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Comparing trunk/src/UseTheForce/ForceField.cpp (file contents):
Revision 1195 by cpuglis, Thu Dec 6 20:04:02 2007 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 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		char* tempPath;
61		tempPath = getenv("FORCE_PARAM_PATH");
62
63		if (tempPath == NULL) {
64	<	//convert a macro from compiler to a string in c++
63	<	STR_DEFINE(ffPath_, FRC_PATH );
64	>	ffPath_ = "ORNULL(FRC_PATH)";
65		} else {
66		ffPath_ = tempPath;
67		}
#	Line 89 | Line 90 | namespace oopse {
90		if (bondType) {
91		return bondType;
92		} else {
93	<	//if no exact match found, try wild card match
94	<	return bondTypeCont_.find(keys, wildCardAtomTypeName_);
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	>	// query atom types for their chains of responsibility
104	>	std::vector<AtomType*> at1Chain = atype1->allYourBase();
105	>	std::vector<AtomType*> at2Chain = atype2->allYourBase();
106	>
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	<
152	>
153		BendType* ForceField::getBendType(const std::string &at1,
154		const std::string &at2,
155		const std::string &at3) {
#	Line 107 | Line 163 | namespace oopse {
163		if (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		}
236
#	Line 122 | Line 244 | namespace oopse {
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;
252		} else {
253	<	//if no exact match found, try wild card match
254	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
255	<	}
256	<
257	<	return torsionTypeCont_.find(keys, wildCardAtomTypeName_);
253	>
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);
#	Line 177 | Line 481 | namespace oopse {
481		keys.push_back(at4);
482		return torsionTypeCont_.find(keys);
483		}
484	<
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
188	–
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;
#	Line 222 | Line 544 | namespace oopse {
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) {
#	Line 250 | Line 585 | namespace oopse {
585		} else {
586		sprintf( painCave.errMsg,
587		"Can not cast GenericData to LJParam\n");
588	<	painCave.severity = OOPSE_ERROR;
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 = OOPSE_ERROR;
594	>	painCave.severity = OPENMD_ERROR;
595		painCave.isFatal = 1;
596		simError();
597		}
#	Line 286 | Line 621 | namespace oopse {
621		"\tHave you tried setting the FORCE_PARAM_PATH environment "
622		"variable?\n",
623		forceFieldFilename.c_str() );
624	<	painCave.severity = OOPSE_ERROR;
624	>	painCave.severity = OPENMD_ERROR;
625		painCave.isFatal = 1;
626		simError();
627		}
#	Line 299 | Line 634 | namespace oopse {
634		forceFieldOptions_.makeFortranOptions(theseFortranOptions);
635		setfForceOptions(&theseFortranOptions);
636		}
637	<	} //end namespace oopse
637	>	} //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.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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

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