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

Comparing:
trunk/src/UseTheForce/ForceField.cpp (file contents), Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (file contents), Revision 1473 by gezelter, Tue Jul 20 15:43:00 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
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 oopse {
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 69 | Line 72 | namespace oopse {
72
73		ForceField::~ForceField() {
74		deleteAtypes();
75	<	deleteSwitch();
75	>	deleteSwitch();
76		}
77
78		AtomType* ForceField::getAtomType(const std::string &at) {
#	Line 89 | Line 92 | namespace oopse {
92		if (bondType) {
93		return bondType;
94		} else {
95	<	//if no exact match found, try wild card match
96	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
95	>	AtomType* atype1;
96	>	AtomType* atype2;
97	>	std::vector<std::string> at1key;
98	>	at1key.push_back(at1);
99	>	atype1 = atomTypeCont_.find(at1key);
100	>
101	>	std::vector<std::string> at2key;
102	>	at2key.push_back(at2);
103	>	atype2 = atomTypeCont_.find(at2key);
104	>
105	>	// query atom types for their chains of responsibility
106	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
107	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
108	>
109	>	std::vector<AtomType*>::iterator i;
110	>	std::vector<AtomType*>::iterator j;
111	>
112	>	int ii = 0;
113	>	int jj = 0;
114	>	int bondTypeScore;
115	>
116	>	std::vector<std::pair<int, std::vector<std::string> > > foundBonds;
117	>
118	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
119	>	jj = 0;
120	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
121	>
122	>	bondTypeScore = ii + jj;
123	>
124	>	std::vector<std::string> myKeys;
125	>	myKeys.push_back((*i)->getName());
126	>	myKeys.push_back((*j)->getName());
127	>
128	>	BondType* bondType = bondTypeCont_.find(myKeys);
129	>	if (bondType) {
130	>	foundBonds.push_back(std::make_pair(bondTypeScore, myKeys));
131	>	}
132	>	jj++;
133	>	}
134	>	ii++;
135	>	}
136	>
137	>
138	>	if (foundBonds.size() > 0) {
139	>	// sort the foundBonds by the score:
140	>	std::sort(foundBonds.begin(), foundBonds.end());
141	>
142	>	int bestScore = foundBonds[0].first;
143	>	std::vector<std::string> theKeys = foundBonds[0].second;
144	>
145	>	BondType* bestType = bondTypeCont_.find(theKeys);
146	>
147	>	return bestType;
148	>	} else {
149	>	//if no exact match found, try wild card match
150	>	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
151	>	}
152		}
153		}
154	<
154	>
155		BendType* ForceField::getBendType(const std::string &at1,
156		const std::string &at2,
157		const std::string &at3) {
#	Line 107 | Line 165 | namespace oopse {
165		if (bendType) {
166		return bendType;
167		} else {
168	<	//if no exact match found, try wild card match
169	<	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
168	>
169	>	AtomType* atype1;
170	>	AtomType* atype2;
171	>	AtomType* atype3;
172	>	std::vector<std::string> at1key;
173	>	at1key.push_back(at1);
174	>	atype1 = atomTypeCont_.find(at1key);
175	>
176	>	std::vector<std::string> at2key;
177	>	at2key.push_back(at2);
178	>	atype2 = atomTypeCont_.find(at2key);
179	>
180	>	std::vector<std::string> at3key;
181	>	at3key.push_back(at3);
182	>	atype3 = atomTypeCont_.find(at3key);
183	>
184	>	// query atom types for their chains of responsibility
185	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
186	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
187	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
188	>
189	>	std::vector<AtomType*>::iterator i;
