ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42	<	/**
43	<	* @file ForceField.cpp
44	<	* @author tlin
45	<	* @date 11/04/2004
46	<	* @time 22:51am
47	<	* @version 1.0
48	<	*/
42	>	/**
43	>	* @file ForceField.cpp
44	>	* @author tlin
45	>	* @date 11/04/2004
46	>	* @time 22:51am
47	>	* @version 1.0
48	>	*/
49
50	+	#include <algorithm>
51		#include "UseTheForce/ForceField.hpp"
52		#include "utils/simError.h"
53	+	#include "utils/Tuple.hpp"
54		#include "UseTheForce/DarkSide/atype_interface.h"
55	<	namespace oopse {
55	>	#include "UseTheForce/DarkSide/fForceOptions_interface.h"
56	>	#include "UseTheForce/DarkSide/switcheroo_interface.h"
57	>	namespace OpenMD {
58
59	<	ForceField::ForceField() {
59	>	ForceField::ForceField() {
60		char* tempPath;
61		tempPath = getenv("FORCE_PARAM_PATH");
62
63		if (tempPath == NULL) {
64	<	//convert a macro from compiler to a string in c++
61	<	STR_DEFINE(ffPath_, FRC_PATH );
64	>	ffPath_ = "ORNULL(FRC_PATH)";
65		} else {
66	<	ffPath_ = tempPath;
66	>	ffPath_ = tempPath;
67		}
68	<	}
68	>	}
69
70
71	<	ForceField::~ForceField() {
71	>	ForceField::~ForceField() {
72		deleteAtypes();
73	<	}
73	>	deleteSwitch();
74	>	}
75
76	<	AtomType* ForceField::getAtomType(const std::string &at) {
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	>	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);
#	Line 83 | Line 88 | BondType* ForceField::getBondType(const std::string &a
88		//try exact match first
89		BondType* bondType = bondTypeCont_.find(keys);
90		if (bondType) {
91	<	return bondType;
91	>	return bondType;
92		} else {
93	<	//if no exact match found, try wild card match
94	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
95	<	}
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	<	}
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	<	BendType* ForceField::getBendType(const std::string &at1, const std::string &at2,
108	<	const std::string &at3) {
107	>	std::vector<AtomType*>::iterator i;
108	>	std::vector<AtomType*>::iterator j;
109	>
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	>	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);
#	Line 101 | Line 161 | BendType* ForceField::getBendType(const std::string &a
161		//try exact match first
162		BendType* bendType = bendTypeCont_.find(keys);
163		if (bendType) {
164	<	return bendType;
164	>	return bendType;
165		} else {
166	<	//if no exact match found, try wild card match
167	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
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	>	// 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	>	int ii = 0;
192	>	int jj = 0;
193	>	int kk = 0;
194	>	int IKscore;
195	>
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	>	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	>	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	<	}
235	>	}
236
237	<	TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2,
238	<	const std::string &at3, const std::string &at4) {
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
247	+
248	+	//try exact match first
249		TorsionType* torsionType = torsionTypeCont_.find(keys);
250		if (torsionType) {
251	<	return torsionType;
251	>	return torsionType;
252		} 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_);
253
254	<	}
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	<	BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){
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	<	return bondTypeCont_.find(keys);
347	<	}
346	>	keys.push_back(at3);
347	>	keys.push_back(at4);
348
349	<	BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2,
350	<	const std::string &at3){
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, const std::string &at2,
474	<	const std::string &at3, const std::string &at4){
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	<	bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
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	<	}
509	>	}
510
511	<	bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) {
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	<
526	<	bool ForceField::addBendType(const std::string &at1, const std::string &at2,
171	<	const std::string &at3, BendType* bendType) {
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, const std::string &at2,
535	<	const std::string &at3, const std::string &at4, TorsionType* torsionType) {
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	<	}
545	>	}
546
547	<	double ForceField::getRcutFromAtomType(AtomType* at) {
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	<	double rcut = 0.0;
573	<
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 = OOPSE_ERROR;
589	<	painCave.isFatal = 1;
590	<	simError();
591	<	}
592	<	} else {
593	<	sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
594	<	painCave.severity = OOPSE_ERROR;
595	<	painCave.isFatal = 1;
596	<	simError();
597	<	}
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		}
219	–
599		return rcut;
600	<	}
600	>	}
601	>
602
603	<
224	<	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
603	>	ifstrstream* ForceField::openForceFieldFile(const std::string& filename) {
604		std::string forceFieldFilename(filename);
605		ifstrstream* ffStream = new ifstrstream();
606
#	Line 229 | Line 608 | ifstrstream* ForceField::openForceFieldFile(const std:
608		ffStream->open(forceFieldFilename.c_str());
609		if(!ffStream->is_open()){
610
611	<	forceFieldFilename = ffPath_ + "/" + forceFieldFilename;
612	<	ffStream->open( forceFieldFilename.c_str() );
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()){
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 = OOPSE_ERROR;
625	<	painCave.isFatal = 1;
626	<	simError();
627	<	}
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		}
250	–
629		return ffStream;
630	+	}
631
632	<	}
633	<
634	<	} //end namespace oopse
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 475 by tim, Tue Apr 12 18:30:37 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines