &at4,
538	>	TorsionType* torsionType) {
539	>	std::vector<std::string> keys;
540	>	keys.push_back(at1);
541	>	keys.push_back(at2);
542	>	keys.push_back(at3);
543	>	keys.push_back(at4);
544	>	return torsionTypeCont_.add(keys, torsionType);
545	>	}
546	>
547	>	bool ForceField::addInversionType(const std::string &at1,
548	>	const std::string &at2,
549	>	const std::string &at3,
550	>	const std::string &at4,
551	>	InversionType* inversionType) {
552	>	std::vector<std::string> keys;
553	>	keys.push_back(at1);
554	>	keys.push_back(at2);
555	>	keys.push_back(at3);
556	>	keys.push_back(at4);
557	>	return inversionTypeCont_.add(keys, inversionType);
558	>	}
559	>
560	>	bool ForceField::addNonBondedInteractionType(const std::string &at1,
561	>	const std::string &at2,
562	>	NonBondedInteractionType* nbiType) {
563	>	std::vector<std::string> keys;
564	>	keys.push_back(at1);
565	>	keys.push_back(at2);
566	>	return nonBondedInteractionTypeCont_.add(keys, nbiType);
567	>	}
568	>
569	>	RealType ForceField::getRcutFromAtomType(AtomType* at) {
570	>	/**@todo */
571	>	GenericData* data;
572	>	RealType rcut = 0.0;
573	>
574	>	if (at->isLennardJones()) {
575	>	data = at->getPropertyByName("LennardJones");
576	>	if (data != NULL) {
577	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
578	>
579	>	if (ljData != NULL) {
580	>	LJParam ljParam = ljData->getData();
581	>
582	>	//by default use 2.5*sigma as cutoff radius
583	>	rcut = 2.5 * ljParam.sigma;
584	>
585	>	} else {
586	>	sprintf( painCave.errMsg,
587	>	"Can not cast GenericData to LJParam\n");
588	>	painCave.severity = OPENMD_ERROR;
589	>	painCave.isFatal = 1;
590	>	simError();
591	>	}
592	>	} else {
593	>	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
594	>	painCave.severity = OPENMD_ERROR;
595	>	painCave.isFatal = 1;
596	>	simError();
597	>	}
598	>	}
599	>	return rcut;
600	>	}
601	>
602	>
603	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
604	>	std::string forceFieldFilename(filename);
605	>	ifstrstream* ffStream = new ifstrstream();
606	>
607	>	//try to open the force filed file in current directory first
608	>	ffStream->open(forceFieldFilename.c_str());
609	>	if(!ffStream->is_open()){
610	>
611	>	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
612	>	ffStream->open( forceFieldFilename.c_str() );
613	>
614	>	//if current directory does not contain the force field file,
615	>	//try to open it in the path
616	>	if(!ffStream->is_open()){
617	>
618	>	sprintf( painCave.errMsg,
619	>	"Error opening the force field parameter file:\n"
620	>	"\t%s\n"
621	>	"\tHave you tried setting the FORCE_PARAM_PATH environment "
622	>	"variable?\n",
623	>	forceFieldFilename.c_str() );
624	>	painCave.severity = OPENMD_ERROR;
625	>	painCave.isFatal = 1;
626	>	simError();
627	>	}
628	>	}
629	>	return ffStream;
630	>	}
631	>
632	>	void ForceField::setFortranForceOptions(){
633	>	ForceOptions theseFortranOptions;
634	>	forceFieldOptions_.makeFortranOptions(theseFortranOptions);
635	>	setfForceOptions(&theseFortranOptions);
636	>	}
637	>	} //end namespace OpenMD

Comparing trunk/src/UseTheForce/ForceField.cpp (property svn:keywords):
Revision 206 by gezelter, Thu Nov 4 20:51:23 2004 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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