190	>	std::vector<AtomType*>::iterator j;
191	>	std::vector<AtomType*>::iterator k;
192	>
193	>	int ii = 0;
194	>	int jj = 0;
195	>	int kk = 0;
196	>	int IKscore;
197	>
198	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundBends;
199	>
200	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
201	>	ii = 0;
202	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
203	>	kk = 0;
204	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
205	>
206	>	IKscore = ii + kk;
207	>
208	>	std::vector<std::string> myKeys;
209	>	myKeys.push_back((*i)->getName());
210	>	myKeys.push_back((*j)->getName());
211	>	myKeys.push_back((*k)->getName());
212	>
213	>	BendType* bendType = bendTypeCont_.find(myKeys);
214	>	if (bendType) {
215	>	foundBends.push_back( make_tuple3(jj, IKscore, myKeys) );
216	>	}
217	>	kk++;
218	>	}
219	>	ii++;
220	>	}
221	>	jj++;
222	>	}
223	>
224	>	if (foundBends.size() > 0) {
225	>	std::sort(foundBends.begin(), foundBends.end());
226	>	int jscore = foundBends[0].first;
227	>	int ikscore = foundBends[0].second;
228	>	std::vector<std::string> theKeys = foundBends[0].third;
229	>
230	>	BendType* bestType = bendTypeCont_.find(theKeys);
231	>	return bestType;
232	>	} else {
233	>	//if no exact match found, try wild card match
234	>	return bendTypeCont_.find(keys, wildCardAtomTypeName_);
235	>	}
236		}
237		}
238
#	Line 122 | Line 246 | namespace oopse {
246		keys.push_back(at3);
247		keys.push_back(at4);
248
249	+
250	+	//try exact match first
251		TorsionType* torsionType = torsionTypeCont_.find(keys);
252		if (torsionType) {
253		return torsionType;
254		} else {
255	<	//if no exact match found, try wild card match
256	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
257	<	}
258	<
259	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
255	>
256	>	AtomType* atype1;
257	>	AtomType* atype2;
258	>	AtomType* atype3;
259	>	AtomType* atype4;
260	>	std::vector<std::string> at1key;
261	>	at1key.push_back(at1);
262	>	atype1 = atomTypeCont_.find(at1key);
263	>
264	>	std::vector<std::string> at2key;
265	>	at2key.push_back(at2);
266	>	atype2 = atomTypeCont_.find(at2key);
267	>
268	>	std::vector<std::string> at3key;
269	>	at3key.push_back(at3);
270	>	atype3 = atomTypeCont_.find(at3key);
271	>
272	>	std::vector<std::string> at4key;
273	>	at4key.push_back(at4);
274	>	atype4 = atomTypeCont_.find(at4key);
275	>
276	>	// query atom types for their chains of responsibility
277	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
278	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
279	>	std::vector<AtomType*> at3Chain = atype3->allYourBase();
280	>	std::vector<AtomType*> at4Chain = atype4->allYourBase();
281	>
282	>	std::vector<AtomType*>::iterator i;
283	>	std::vector<AtomType*>::iterator j;
284	>	std::vector<AtomType*>::iterator k;
285	>	std::vector<AtomType*>::iterator l;
286	>
287	>	int ii = 0;
288	>	int jj = 0;
289	>	int kk = 0;
290	>	int ll = 0;
291	>	int ILscore;
292	>	int JKscore;
293	>
294	>	std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions;
295	>
296	>	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
297	>	kk = 0;
298	>	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
299	>	ii = 0;
300	>	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
301	>	ll = 0;
302	>	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
303	>
304	>	ILscore = ii + ll;
305	>	JKscore = jj + kk;
306	>
307	>	std::vector<std::string> myKeys;
308	>	myKeys.push_back((*i)->getName());
309	>	myKeys.push_back((*j)->getName());
310	>	myKeys.push_back((*k)->getName());
311	>	myKeys.push_back((*l)->getName());
312	>
313	>	TorsionType* torsionType = torsionTypeCont_.find(myKeys);
314	>	if (torsionType) {
315	>	foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) );
316	>	}
317	>	ll++;
318	>	}
319	>	ii++;
320	>	}
321	>	kk++;
322	>	}
323	>	jj++;
324	>	}
325	>
326	>	if (foundTorsions.size() > 0) {
327	>	std::sort(foundTorsions.begin(), foundTorsions.end());
328	>	int jkscore = foundTorsions[0].first;
329	>	int ilscore = foundTorsions[0].second;
330	>	std::vector<std::string> theKeys = foundTorsions[0].third;
331	>
332	>	TorsionType* bestType = torsionTypeCont_.find(theKeys);
333	>	return bestType;
334	>	} else {
335	>	//if no exact match found, try wild card match
336	>	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
337	>	}
338	>	}
339		}
340	+
341	+	InversionType* ForceField::getInversionType(const std::string &at1,
342	+	const std::string &at2,
343	+	const std::string &at3,
344	+	const std::string &at4) {
345	+	std::vector<std::string> keys;
346	+	keys.push_back(at1);
347	+	keys.push_back(at2);
348	+	keys.push_back(at3);
349	+	keys.push_back(at4);
350	+
351	+	//try exact match first
352	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys);
353	+	if (inversionType) {
354	+	return inversionType;
355	+	} else {
356	+
357	+	AtomType* atype1;
358	+	AtomType* atype2;
359	+	AtomType* atype3;
360	+	AtomType* atype4;
361	+	std::vector<std::string> at1key;
362	+	at1key.push_back(at1);
363	+	atype1 = atomTypeCont_.find(at1key);
364	+
365	+	std::vector<std::string> at2key;
366	+	at2key.push_back(at2);
367	+	atype2 = atomTypeCont_.find(at2key);
368	+
369	+	std::vector<std::string> at3key;
370	+	at3key.push_back(at3);
371	+	atype3 = atomTypeCont_.find(at3key);
372	+
373	+	std::vector<std::string> at4key;
374	+	at4key.push_back(at4);
375	+	atype4 = atomTypeCont_.find(at4key);
376	+
377	+	// query atom types for their chains of responsibility
378	+	std::vector<AtomType*> at1Chain = atype1->allYourBase();
379	+	std::vector<AtomType*> at2Chain = atype2->allYourBase();
380	+	std::vector<AtomType*> at3Chain = atype3->allYourBase();
381	+	std::vector<AtomType*> at4Chain = atype4->allYourBase();
382	+
383	+	std::vector<AtomType*>::iterator i;
384	+	std::vector<AtomType*>::iterator j;
385	+	std::vector<AtomType*>::iterator k;
386	+	std::vector<AtomType*>::iterator l;
387
388	+	int ii = 0;
389	+	int jj = 0;
390	+	int kk = 0;
391	+	int ll = 0;
392	+	int Iscore;
393	+	int JKLscore;
394	+
395	+	std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions;
396	+
397	+	for (j = at2Chain.begin(); j != at2Chain.end(); j++) {
398	+	kk = 0;
399	+	for (k = at3Chain.begin(); k != at3Chain.end(); k++) {
400	+	ii = 0;
401	+	for (i = at1Chain.begin(); i != at1Chain.end(); i++) {
402	+	ll = 0;
403	+	for (l = at4Chain.begin(); l != at4Chain.end(); l++) {
404	+
405	+	Iscore = ii;
406	+	JKLscore = jj + kk + ll;
407	+
408	+	std::vector<std::string> myKeys;
409	+	myKeys.push_back((*i)->getName());
410	+	myKeys.push_back((*j)->getName());
411	+	myKeys.push_back((*k)->getName());
412	+	myKeys.push_back((*l)->getName());
413	+
414	+	InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys);
415	+	if (inversionType) {
416	+	foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) );
417	+	}
418	+	ll++;
419	+	}
420	+	ii++;
421	+	}
422	+	kk++;
423	+	}
424	+	jj++;
425	+	}
426	+
427	+	if (foundInversions.size() > 0) {
428	+	std::sort(foundInversions.begin(), foundInversions.end());
429	+	int iscore = foundInversions[0].first;
430	+	int jklscore = foundInversions[0].second;
431	+	std::vector<std::string> theKeys = foundInversions[0].third;
432	+
433	+	InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys);
434	+	return bestType;
435	+	} else {
436	+	//if no exact match found, try wild card match
437	+	return inversionTypeCont_.find(keys, wildCardAtomTypeName_);
438	+	}
439	+	}
440	+	}
441	+
442		NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) {
443		std::vector<std::string> keys;
444		keys.push_back(at1);
#	Line 177 | Line 483 | namespace oopse {
483		keys.push_back(at4);
484		return torsionTypeCont_.find(keys);
485		}
486	<
486	>
487	>	InversionType* ForceField::getExactInversionType(const std::string &at1,
488	>	const std::string &at2,
489	>	const std::string &at3,
490	>	const std::string &at4){
491	>	std::vector<std::string> keys;
492	>	keys.push_back(at1);
493	>	keys.push_back(at2);
494	>	keys.push_back(at3);
495	>	keys.push_back(at4);
496	>	return inversionTypeCont_.find(keys);
497	>	}
498	>
499		NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){
500		std::vector<std::string> keys;
501		keys.push_back(at1);
502		keys.push_back(at2);
503		return nonBondedInteractionTypeCont_.find(keys);
504		}
505	+
506
188	–
507		bool ForceField::addAtomType(const std::string &at, AtomType* atomType) {
508		std::vector<std::string> keys;
509		keys.push_back(at);
510		return atomTypeCont_.add(keys, atomType);
511		}
512
513	+	bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) {
514	+	std::vector<std::string> keys;
515	+	keys.push_back(at);
516	+	return atomTypeCont_.replace(keys, atomType);
517	+	}
518	+
519		bool ForceField::addBondType(const std::string &at1, const std::string &at2,
520		BondType* bondType) {
521		std::vector<std::string> keys;
#	Line 222 | Line 546 | namespace oopse {
546		return torsionTypeCont_.add(keys, torsionType);
547		}
548
549	+	bool ForceField::addInversionType(const std::string &at1,
550	+	const std::string &at2,
551	+	const std::string &at3,
552	+	const std::string &at4,
553	+	InversionType* inversionType) {
554	+	std::vector<std::string> keys;
555	+	keys.push_back(at1);
556	+	keys.push_back(at2);
557	+	keys.push_back(at3);
558	+	keys.push_back(at4);
559	+	return inversionTypeCont_.add(keys, inversionType);
560	+	}
561	+
562		bool ForceField::addNonBondedInteractionType(const std::string &at1,
563		const std::string &at2,
564		NonBondedInteractionType* nbiType) {
#	Line 250 | Line 587 | namespace oopse {
587		} else {
588		sprintf( painCave.errMsg,
589		"Can not cast GenericData to LJParam\n");
590	<	painCave.severity = OOPSE_ERROR;
590	>	painCave.severity = OPENMD_ERROR;
591		painCave.isFatal = 1;
592		simError();
593		}
594		} else {
595		sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
596	<	painCave.severity = OOPSE_ERROR;
596	>	painCave.severity = OPENMD_ERROR;
597		painCave.isFatal = 1;
598		simError();
599		}
#	Line 286 | Line 623 | namespace oopse {
623		"\tHave you tried setting the FORCE_PARAM_PATH environment "
624		"variable?\n",
625		forceFieldFilename.c_str() );
626	<	painCave.severity = OOPSE_ERROR;
626	>	painCave.severity = OPENMD_ERROR;
627		painCave.isFatal = 1;
628		simError();
629		}
#	Line 299 | Line 636 | namespace oopse {
636		forceFieldOptions_.makeFortranOptions(theseFortranOptions);
637		setfForceOptions(&theseFortranOptions);
638		}
639	<	} //end namespace oopse
639	>	} //end namespace OpenMD

Comparing:
trunk/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
branches/development/src/UseTheForce/ForceField.cpp (property svn:keywords), Revision 1473 by gezelter, Tue Jul 20 15:43:00 2010 UTC

#	Line 0 | Line 1
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